From 20face60a1b8788e73b6df79a231596ac227b2fd Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jul 2023 11:47:42 +0200
Subject: [PATCH 01/41] Add basic Invenio file source plugin

Currently only basic support for listing records and downloading files in public records.
---
 lib/galaxy/files/sources/invenio.py | 143 ++++++++++++++++++++++++++++
 1 file changed, 143 insertions(+)
 create mode 100644 lib/galaxy/files/sources/invenio.py

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
new file mode 100644
index 000000000000..64e4ca597756
--- /dev/null
+++ b/lib/galaxy/files/sources/invenio.py
@@ -0,0 +1,143 @@
+import ssl
+import urllib.request
+from typing import (
+    cast,
+    Optional,
+)
+from urllib.parse import urljoin
+
+import requests
+from typing_extensions import Unpack
+
+from galaxy.files.sources import (
+    BaseFilesSource,
+    FilesSourceOptions,
+    FilesSourceProperties,
+)
+from galaxy.util import (
+    DEFAULT_SOCKET_TIMEOUT,
+    get_charset_from_http_headers,
+    stream_to_open_named_file,
+)
+
+# TODO: Remove this block. Ignoring SSL errors for testing purposes.
+VERIFY = False
+SSL_CONTEXT = ssl.create_default_context()
+SSL_CONTEXT.check_hostname = False
+SSL_CONTEXT.verify_mode = ssl.CERT_NONE
+
+
+class InvenioFilesSourceProperties(FilesSourceProperties):
+    url: str
+
+
+class InvenioFilesSource(BaseFilesSource):
+    """A files source for Invenio turn-key research data management repository."""
+
+    plugin_type = "inveniordm"
+
+    def __init__(self, **kwd: Unpack[InvenioFilesSourceProperties]):
+        props = self._parse_common_config_opts(kwd)
+        base_url = props.get("url", None)
+        if not base_url:
+            raise Exception("InvenioFilesSource requires a url")
+        self._invenio_url = base_url
+        self._props = props
+
+    def _list(self, path="/", recursive=True, user_context=None, opts: Optional[FilesSourceOptions] = None):
+        is_listing_records = path == "/"
+        if is_listing_records:
+            # TODO: This is limited to 25 records by default. We should add pagination support.
+            request_url = urljoin(self._invenio_url, "api/records")
+        else:
+            # listing a record's files
+            request_url = urljoin(self._invenio_url, f"{path}/files")
+
+        rval = []
+        headers = self._get_request_headers(user_context)
+        response = requests.get(request_url, headers=headers, verify=VERIFY)
+        if response.status_code == 200:
+            response_json = response.json()
+            if is_listing_records:
+                rval = self._get_records_from_response(path, response_json)
+            else:
+                rval = self._get_record_files_from_response(path, response_json)
+        else:
+            raise Exception(f"Request to {request_url} failed with status code {response.status_code}")
+        return rval
+
+    def _get_request_headers(self, user_context):
+        preferences = user_context.preferences if user_context else None
+        token = preferences.get(f"{self.id}|token", None) if preferences else None
+        headers = {"Authorization": f"Bearer {token}"} if token else {}
+        return headers
+
+    def _get_records_from_response(self, path: str, response: dict):
+        records = response["hits"]["hits"]
+        rval = []
+        for record in records:
+            uri = self._to_plugin_uri(record["links"]["self"])
+            rval.append(
+                {
+                    "class": "Directory",
+                    "name": record["metadata"]["title"],
+                    "ctime": record["created"],
+                    "uri": uri,
+                    "path": path,
+                }
+            )
+
+        return rval
+
+    def _get_record_files_from_response(self, path: str, response: dict):
+        files_enabled = response.get("enabled", False)
+        if not files_enabled:
+            return []
+        entries = response["entries"]
+        rval = []
+        for entry in entries:
+            if entry.get("status") == "completed":
+                uri = self._to_plugin_uri(entry["links"]["content"])
+                rval.append(
+                    {
+                        "class": "File",
+                        "name": entry["key"],
+                        "size": entry["size"],
+                        "ctime": entry["created"],
+                        "uri": uri,
+                        "path": path,
+                    }
+                )
+        return rval
+
+    def _to_plugin_uri(self, uri: str) -> str:
+        return uri.replace(self._invenio_url, self.get_uri_root())
+
+    def _realize_to(
+        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+    ):
+        remote_path = urljoin(self._invenio_url, source_path)
+        # TODO: user_context is always None here when called from a data fetch.
+        # This prevents downloading files that require authentication even if the user provided a token.
+        headers = self._get_request_headers(user_context)
+        req = urllib.request.Request(remote_path, headers=headers)
+        with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT, context=SSL_CONTEXT) as page:
+            f = open(native_path, "wb")
+            return stream_to_open_named_file(
+                page, f.fileno(), native_path, source_encoding=get_charset_from_http_headers(page.headers)
+            )
+
+    def _write_from(
+        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+    ):
+        raise NotImplementedError()
+
+    def _serialization_props(self, user_context=None) -> InvenioFilesSourceProperties:
+        effective_props = {}
+        for key, val in self._props.items():
+            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
+        effective_props["url"] = self._invenio_url
+        return cast(InvenioFilesSourceProperties, effective_props)
+
+
+__all__ = ("InvenioFilesSource",)

From e06e295f56ecf0b1c9e23e391c3d3e11b523601b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 7 Jul 2023 13:31:14 +0200
Subject: [PATCH 02/41] Add Invenio RDM plugin configuration sample

---
 lib/galaxy/config/sample/file_sources_conf.yml.sample | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index f7ab5e7b40e5..e8fdf524b5d9 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -191,3 +191,9 @@
   label: Stock DRS filesource
   id: drsstock
   doc: Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.
+
+- type: inveniordm
+  id: invenio
+  doc: Invenio RDM turn-key research data management repository
+  label: Invenio RDM Demo Repository
+  url: https://inveniordm.web.cern.ch/

From 6b4d9e783433ab127a7b237968dcf3d32af4360e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 10 Jul 2023 16:05:12 +0200
Subject: [PATCH 03/41] Explore record publishing

This has a severe limitation.
We can export a record with files (without much metadata) but we cannot reference it back directly form an export URI.
 The reason is how we construct the URI for regular file sources, which obviously are just file paths, while with DOI repositories, we need to differentiate between records and files only.
---
 lib/galaxy/files/sources/invenio.py | 268 ++++++++++++++++++++++++----
 1 file changed, 229 insertions(+), 39 deletions(-)

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 64e4ca597756..42cd737a0c08 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -1,13 +1,21 @@
+import datetime
+import json
+import os
 import ssl
 import urllib.request
 from typing import (
     cast,
+    List,
     Optional,
 )
 from urllib.parse import urljoin
 
 import requests
-from typing_extensions import Unpack
+from typing_extensions import (
+    Literal,
+    TypedDict,
+    Unpack,
+)
 
 from galaxy.files.sources import (
     BaseFilesSource,
@@ -27,10 +35,82 @@
 SSL_CONTEXT.verify_mode = ssl.CERT_NONE
 
 
+AccessStatus = Literal["public", "restricted"]
+
+
 class InvenioFilesSourceProperties(FilesSourceProperties):
     url: str
 
 
+class ResourceType(TypedDict):
+    id: str
+
+
+class RecordAccess(TypedDict):
+    record: AccessStatus
+    files: AccessStatus
+
+
+class RecordFiles(TypedDict):
+    enabled: bool
+
+
+class IdentifierEntry(TypedDict):
+    scheme: str
+    identifier: str
+
+
+class AffiliationEntry(TypedDict):
+    id: str
+    name: str
+
+
+class RecordPersonOrOrg(TypedDict):
+    family_name: str
+    given_name: str
+    type: Literal["personal", "organizational"]
+    name: str
+    identifiers: List[IdentifierEntry]
+
+
+class Creator(TypedDict):
+    person_or_org: RecordPersonOrOrg
+    affiliations: Optional[List[AffiliationEntry]]
+
+
+class RecordMetadata(TypedDict):
+    title: str
+    resource_type: ResourceType
+    publication_date: str
+    creators: List[Creator]
+
+
+class RecordLinks(TypedDict):
+    self: str
+    self_html: str
+    self_iiif_manifest: str
+    self_iiif_sequence: str
+    files: str
+    record: str
+    record_html: str
+    publish: str
+    review: str
+    versions: str
+    access_links: str
+    reserve_doi: str
+
+
+class InvenioRecord(TypedDict):
+    id: str
+    title: str
+    resource_type: ResourceType
+    publication_date: str
+    access: RecordAccess
+    files: RecordFiles
+    metadata: RecordMetadata
+    links: RecordLinks
+
+
 class InvenioFilesSource(BaseFilesSource):
     """A files source for Invenio turn-key research data management repository."""
 
@@ -45,26 +125,56 @@ def __init__(self, **kwd: Unpack[InvenioFilesSourceProperties]):
         self._props = props
 
     def _list(self, path="/", recursive=True, user_context=None, opts: Optional[FilesSourceOptions] = None):
-        is_listing_records = path == "/"
-        if is_listing_records:
-            # TODO: This is limited to 25 records by default. We should add pagination support.
-            request_url = urljoin(self._invenio_url, "api/records")
-        else:
-            # listing a record's files
-            request_url = urljoin(self._invenio_url, f"{path}/files")
+        is_root_path = path == "/"
+        if is_root_path:
+            return self._list_records(user_context)
+        return self._list_record_files(path, user_context)
 
-        rval = []
+    def _realize_to(
+        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+    ):
+        # TODO: source_path will be wrong when constructed from the UI as it assumes the target_uri is `get_root_uri() + filename`
+
+        remote_path = urljoin(self._invenio_url, source_path)
+        # TODO: user_context is always None here when called from a data fetch.
+        # This prevents downloading files that require authentication even if the user provided a token.
+        headers = self._get_request_headers(user_context)
+        req = urllib.request.Request(remote_path, headers=headers)
+        with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT, context=SSL_CONTEXT) as page:
+            f = open(native_path, "wb")
+            return stream_to_open_named_file(
+                page, f.fileno(), native_path, source_encoding=get_charset_from_http_headers(page.headers)
+            )
+
+    def _write_from(
+        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+    ):
+        filename = os.path.basename(target_path)
+        record_title = f"{filename} (exported by Galaxy)"
+        draft_record = self._create_draft_record(title=record_title, user_context=user_context)
+        try:
+            self._upload_file_to_draft_record(draft_record, filename, native_path, user_context=user_context)
+            self._publish_draft_record(draft_record, user_context=user_context)
+        except Exception:
+            self._delete_draft_record(draft_record, user_context)
+            raise
+
+    def _list_records(self, user_context=None):
+        # TODO: This is limited to 25 records by default. Add pagination support?
+        request_url = urljoin(self._invenio_url, "api/records")
+        response_data = self._get_response(user_context, request_url)
+        return self._get_records_from_response(response_data)
+
+    def _list_record_files(self, path, user_context=None):
+        request_url = urljoin(self._invenio_url, f"{path}/files")
+        response_data = self._get_response(user_context, request_url)
+        return self._get_record_files_from_response(path, response_data)
+
+    def _get_response(self, user_context, request_url: str) -> dict:
         headers = self._get_request_headers(user_context)
         response = requests.get(request_url, headers=headers, verify=VERIFY)
-        if response.status_code == 200:
-            response_json = response.json()
-            if is_listing_records:
-                rval = self._get_records_from_response(path, response_json)
-            else:
-                rval = self._get_record_files_from_response(path, response_json)
-        else:
-            raise Exception(f"Request to {request_url} failed with status code {response.status_code}")
-        return rval
+        self._ensure_response_has_expected_status_code(response, 200)
+        return response.json()
 
     def _get_request_headers(self, user_context):
         preferences = user_context.preferences if user_context else None
@@ -72,7 +182,7 @@ def _get_request_headers(self, user_context):
         headers = {"Authorization": f"Bearer {token}"} if token else {}
         return headers
 
-    def _get_records_from_response(self, path: str, response: dict):
+    def _get_records_from_response(self, response: dict):
         records = response["hits"]["hits"]
         rval = []
         for record in records:
@@ -83,7 +193,7 @@ def _get_records_from_response(self, path: str, response: dict):
                     "name": record["metadata"]["title"],
                     "ctime": record["created"],
                     "uri": uri,
-                    "path": path,
+                    "path": f"/{record['id']}",
                 }
             )
 
@@ -98,6 +208,7 @@ def _get_record_files_from_response(self, path: str, response: dict):
         for entry in entries:
             if entry.get("status") == "completed":
                 uri = self._to_plugin_uri(entry["links"]["content"])
+                path = self._to_plugin_uri(entry["links"]["self"])
                 rval.append(
                     {
                         "class": "File",
@@ -113,25 +224,6 @@ def _get_record_files_from_response(self, path: str, response: dict):
     def _to_plugin_uri(self, uri: str) -> str:
         return uri.replace(self._invenio_url, self.get_uri_root())
 
-    def _realize_to(
-        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
-    ):
-        remote_path = urljoin(self._invenio_url, source_path)
-        # TODO: user_context is always None here when called from a data fetch.
-        # This prevents downloading files that require authentication even if the user provided a token.
-        headers = self._get_request_headers(user_context)
-        req = urllib.request.Request(remote_path, headers=headers)
-        with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT, context=SSL_CONTEXT) as page:
-            f = open(native_path, "wb")
-            return stream_to_open_named_file(
-                page, f.fileno(), native_path, source_encoding=get_charset_from_http_headers(page.headers)
-            )
-
-    def _write_from(
-        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
-    ):
-        raise NotImplementedError()
-
     def _serialization_props(self, user_context=None) -> InvenioFilesSourceProperties:
         effective_props = {}
         for key, val in self._props.items():
@@ -139,5 +231,103 @@ def _serialization_props(self, user_context=None) -> InvenioFilesSourcePropertie
         effective_props["url"] = self._invenio_url
         return cast(InvenioFilesSourceProperties, effective_props)
 
+    def _create_draft_record(self, title: str, user_context=None) -> InvenioRecord:
+        today = datetime.date.today().isoformat()
+        creator = self._get_creator_from_user_context(user_context)
+        should_publish = self._get_public_records_user_setting_enabled_status(user_context)
+        access = "public" if should_publish else "restricted"
+        create_record_request = {
+            "access": {"record": access, "files": access},
+            "files": {"enabled": True},
+            "metadata": {
+                "title": title,
+                "publication_date": today,
+                "resource_type": {"id": "dataset"},
+                "creators": [
+                    creator,
+                ],
+            },
+        }
+
+        headers = self._get_request_headers(user_context)
+        if "Authorization" not in headers:
+            raise Exception(
+                "Cannot create record without authentication token. Please set your personal access token in your Galaxy preferences."
+            )
+
+        create_record_url = urljoin(self._invenio_url, "api/records")
+        response = requests.post(create_record_url, json=create_record_request, headers=headers, verify=VERIFY)
+        self._ensure_response_has_expected_status_code(response, 201)
+        record = response.json()
+        return record
+
+    def _delete_draft_record(self, record: InvenioRecord, user_context=None):
+        delete_record_url = record["links"]["self"]
+        headers = self._get_request_headers(user_context)
+        response = requests.delete(delete_record_url, headers=headers, verify=VERIFY)
+        self._ensure_response_has_expected_status_code(response, 204)
+
+    def _upload_file_to_draft_record(self, record: InvenioRecord, filename: str, native_path: str, user_context=None):
+        upload_file_url = urljoin(self._invenio_url, f"api/records/{record['id']}/draft/files")
+        headers = self._get_request_headers(user_context)
+
+        # Add file metadata
+        response = requests.post(upload_file_url, json=[{"key": filename}], headers=headers, verify=VERIFY)
+        self._ensure_response_has_expected_status_code(response, 201)
+
+        # Upload file content
+        file_entry = response.json()["entries"][0]
+        upload_file_content_url = file_entry["links"]["content"]
+        commit_file_upload_url = file_entry["links"]["commit"]
+        with open(native_path, "rb") as file:
+            response = requests.put(upload_file_content_url, data=file, headers=headers, verify=VERIFY)
+            self._ensure_response_has_expected_status_code(response, 200)
+
+        # Commit file upload
+        response = requests.post(commit_file_upload_url, headers=headers, verify=VERIFY)
+        self._ensure_response_has_expected_status_code(response, 200)
+
+    def _publish_draft_record(self, record: InvenioRecord, user_context=None):
+        publish_record_url = urljoin(self._invenio_url, f"api/records/{record['id']}/draft/actions/publish")
+        headers = self._get_request_headers(user_context)
+        response = requests.post(publish_record_url, headers=headers, verify=VERIFY)
+        self._ensure_response_has_expected_status_code(response, 202)
+
+    def _get_creator_from_user_context(self, user_context):
+        preferences = user_context.preferences if user_context else None
+        public_name = preferences.get(f"{self.id}|public_name", None) if preferences else None
+        family_name = "Galaxy User"
+        given_name = "Anonymous"
+        if public_name:
+            tokens = public_name.split(", ")
+            if len(tokens) == 2:
+                family_name = tokens[0]
+                given_name = tokens[1]
+            else:
+                given_name = public_name
+        return {"person_or_org": {"family_name": family_name, "given_name": given_name, "type": "personal"}}
+
+    def _get_public_records_user_setting_enabled_status(self, user_context) -> bool:
+        preferences = user_context.preferences if user_context else None
+        public_records = preferences.get(f"{self.id}|public_records", None) if preferences else None
+        if public_records:
+            return True
+        return False
+
+    def _ensure_response_has_expected_status_code(self, response, expected_status_code: int):
+        if response.status_code != expected_status_code:
+            error_message = self._get_response_error_message(response)
+            raise Exception(
+                f"Request to {response.url} failed with status code {response.status_code}: {error_message}"
+            )
+
+    def _get_response_error_message(self, response):
+        response_json = response.json()
+        error_message = response_json.get("message") if response.status_code == 400 else response.text
+        errors = response_json.get("errors", [])
+        for error in errors:
+            error_message += f"\n{json.dumps(error)}"
+        return error_message
+
 
 __all__ = ("InvenioFilesSource",)

From 333b251efe93f1a2353a873a4bd2459ec45d4d62 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 11 Jul 2023 14:26:04 +0200
Subject: [PATCH 04/41] Use vault secret to store personal token

Also add example config to user_preferences_extra_conf.yml.sample
---
 .../user_preferences_extra_conf.yml.sample    | 17 +++++
 lib/galaxy/files/sources/invenio.py           | 63 ++++++++++++++-----
 2 files changed, 64 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
index d0280966e40e..17c7fbf41572 100644
--- a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
+++ b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
@@ -94,3 +94,20 @@ preferences:
               label: Password
               type:  password
               required: False
+
+    invenio:
+        description: Your Invenio RDM Account
+        inputs:
+            - name: token
+              label: Personal Token to publish records to Invenio RDM
+              type: secret
+              store: vault # Requires setting up vault_config_file in your galaxy.yml
+              required: False
+            - name: public_name
+              label: Public name to publish records (formatted as "Lastname, Firstname")
+              type: text
+              required: False
+            - name: public_records
+              label: Whether to publish records (file exports) or make them restricted. Only public records can be imported back.
+              type: boolean
+              required: False
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 42cd737a0c08..1aa70ed0c6af 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -17,6 +17,7 @@
     Unpack,
 )
 
+from galaxy.files import ProvidesUserFileSourcesUserContext
 from galaxy.files.sources import (
     BaseFilesSource,
     FilesSourceOptions,
@@ -124,14 +125,24 @@ def __init__(self, **kwd: Unpack[InvenioFilesSourceProperties]):
         self._invenio_url = base_url
         self._props = props
 
-    def _list(self, path="/", recursive=True, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _list(
+        self,
+        path="/",
+        recursive=True,
+        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         is_root_path = path == "/"
         if is_root_path:
             return self._list_records(user_context)
         return self._list_record_files(path, user_context)
 
     def _realize_to(
-        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         # TODO: source_path will be wrong when constructed from the UI as it assumes the target_uri is `get_root_uri() + filename`
 
@@ -147,7 +158,11 @@ def _realize_to(
             )
 
     def _write_from(
-        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         filename = os.path.basename(target_path)
         record_title = f"{filename} (exported by Galaxy)"
@@ -159,26 +174,26 @@ def _write_from(
             self._delete_draft_record(draft_record, user_context)
             raise
 
-    def _list_records(self, user_context=None):
+    def _list_records(self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
         # TODO: This is limited to 25 records by default. Add pagination support?
         request_url = urljoin(self._invenio_url, "api/records")
         response_data = self._get_response(user_context, request_url)
         return self._get_records_from_response(response_data)
 
-    def _list_record_files(self, path, user_context=None):
+    def _list_record_files(self, path, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
         request_url = urljoin(self._invenio_url, f"{path}/files")
         response_data = self._get_response(user_context, request_url)
         return self._get_record_files_from_response(path, response_data)
 
-    def _get_response(self, user_context, request_url: str) -> dict:
+    def _get_response(self, user_context: Optional[ProvidesUserFileSourcesUserContext], request_url: str) -> dict:
         headers = self._get_request_headers(user_context)
         response = requests.get(request_url, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 200)
         return response.json()
 
-    def _get_request_headers(self, user_context):
-        preferences = user_context.preferences if user_context else None
-        token = preferences.get(f"{self.id}|token", None) if preferences else None
+    def _get_request_headers(self, user_context: Optional[ProvidesUserFileSourcesUserContext]):
+        vault = user_context.user_vault if user_context else None
+        token = vault.read_secret(f"preferences/{self.id}/token") if vault else None
         headers = {"Authorization": f"Bearer {token}"} if token else {}
         return headers
 
@@ -224,14 +239,18 @@ def _get_record_files_from_response(self, path: str, response: dict):
     def _to_plugin_uri(self, uri: str) -> str:
         return uri.replace(self._invenio_url, self.get_uri_root())
 
-    def _serialization_props(self, user_context=None) -> InvenioFilesSourceProperties:
+    def _serialization_props(
+        self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
+    ) -> InvenioFilesSourceProperties:
         effective_props = {}
         for key, val in self._props.items():
             effective_props[key] = self._evaluate_prop(val, user_context=user_context)
         effective_props["url"] = self._invenio_url
         return cast(InvenioFilesSourceProperties, effective_props)
 
-    def _create_draft_record(self, title: str, user_context=None) -> InvenioRecord:
+    def _create_draft_record(
+        self, title: str, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
+    ) -> InvenioRecord:
         today = datetime.date.today().isoformat()
         creator = self._get_creator_from_user_context(user_context)
         should_publish = self._get_public_records_user_setting_enabled_status(user_context)
@@ -261,13 +280,21 @@ def _create_draft_record(self, title: str, user_context=None) -> InvenioRecord:
         record = response.json()
         return record
 
-    def _delete_draft_record(self, record: InvenioRecord, user_context=None):
+    def _delete_draft_record(
+        self, record: InvenioRecord, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
+    ):
         delete_record_url = record["links"]["self"]
         headers = self._get_request_headers(user_context)
         response = requests.delete(delete_record_url, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 204)
 
-    def _upload_file_to_draft_record(self, record: InvenioRecord, filename: str, native_path: str, user_context=None):
+    def _upload_file_to_draft_record(
+        self,
+        record: InvenioRecord,
+        filename: str,
+        native_path: str,
+        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+    ):
         upload_file_url = urljoin(self._invenio_url, f"api/records/{record['id']}/draft/files")
         headers = self._get_request_headers(user_context)
 
@@ -287,13 +314,15 @@ def _upload_file_to_draft_record(self, record: InvenioRecord, filename: str, nat
         response = requests.post(commit_file_upload_url, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 200)
 
-    def _publish_draft_record(self, record: InvenioRecord, user_context=None):
+    def _publish_draft_record(
+        self, record: InvenioRecord, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
+    ):
         publish_record_url = urljoin(self._invenio_url, f"api/records/{record['id']}/draft/actions/publish")
         headers = self._get_request_headers(user_context)
         response = requests.post(publish_record_url, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 202)
 
-    def _get_creator_from_user_context(self, user_context):
+    def _get_creator_from_user_context(self, user_context: Optional[ProvidesUserFileSourcesUserContext]):
         preferences = user_context.preferences if user_context else None
         public_name = preferences.get(f"{self.id}|public_name", None) if preferences else None
         family_name = "Galaxy User"
@@ -307,7 +336,9 @@ def _get_creator_from_user_context(self, user_context):
                 given_name = public_name
         return {"person_or_org": {"family_name": family_name, "given_name": given_name, "type": "personal"}}
 
-    def _get_public_records_user_setting_enabled_status(self, user_context) -> bool:
+    def _get_public_records_user_setting_enabled_status(
+        self, user_context: Optional[ProvidesUserFileSourcesUserContext]
+    ) -> bool:
         preferences = user_context.preferences if user_context else None
         public_records = preferences.get(f"{self.id}|public_records", None) if preferences else None
         if public_records:

From 6fb9349541c36263883114ec2701e3bcbafa7c23 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 16:28:37 +0200
Subject: [PATCH 05/41] Add write intent option to File Sources

This options helps to identify when we are browsing a file source with the "intent to write" to it.

This is helpful to avoid listing those elements (directories/records) that might not be writable (protected, read-only, etc.) even if the file source itself is writable.

The plugin implementation should handle this option accordingly if necessary.
---
 lib/galaxy/files/sources/__init__.py          |  7 ++++++-
 lib/galaxy/managers/remote_files.py           | 12 +++++++++++-
 lib/galaxy/webapps/galaxy/api/remote_files.py | 12 +++++++++++-
 3 files changed, 28 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index d369fcfe4293..272547bc26f8 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -53,7 +53,12 @@ class FilesSourceProperties(TypedDict):
 
 
 class FilesSourceOptions:
-    """Options to control behaviour of filesource operations, such as realize_to and write_from"""
+    """Options to control behavior of file source operations, such as realize_to, write_from and list."""
+
+    # Indicates access to the FS operation with intent to write.
+    # A file source can be "writeable" but, for example, some directories (or elements) may be restricted or read-only
+    # so those should be skipped while browsing with write_intent=True.
+    write_intent: Optional[bool]
 
     # Property overrides for values initially configured through the constructor. For example
     # the HTTPFilesSource passes in additional http_headers through these properties, which
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index fd577e546b69..fb589880133f 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -8,6 +8,7 @@
     ConfiguredFileSources,
     ProvidesUserFileSourcesUserContext,
 )
+from galaxy.files.sources import FilesSourceOptions
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.schema.remote_files import (
     AnyRemoteFilesListResponse,
@@ -41,6 +42,7 @@ def index(
         format: Optional[RemoteFilesFormat],
         recursive: Optional[bool],
         disable: Optional[RemoteFilesDisableMode],
+        write_intent: Optional[bool] = False,
     ) -> AnyRemoteFilesListResponse:
         """Returns a list of remote files available to the user."""
 
@@ -75,8 +77,16 @@ def index(
 
         file_source_path = self._file_sources.get_file_source_path(uri)
         file_source = file_source_path.file_source
+
+        opts = FilesSourceOptions()
+        opts.write_intent = write_intent or False
         try:
-            index = file_source.list(file_source_path.path, recursive=recursive, user_context=user_file_source_context)
+            index = file_source.list(
+                file_source_path.path,
+                recursive=recursive,
+                user_context=user_file_source_context,
+                opts=opts,
+            )
         except exceptions.MessageException:
             log.warning(f"Problem listing file source path {file_source_path}", exc_info=True)
             raise
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 39f21c872768..84957a11018e 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -59,6 +59,15 @@
     ),
 )
 
+WriteIntentQueryParam: Optional[bool] = Query(
+    default=None,
+    title="Write Intent",
+    description=(
+        "Whether the query is made with the intention of writing to the source."
+        " If set to True, only entries that can be written to will be accessible."
+    ),
+)
+
 BrowsableQueryParam: Optional[bool] = Query(
     default=True,
     title="Browsable filesources only",
@@ -90,9 +99,10 @@ async def index(
         format: Optional[RemoteFilesFormat] = FormatQueryParam,
         recursive: Optional[bool] = RecursiveQueryParam,
         disable: Optional[RemoteFilesDisableMode] = DisableModeQueryParam,
+        write_intent: Optional[bool] = WriteIntentQueryParam,
     ) -> AnyRemoteFilesListResponse:
         """Lists all remote files available to the user from different sources."""
-        return self.manager.index(user_ctx, target, format, recursive, disable)
+        return self.manager.index(user_ctx, target, format, recursive, disable, write_intent=write_intent)
 
     @router.get(
         "/api/remote_files/plugins",

From bf15a1df556c22dd5afd21172a0f89d19f1b318e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 16:38:44 +0200
Subject: [PATCH 06/41] Add create_entry endpoint for File sources

This allows to create a new entry (directory/record) in those remote file sources
that supports it. By default, the endpoint will raise NotImplementedError unless
the plugin implements the _create_entry method.
---
 lib/galaxy/files/sources/__init__.py          | 31 +++++++++++++++--
 lib/galaxy/managers/remote_files.py           | 21 ++++++++++++
 lib/galaxy/schema/remote_files.py             | 34 +++++++++++++++++++
 lib/galaxy/webapps/galaxy/api/remote_files.py | 20 ++++++++++-
 4 files changed, 103 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index 272547bc26f8..863dfb03e3d5 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -67,6 +67,18 @@ class FilesSourceOptions:
     extra_props: Optional[FilesSourceProperties]
 
 
+class EntryData(TypedDict):
+    name: str
+    # May contain additional properties depending on the file source
+
+
+class Entry(TypedDict):
+    name: str
+    uri: str
+    # May contain additional properties depending on the file source
+    external_link: NotRequired[str]
+
+
 class SingleFileSource(metaclass=abc.ABCMeta):
     """
     Represents a protocol handler for a single remote file that can be read by or written to by Galaxy.
@@ -298,9 +310,20 @@ def list(self, path="/", recursive=False, user_context=None, opts: Optional[File
     def _list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None):
         pass
 
+    def create_entry(
+        self, entry_data: EntryData, user_context=None, opts: Optional[FilesSourceOptions] = None
+    ) -> Entry:
+        self._ensure_writeable()
+        self._check_user_access(user_context)
+        return self._create_entry(entry_data, user_context, opts)
+
+    def _create_entry(
+        self, entry_data: EntryData, user_context=None, opts: Optional[FilesSourceOptions] = None
+    ) -> Entry:
+        raise NotImplementedError()
+
     def write_from(self, target_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
-        if not self.get_writable():
-            raise Exception("Cannot write to a non-writable file source.")
+        self._ensure_writeable()
         self._check_user_access(user_context)
         self._write_from(target_path, native_path, user_context=user_context, opts=opts)
 
@@ -316,6 +339,10 @@ def realize_to(self, source_path, native_path, user_context=None, opts: Optional
     def _realize_to(self, source_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
         pass
 
+    def _ensure_writeable(self):
+        if not self.get_writable():
+            raise Exception("Cannot write to a non-writable file source.")
+
     def _check_user_access(self, user_context):
         """Raises an exception if the given user doesn't have the rights to access this file source.
 
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index fb589880133f..470ae5cb3307 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -12,6 +12,8 @@
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.schema.remote_files import (
     AnyRemoteFilesListResponse,
+    CreatedEntryResponse,
+    CreateEntryPayload,
     FilesSourcePlugin,
     FilesSourcePluginList,
     RemoteFilesDisableMode,
@@ -139,3 +141,22 @@ def get_files_source_plugins(
     @property
     def _file_sources(self) -> ConfiguredFileSources:
         return self._app.file_sources
+
+    def create_entry(self, user_ctx: ProvidesUserContext, entry_data: CreateEntryPayload) -> CreatedEntryResponse:
+        """Create an entry (directory or record) in a remote files location."""
+        target = entry_data.target
+        user_file_source_context = ProvidesUserFileSourcesUserContext(user_ctx)
+        self._file_sources.validate_uri_root(target, user_context=user_file_source_context)
+        file_source_path = self._file_sources.get_file_source_path(target)
+        file_source = file_source_path.file_source
+        try:
+            result = file_source.create_entry(entry_data.dict(), user_context=user_file_source_context)
+        except Exception:
+            message = f"Problem creating entry {entry_data.name} in file source {entry_data.target}"
+            log.warning(message, exc_info=True)
+            raise exceptions.InternalServerError(message)
+        return CreatedEntryResponse(
+            name=result["name"],
+            uri=result["uri"],
+            external_link=result.get("external_link", None),
+        )
diff --git a/lib/galaxy/schema/remote_files.py b/lib/galaxy/schema/remote_files.py
index 66302390ea92..a408f076a9c8 100644
--- a/lib/galaxy/schema/remote_files.py
+++ b/lib/galaxy/schema/remote_files.py
@@ -149,3 +149,37 @@ class ListUriResponse(Model):
 
 
 AnyRemoteFilesListResponse = Union[ListUriResponse, ListJstreeResponse]
+
+
+class CreateEntryPayload(Model):
+    target: str = Field(
+        Required,
+        title="Target",
+        description="The target file source to create the entry in.",
+    )
+    name: str = Field(
+        Required,
+        title="Name",
+        description="The name of the entry to create.",
+        example="my_new_entry",
+    )
+
+
+class CreatedEntryResponse(Model):
+    name: str = Field(
+        Required,
+        title="Name",
+        description="The name of the created entry.",
+        example="my_new_entry",
+    )
+    uri: str = Field(
+        Required,
+        title="URI",
+        description="The URI of the created entry.",
+        example="gxfiles://my_new_entry",
+    )
+    external_link: Optional[str] = Field(
+        default=None,
+        title="External link",
+        description="An optional external link to the created entry if available.",
+    )
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 84957a11018e..16284e265e3c 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -4,12 +4,15 @@
 import logging
 from typing import Optional
 
+from fastapi import Body
 from fastapi.param_functions import Query
 
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.remote_files import RemoteFilesManager
 from galaxy.schema.remote_files import (
     AnyRemoteFilesListResponse,
+    CreatedEntryResponse,
+    CreateEntryPayload,
     FilesSourcePluginList,
     RemoteFilesDisableMode,
     RemoteFilesFormat,
@@ -115,4 +118,19 @@ async def plugins(
         browsable_only: Optional[bool] = BrowsableQueryParam,
     ) -> FilesSourcePluginList:
         """Display plugin information for each of the gxfiles:// URI targets available."""
-        return self.manager.get_files_source_plugins(user_ctx, browsable_only)
+
+    @router.post(
+        "/api/remote_files",
+        summary="Creates a new entry (directory/record) on the remote files source.",
+    )
+    async def create_entry(
+        self,
+        user_ctx: ProvidesUserContext = DependsOnTrans,
+        payload: CreateEntryPayload = Body(
+            ...,
+            title="Entry Data",
+            description="Information about the entry to create. Depends on the target file source.",
+        ),
+    ) -> CreatedEntryResponse:
+        """Creates a new entry on the remote files source."""
+        return self.manager.create_entry(user_ctx, payload)

From 35dfa9c2aced221e185179bd4e11617ccdf7aed4 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 17:23:53 +0200
Subject: [PATCH 07/41] Add RDMFilesSource subclass

Implement the _create_entry method for InvenioRDMFilesSource and some additional refactors.
---
 lib/galaxy/files/sources/_rdm.py    |  61 +++++++++++++++
 lib/galaxy/files/sources/invenio.py | 116 +++++++++++++++++-----------
 2 files changed, 133 insertions(+), 44 deletions(-)
 create mode 100644 lib/galaxy/files/sources/_rdm.py

diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
new file mode 100644
index 000000000000..9479982be50a
--- /dev/null
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -0,0 +1,61 @@
+import logging
+from typing import (
+    cast,
+    Optional,
+)
+
+from typing_extensions import Unpack
+
+from galaxy.files import ProvidesUserFileSourcesUserContext
+from galaxy.files.sources import (
+    BaseFilesSource,
+    FilesSourceProperties,
+)
+
+log = logging.getLogger(__name__)
+
+
+class RDMFilesSourceProperties(FilesSourceProperties):
+    url: str
+
+
+class RDMFilesSource(BaseFilesSource):
+    """Base class for Research Data Management (RDM) file sources.
+
+    This class is not intended to be used directly, but rather to be subclassed
+    by file sources that interact with RDM repositories.
+
+    A RDM file source is similar to a regular file source, but instead of tree of
+    files and directories, it provides a (one level) list of records (representing directories)
+    that can contain only files (no subdirectories).
+
+    In addition, RDM file sources might need to create a new record (directory) in advance in the
+    repository, and then upload a file to it. This is done by calling the `create_entry`
+    method.
+
+    """
+
+    # This allows to filter out the RDM file sources from the list of available
+    # file sources.
+    supports_rdm = True
+
+    def __init__(self, **kwd: Unpack[FilesSourceProperties]):
+        props = self._parse_common_config_opts(kwd)
+        base_url = props.get("url", None)
+        if not base_url:
+            raise Exception("URL for RDM repository must be provided in configuration")
+        self._repository_url = base_url
+        self._props = props
+
+    @property
+    def repository_url(self) -> str:
+        return self._repository_url
+
+    def _serialization_props(
+        self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
+    ) -> RDMFilesSourceProperties:
+        effective_props = {}
+        for key, val in self._props.items():
+            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
+        effective_props["url"] = self.repository_url
+        return cast(RDMFilesSourceProperties, effective_props)
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 1aa70ed0c6af..d1765f0eafc7 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -4,7 +4,6 @@
 import ssl
 import urllib.request
 from typing import (
-    cast,
     List,
     Optional,
 )
@@ -14,15 +13,15 @@
 from typing_extensions import (
     Literal,
     TypedDict,
-    Unpack,
 )
 
 from galaxy.files import ProvidesUserFileSourcesUserContext
 from galaxy.files.sources import (
-    BaseFilesSource,
+    Entry,
+    EntryData,
     FilesSourceOptions,
-    FilesSourceProperties,
 )
+from galaxy.files.sources._rdm import RDMFilesSource
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     get_charset_from_http_headers,
@@ -39,10 +38,6 @@
 AccessStatus = Literal["public", "restricted"]
 
 
-class InvenioFilesSourceProperties(FilesSourceProperties):
-    url: str
-
-
 class ResourceType(TypedDict):
     id: str
 
@@ -104,6 +99,8 @@ class RecordLinks(TypedDict):
 class InvenioRecord(TypedDict):
     id: str
     title: str
+    created: str
+    updated: str
     resource_type: ResourceType
     publication_date: str
     access: RecordAccess
@@ -112,19 +109,11 @@ class InvenioRecord(TypedDict):
     links: RecordLinks
 
 
-class InvenioFilesSource(BaseFilesSource):
+class InvenioRDMFilesSource(RDMFilesSource):
     """A files source for Invenio turn-key research data management repository."""
 
     plugin_type = "inveniordm"
 
-    def __init__(self, **kwd: Unpack[InvenioFilesSourceProperties]):
-        props = self._parse_common_config_opts(kwd)
-        base_url = props.get("url", None)
-        if not base_url:
-            raise Exception("InvenioFilesSource requires a url")
-        self._invenio_url = base_url
-        self._props = props
-
     def _list(
         self,
         path="/",
@@ -132,10 +121,24 @@ def _list(
         user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
         opts: Optional[FilesSourceOptions] = None,
     ):
+        write_intent = opts and opts.write_intent or False
         is_root_path = path == "/"
         if is_root_path:
-            return self._list_records(user_context)
-        return self._list_record_files(path, user_context)
+            return self._list_records(write_intent, user_context)
+        return self._list_record_files(path, write_intent, user_context)
+
+    def _create_entry(
+        self,
+        entry_data: EntryData,
+        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ) -> Entry:
+        record = self._create_draft_record(entry_data["name"], user_context=user_context)
+        return {
+            "uri": self._to_plugin_uri(record["links"]["record"]),
+            "name": record["metadata"]["title"],
+            "external_link": record["links"]["self_html"],
+        }
 
     def _realize_to(
         self,
@@ -144,9 +147,8 @@ def _realize_to(
         user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
         opts: Optional[FilesSourceOptions] = None,
     ):
-        # TODO: source_path will be wrong when constructed from the UI as it assumes the target_uri is `get_root_uri() + filename`
-
-        remote_path = urljoin(self._invenio_url, source_path)
+        # source_path = '/api/records/pxpnk-7c133/Tester.rocrate.zip'
+        remote_path = urljoin(self.repository_url, source_path)
         # TODO: user_context is always None here when called from a data fetch.
         # This prevents downloading files that require authentication even if the user provided a token.
         headers = self._get_request_headers(user_context)
@@ -165,23 +167,48 @@ def _write_from(
         opts: Optional[FilesSourceOptions] = None,
     ):
         filename = os.path.basename(target_path)
-        record_title = f"{filename} (exported by Galaxy)"
-        draft_record = self._create_draft_record(title=record_title, user_context=user_context)
+        dirname = os.path.dirname(target_path)
+        record_id = dirname.replace("/api/records/", "")
+        use_existing_record = len(record_id) > 5
+
+        # TODO: if we create the record here, then the target_path of the export will not have the record id and it will not be possible to import it back.
+        # We need to create the record before the export and then use the record id in the target_path.
+
+        if use_existing_record:
+            draft_record = self._get_draft_record(record_id, user_context=user_context)
+        else:
+            record_title = f"{filename} (exported by Galaxy)"
+            draft_record = self._create_draft_record(title=record_title, user_context=user_context)
         try:
             self._upload_file_to_draft_record(draft_record, filename, native_path, user_context=user_context)
             self._publish_draft_record(draft_record, user_context=user_context)
         except Exception:
-            self._delete_draft_record(draft_record, user_context)
+            if not use_existing_record:
+                self._delete_draft_record(draft_record, user_context)
             raise
 
-    def _list_records(self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
+    def _list_records(self, write_intent: bool, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
+        if write_intent:
+            return self._list_writeable_records(user_context)
+        return self._list_all_records(user_context)
+
+    def _list_all_records(self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
+        # TODO: This is limited to 25 records by default. Add pagination support?
+        request_url = urljoin(self.repository_url, "api/records")
+        response_data = self._get_response(user_context, request_url)
+        return self._get_records_from_response(response_data)
+
+    def _list_writeable_records(self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
         # TODO: This is limited to 25 records by default. Add pagination support?
-        request_url = urljoin(self._invenio_url, "api/records")
+        # Only draft records can be written to.
+        request_url = urljoin(self.repository_url, "api/user/records?is_published=false")
         response_data = self._get_response(user_context, request_url)
         return self._get_records_from_response(response_data)
 
-    def _list_record_files(self, path, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
-        request_url = urljoin(self._invenio_url, f"{path}/files")
+    def _list_record_files(
+        self, path: str, write_intent: bool, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
+    ):
+        request_url = urljoin(self.repository_url, f"{path}{'/draft' if write_intent else '' }/files")
         response_data = self._get_response(user_context, request_url)
         return self._get_record_files_from_response(path, response_data)
 
@@ -199,9 +226,13 @@ def _get_request_headers(self, user_context: Optional[ProvidesUserFileSourcesUse
 
     def _get_records_from_response(self, response: dict):
         records = response["hits"]["hits"]
+        return self._get_records_as_directories(records)
+
+    def _get_records_as_directories(self, records):
         rval = []
         for record in records:
             uri = self._to_plugin_uri(record["links"]["self"])
+            # TODO: define model for Directory and File
             rval.append(
                 {
                     "class": "Directory",
@@ -237,16 +268,12 @@ def _get_record_files_from_response(self, path: str, response: dict):
         return rval
 
     def _to_plugin_uri(self, uri: str) -> str:
-        return uri.replace(self._invenio_url, self.get_uri_root())
+        return uri.replace(self.repository_url, self.get_uri_root())
 
-    def _serialization_props(
-        self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
-    ) -> InvenioFilesSourceProperties:
-        effective_props = {}
-        for key, val in self._props.items():
-            effective_props[key] = self._evaluate_prop(val, user_context=user_context)
-        effective_props["url"] = self._invenio_url
-        return cast(InvenioFilesSourceProperties, effective_props)
+    def _get_draft_record(self, record_id: str, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
+        request_url = urljoin(self.repository_url, f"api/records/{record_id}/draft")
+        draft_record = self._get_response(user_context, request_url)
+        return draft_record
 
     def _create_draft_record(
         self, title: str, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
@@ -274,7 +301,7 @@ def _create_draft_record(
                 "Cannot create record without authentication token. Please set your personal access token in your Galaxy preferences."
             )
 
-        create_record_url = urljoin(self._invenio_url, "api/records")
+        create_record_url = urljoin(self.repository_url, "api/records")
         response = requests.post(create_record_url, json=create_record_request, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 201)
         record = response.json()
@@ -295,15 +322,16 @@ def _upload_file_to_draft_record(
         native_path: str,
         user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
     ):
-        upload_file_url = urljoin(self._invenio_url, f"api/records/{record['id']}/draft/files")
+        upload_file_url = record["links"]["files"]
         headers = self._get_request_headers(user_context)
 
-        # Add file metadata
+        # Add file metadata entry
         response = requests.post(upload_file_url, json=[{"key": filename}], headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 201)
 
         # Upload file content
-        file_entry = response.json()["entries"][0]
+        entries = response.json()["entries"]
+        file_entry = next(entry for entry in entries if entry["key"] == filename)
         upload_file_content_url = file_entry["links"]["content"]
         commit_file_upload_url = file_entry["links"]["commit"]
         with open(native_path, "rb") as file:
@@ -317,7 +345,7 @@ def _upload_file_to_draft_record(
     def _publish_draft_record(
         self, record: InvenioRecord, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
     ):
-        publish_record_url = urljoin(self._invenio_url, f"api/records/{record['id']}/draft/actions/publish")
+        publish_record_url = urljoin(self.repository_url, f"api/records/{record['id']}/draft/actions/publish")
         headers = self._get_request_headers(user_context)
         response = requests.post(publish_record_url, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 202)
@@ -361,4 +389,4 @@ def _get_response_error_message(self, response):
         return error_message
 
 
-__all__ = ("InvenioFilesSource",)
+__all__ = ("InvenioRDMFilesSource",)

From 772292bac2308faa66d8b21248be81e81a9ef2b0 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 17:26:32 +0200
Subject: [PATCH 08/41] Allow filtering only RDM plugins in the API

---
 lib/galaxy/files/__init__.py                  |  3 +++
 lib/galaxy/managers/remote_files.py           |  8 ++++++--
 lib/galaxy/webapps/galaxy/api/remote_files.py | 10 ++++++++++
 3 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/files/__init__.py b/lib/galaxy/files/__init__.py
index 88184c7862bc..97f8c4765054 100644
--- a/lib/galaxy/files/__init__.py
+++ b/lib/galaxy/files/__init__.py
@@ -165,11 +165,14 @@ def plugins_to_dict(
         for_serialization: bool = False,
         user_context: Optional["FileSourceDictifiable"] = None,
         browsable_only: Optional[bool] = False,
+        rdm_only: Optional[bool] = False,
     ) -> List[Dict[str, Any]]:
         rval = []
         for file_source in self._file_sources:
             if not file_source.user_has_access(user_context):
                 continue
+            if rdm_only and not getattr(file_source, "supports_rdm", False):
+                continue
             if browsable_only and not file_source.get_browsable():
                 continue
             el = file_source.to_dict(for_serialization=for_serialization, user_context=user_context)
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index 470ae5cb3307..863c0494436c 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -128,12 +128,16 @@ def index(
         return index
 
     def get_files_source_plugins(
-        self, user_context: ProvidesUserContext, browsable_only: Optional[bool] = True
+        self, user_context: ProvidesUserContext, browsable_only: Optional[bool] = True, rdm_only: Optional[bool] = False
     ) -> FilesSourcePluginList:
         """Display plugin information for each of the gxfiles:// URI targets available."""
         user_file_source_context = ProvidesUserFileSourcesUserContext(user_context)
+        browsable_only = True if browsable_only is None else browsable_only
+        rdm_only = rdm_only or False
         plugins_dict = self._file_sources.plugins_to_dict(
-            user_context=user_file_source_context, browsable_only=True if browsable_only is None else browsable_only
+            user_context=user_file_source_context,
+            browsable_only=browsable_only,
+            rdm_only=rdm_only,
         )
         plugins = [FilesSourcePlugin(**plugin_dict) for plugin_dict in plugins_dict]
         return FilesSourcePluginList.construct(__root__=plugins)
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 16284e265e3c..ce930ebd0e11 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -80,6 +80,14 @@
     ),
 )
 
+RDMOnlyQueryParam: Optional[bool] = Query(
+    default=False,
+    title="RDM only",
+    description=(
+        "Whether to return only RDM compatible plugins. The default is `False`, which will return all plugins."
+    ),
+)
+
 
 @router.cbv
 class FastAPIRemoteFiles:
@@ -116,8 +124,10 @@ async def plugins(
         self,
         user_ctx: ProvidesUserContext = DependsOnTrans,
         browsable_only: Optional[bool] = BrowsableQueryParam,
+        rdm_only: Optional[bool] = RDMOnlyQueryParam,
     ) -> FilesSourcePluginList:
         """Display plugin information for each of the gxfiles:// URI targets available."""
+        return self.manager.get_files_source_plugins(user_ctx, browsable_only, rdm_only)
 
     @router.post(
         "/api/remote_files",

From 31000c101f551f56b9626a115c9d2f7e0df16e2a Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 17:27:59 +0200
Subject: [PATCH 09/41] Update client API schema

---
 client/src/schema/schema.ts | 82 +++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)

diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index 5961148ca6a9..6668bfebbff0 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -1232,6 +1232,11 @@ export interface paths {
          * @description Lists all remote files available to the user from different sources.
          */
         get: operations["index_api_remote_files_get"];
+        /**
+         * Creates a new entry (directory/record) on the remote files source.
+         * @description Creates a new entry on the remote files source.
+         */
+        post: operations["create_entry_api_remote_files_post"];
     };
     "/api/remote_files/plugins": {
         /**
@@ -2597,6 +2602,23 @@ export interface components {
         ConvertedDatasetsMap: {
             [key: string]: string | undefined;
         };
+        /**
+         * CreateEntryPayload
+         * @description Base model definition with common configuration used by all derived models.
+         */
+        CreateEntryPayload: {
+            /**
+             * Name
+             * @description The name of the entry to create.
+             * @example my_new_entry
+             */
+            name: string;
+            /**
+             * Target
+             * @description The target file source to create the entry in.
+             */
+            target: string;
+        };
         /**
          * CreateHistoryContentFromStore
          * @description Base model definition with common configuration used by all derived models.
@@ -2968,6 +2990,29 @@ export interface components {
              */
             url: string;
         };
+        /**
+         * CreatedEntryResponse
+         * @description Base model definition with common configuration used by all derived models.
+         */
+        CreatedEntryResponse: {
+            /**
+             * External link
+             * @description An optional external link to the created entry if available.
+             */
+            external_link?: string;
+            /**
+             * Name
+             * @description The name of the created entry.
+             * @example my_new_entry
+             */
+            name: string;
+            /**
+             * URI
+             * @description The URI of the created entry.
+             * @example gxfiles://my_new_entry
+             */
+            uri: string;
+        };
         /**
          * CreatedUserModel
          * @description User in a transaction context.
@@ -11122,11 +11167,13 @@ export interface operations {
             /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
             /** @description Wether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
             /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
+            /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be accessible. */
             query?: {
                 target?: string;
                 format?: components["schemas"]["RemoteFilesFormat"];
                 recursive?: boolean;
                 disable?: components["schemas"]["RemoteFilesDisableMode"];
+                write_intent?: boolean;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -16081,11 +16128,13 @@ export interface operations {
             /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
             /** @description Wether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
             /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
+            /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be accessible. */
             query?: {
                 target?: string;
                 format?: components["schemas"]["RemoteFilesFormat"];
                 recursive?: boolean;
                 disable?: components["schemas"]["RemoteFilesDisableMode"];
+                write_intent?: boolean;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -16109,6 +16158,37 @@ export interface operations {
             };
         };
     };
+    create_entry_api_remote_files_post: {
+        /**
+         * Creates a new entry (directory/record) on the remote files source.
+         * @description Creates a new entry on the remote files source.
+         */
+        parameters?: {
+            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            header?: {
+                "run-as"?: string;
+            };
+        };
+        requestBody: {
+            content: {
+                "application/json": components["schemas"]["CreateEntryPayload"];
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["CreatedEntryResponse"];
+                };
+            };
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"];
+                };
+            };
+        };
+    };
     plugins_api_remote_files_plugins_get: {
         /**
          * Display plugin information for each of the gxfiles:// URI targets available.
@@ -16116,8 +16196,10 @@ export interface operations {
          */
         parameters?: {
             /** @description Whether to return browsable filesources only. The default is `True`, which will omit filesourceslike `http` and `base64` that do not implement a list method. */
+            /** @description Whether to return only RDM compatible plugins. The default is `False`, which will return all plugins. */
             query?: {
                 browsable_only?: boolean;
+                rdm_only?: boolean;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {

From 6db572393250a2c60d035d2cf5f2e744e58b7223 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 17:33:42 +0200
Subject: [PATCH 10/41] Update FilesDialog services

- Add new API parameters
- Add new POST endpoint for creating entries
- Add some code docs
---
 client/src/components/FilesDialog/services.ts | 34 ++++++++++++++++---
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/client/src/components/FilesDialog/services.ts b/client/src/components/FilesDialog/services.ts
index f022c7c4a0d4..12ad338dc08d 100644
--- a/client/src/components/FilesDialog/services.ts
+++ b/client/src/components/FilesDialog/services.ts
@@ -5,17 +5,43 @@ export type FilesSourcePlugin = components["schemas"]["FilesSourcePlugin"];
 export type RemoteFile = components["schemas"]["RemoteFile"];
 export type RemoteDirectory = components["schemas"]["RemoteDirectory"];
 export type RemoteEntry = RemoteFile | RemoteDirectory;
+export type CreatedEntry = components["schemas"]["CreatedEntryResponse"];
 
 const getRemoteFilesPlugins = fetcher.path("/api/remote_files/plugins").method("get").create();
 
-export async function getFileSources(): Promise<FilesSourcePlugin[]> {
-    const { data } = await getRemoteFilesPlugins({ browsable_only: true });
+/**
+ * Get the list of available file sources from the server that can be browsed.
+ * @param rdm_only Whether to only include Research Data Management (RDM) specific file sources.
+ * @returns The list of available file sources from the server.
+ */
+export async function getFileSources(rdm_only = false): Promise<FilesSourcePlugin[]> {
+    const { data } = await getRemoteFilesPlugins({ browsable_only: true, rdm_only: rdm_only });
     return data;
 }
 
 const getRemoteFiles = fetcher.path("/api/remote_files").method("get").create();
 
-export async function browseRemoteFiles(uri: string, isRecursive = false): Promise<RemoteEntry[]> {
-    const { data } = await getRemoteFiles({ target: uri, recursive: isRecursive });
+/**
+ * Get the list of files and directories from the server for the given file source URI.
+ * @param uri The file source URI to browse.
+ * @param isRecursive Whether to recursively retrieve all files inside subdirectories.
+ * @param writeIntent Whether to include only entries that can be written to.
+ * @returns The list of files and directories from the server for the given URI.
+ */
+export async function browseRemoteFiles(uri: string, isRecursive = false, writeIntent = false): Promise<RemoteEntry[]> {
+    const { data } = await getRemoteFiles({ target: uri, recursive: isRecursive, write_intent: writeIntent });
     return data as RemoteEntry[];
 }
+
+const createEntry = fetcher.path("/api/remote_files").method("post").create();
+
+/**
+ * Create a new entry (directory/record) on the given file source URI.
+ * @param uri The file source URI to create the entry in.
+ * @param name The name of the entry to create.
+ * @returns The created entry details.
+ */
+export async function createRemoteEntry(uri: string, name: string): Promise<CreatedEntry> {
+    const { data } = await createEntry({ target: uri, name: name });
+    return data;
+}

From 6af8aad7b502c1b5b2e93dbd12b29d23cf83ed18 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 17:34:37 +0200
Subject: [PATCH 11/41] Allow to filter RDM FS in composable

---
 client/src/composables/fileSources.ts | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/client/src/composables/fileSources.ts b/client/src/composables/fileSources.ts
index 67eb3d635676..d2a378b19350 100644
--- a/client/src/composables/fileSources.ts
+++ b/client/src/composables/fileSources.ts
@@ -4,14 +4,16 @@ import { FilesSourcePlugin, getFileSources } from "@/components/FilesDialog/serv
 
 /**
  * Composable for accessing and working with file sources.
+ *
+ * @param rdmOnly Whether to only include Research Data Management (RDM) specific file sources.
  */
-export function useFileSources() {
+export function useFileSources(rdmOnly = false) {
     const isLoading = ref(true);
     const hasWritable = ref(false);
     const fileSources = ref<FilesSourcePlugin[]>([]);
 
     onMounted(async () => {
-        fileSources.value = await getFileSources();
+        fileSources.value = await getFileSources(rdmOnly);
         hasWritable.value = fileSources.value.some((fs) => fs.writable);
         isLoading.value = false;
     });

From 314ca8b3a280d72c155befcf96d4ce50956032b6 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 17:37:06 +0200
Subject: [PATCH 12/41] Allow to filter RDM FS in FilesInput

---
 client/src/components/FilesDialog/FilesInput.vue | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/src/components/FilesDialog/FilesInput.vue b/client/src/components/FilesDialog/FilesInput.vue
index 11a1abcd5d8d..c7a0c88f680a 100644
--- a/client/src/components/FilesDialog/FilesInput.vue
+++ b/client/src/components/FilesDialog/FilesInput.vue
@@ -8,6 +8,7 @@ interface Props {
     value: string;
     mode?: "file" | "directory";
     requireWritable?: boolean;
+    rdmOnly?: boolean;
 }
 
 interface SelectableFile {
@@ -36,6 +37,7 @@ const selectFile = () => {
     const dialogProps = {
         mode: props.mode,
         requireWritable: props.requireWritable,
+        rdmOnly: props.rdmOnly,
     };
     filesDialog((selected: SelectableFile) => {
         currentValue.value = selected?.url;

From f1aaaf98ee6ddaffa62522a56c5fe23e42b021d2 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 20 Jul 2023 17:39:12 +0200
Subject: [PATCH 13/41] Update FilesDialog

- Add new mode "source" to select only the root level of a file source.
- Allow filtering FS by RDM support
- Document props
---
 .../components/FilesDialog/FilesDialog.vue    | 25 ++++++++++++++++---
 1 file changed, 22 insertions(+), 3 deletions(-)

diff --git a/client/src/components/FilesDialog/FilesDialog.vue b/client/src/components/FilesDialog/FilesDialog.vue
index f4ff8a8e57ba..2a6e7a570881 100644
--- a/client/src/components/FilesDialog/FilesDialog.vue
+++ b/client/src/components/FilesDialog/FilesDialog.vue
@@ -21,9 +21,19 @@ import SelectionDialog from "@/components/SelectionDialog/SelectionDialog.vue";
 library.add(faCaretLeft);
 
 interface FilesDialogProps {
+    /** Whether to allow multiple selections */
     multiple?: boolean;
-    mode?: "file" | "directory";
+    /** The browsing mode:
+     * - `file` - allows to select files or directories contained in a source (default)
+     * - `directory` - allows to select directories (paths) only
+     * - `source` - allows to select a source plugin root and doesn't list its contents
+     */
+    mode?: "file" | "directory" | "source";
+    /** Whether to show only writable sources */
     requireWritable?: boolean;
+    /** Whether to show only RDM sources */
+    rdmOnly?: boolean;
+    /** Callback function to be called passing the results when selection is complete */
     callback?: (files: any) => void;
 }
 
@@ -31,6 +41,7 @@ const props = withDefaults(defineProps<FilesDialogProps>(), {
     multiple: false,
     mode: "file",
     requireWritable: false,
+    rdmOnly: false,
     callback: () => {},
 });
 
@@ -204,7 +215,7 @@ function load(record?: DirectoryRecord) {
     undoShow.value = !urlTracker.value.atRoot();
     if (urlTracker.value.atRoot() || errorMessage.value) {
         errorMessage.value = undefined;
-        getFileSources()
+        getFileSources(props.rdmOnly)
             .then((results) => {
                 const convertedItems = results
                     .filter((item) => !props.requireWritable || item.writable)
@@ -222,7 +233,15 @@ function load(record?: DirectoryRecord) {
         if (!currentDirectory.value) {
             return;
         }
-        browseRemoteFiles(currentDirectory.value?.url)
+        if (props.mode === "source") {
+            // In source mode, only show sources, not contents
+            items.value = [];
+            optionsShow.value = true;
+            showTime.value = false;
+            showDetails.value = false;
+            return;
+        }
+        browseRemoteFiles(currentDirectory.value?.url, false, props.requireWritable)
             .then((results) => {
                 items.value = filterByMode(results).map(entryToRecord);
                 formatRows();

From 556160ddaab9c447e9eb347fdb23984b62c603a0 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 21 Jul 2023 14:15:08 +0200
Subject: [PATCH 14/41] Add ExportDOIForm component

This component allows to select or create new records in a DOI repository (RDM file source) for uploading exported artifacts (histories, datasets, etc.) to them.
---
 .../src/components/Common/ExportDOIForm.vue   | 162 ++++++++++++++++++
 1 file changed, 162 insertions(+)
 create mode 100644 client/src/components/Common/ExportDOIForm.vue

diff --git a/client/src/components/Common/ExportDOIForm.vue b/client/src/components/Common/ExportDOIForm.vue
new file mode 100644
index 000000000000..d16b05a6b6db
--- /dev/null
+++ b/client/src/components/Common/ExportDOIForm.vue
@@ -0,0 +1,162 @@
+<script setup lang="ts">
+import { BButton, BCard, BFormGroup, BFormInput, BFormRadio, BFormRadioGroup } from "bootstrap-vue";
+import { computed, ref } from "vue";
+
+import { CreatedEntry, createRemoteEntry } from "@/components/FilesDialog/services";
+import localize from "@/utils/localization";
+
+import ExternalLink from "@/components/ExternalLink.vue";
+import FilesInput from "@/components/FilesDialog/FilesInput.vue";
+
+interface Props {
+    what?: string;
+    clearInputAfterExport?: boolean;
+    defaultRecordName?: string;
+    defaultFilename?: string;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    what: "archive",
+    clearInputAfterExport: false,
+    defaultRecordName: "",
+    defaultFilename: "",
+});
+
+const emit = defineEmits<{
+    (e: "export", recordUri: string, fileName: string, newRecordName?: string): void;
+}>();
+
+type ExportChoice = "existing" | "new";
+
+const recordUri = ref<string>("");
+const sourceUri = ref<string>("");
+const fileName = ref<string>(props.defaultFilename);
+const exportChoice = ref<ExportChoice>("new");
+const recordName = ref<string>(props.defaultRecordName);
+const newEntry = ref<CreatedEntry>();
+
+const canCreateRecord = computed(() => Boolean(sourceUri.value) && Boolean(recordName.value));
+
+const canExport = computed(() => Boolean(recordUri.value) && Boolean(fileName.value));
+
+const repositoryRecordDescription = computed(() => localize(`Select a repository to export ${props.what} to.`));
+
+const nameDescription = computed(() => localize("Give the exported file a name."));
+const recordNameDescription = computed(() => localize("Give the new record a name or title."));
+
+const namePlaceholder = computed(() => localize("File name"));
+const recordNamePlaceholder = computed(() => localize("Record name"));
+
+function doExport() {
+    emit("export", recordUri.value, fileName.value);
+
+    if (props.clearInputAfterExport) {
+        clearInputs();
+    }
+}
+
+async function doCreateRecord() {
+    //TODO: handle errors
+    newEntry.value = await createRemoteEntry(sourceUri.value, recordName.value);
+    recordUri.value = newEntry.value.uri;
+}
+
+function clearInputs() {
+    recordUri.value = "";
+    sourceUri.value = "";
+    fileName.value = "";
+    newEntry.value = undefined;
+}
+</script>
+
+<template>
+    <div class="export-to-doi-repository">
+        <BFormGroup id="fieldset-name" label-for="name" :description="nameDescription" class="mt-3">
+            <BFormInput id="name" v-model="fileName" :placeholder="namePlaceholder" required />
+        </BFormGroup>
+
+        <BFormRadioGroup v-model="exportChoice" class="export-radio-group">
+            <BFormRadio v-localize name="exportChoice" value="new"> Export to new record </BFormRadio>
+            <BFormRadio v-localize name="exportChoice" value="existing"> Export to existing draft record </BFormRadio>
+        </BFormRadioGroup>
+
+        <div v-if="exportChoice === 'new'">
+            <div v-if="newEntry">
+                <BCard>
+                    <p v-localize>
+                        A new draft record with name <b>{{ newEntry.name }}</b> has been created in the repository.
+                    </p>
+                    <p v-if="newEntry.external_link">
+                        You can preview the record in the repository and further edit its metadata at
+                        <ExternalLink :href="newEntry.external_link">
+                            <b>{{ newEntry.external_link }}</b>
+                        </ExternalLink>
+                    </p>
+                    <p v-localize>Please use the button below to upload the exported {{ props.what }} to the record.</p>
+                    <BButton
+                        v-localize
+                        class="export-button"
+                        variant="primary"
+                        :disabled="!canExport"
+                        @click.prevent="doExport">
+                        Export to this record
+                    </BButton>
+                </BCard>
+            </div>
+            <div v-else>
+                <BFormGroup
+                    id="fieldset-record"
+                    label-for="source-selector"
+                    :description="repositoryRecordDescription"
+                    class="mt-3">
+                    <FilesInput
+                        id="repository-selector"
+                        v-model="sourceUri"
+                        mode="source"
+                        :require-writable="true"
+                        :rdm-only="true" />
+                </BFormGroup>
+                <BFormGroup
+                    id="fieldset-record-name"
+                    label-for="record-name"
+                    :description="recordNameDescription"
+                    class="mt-3">
+                    <BFormInput id="record-name" v-model="recordName" :placeholder="recordNamePlaceholder" required />
+                </BFormGroup>
+                <p v-localize>
+                    You need to create the new record in a repository before exporting the {{ props.what }} to it.
+                </p>
+                <BButton
+                    v-localize
+                    class="export-button"
+                    variant="primary"
+                    :disabled="!canCreateRecord"
+                    @click.prevent="doCreateRecord">
+                    Create new record
+                </BButton>
+            </div>
+        </div>
+        <div v-else>
+            <BFormGroup
+                id="fieldset-record"
+                label-for="existing-record-selector"
+                :description="repositoryRecordDescription"
+                class="mt-3">
+                <FilesInput
+                    id="existing-record-selector"
+                    v-model="recordUri"
+                    mode="directory"
+                    :require-writable="true"
+                    :rdm-only="true" />
+            </BFormGroup>
+            <BButton
+                v-localize
+                class="export-button"
+                variant="primary"
+                :disabled="!canExport"
+                @click.prevent="doExport">
+                Export to existing record
+            </BButton>
+        </div>
+    </div>
+</template>

From 5cbc993c97699e8f79b011dd9847e754112fa95f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 21 Jul 2023 14:16:06 +0200
Subject: [PATCH 15/41] Add option to export histories to DOI repository

---
 .../History/Export/HistoryExport.vue          | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue
index 4ff671873a99..1262b53c32ec 100644
--- a/client/src/components/History/Export/HistoryExport.vue
+++ b/client/src/components/History/Export/HistoryExport.vue
@@ -10,6 +10,7 @@ import { DEFAULT_EXPORT_PARAMS, useShortTermStorage } from "composables/shortTer
 import { useTaskMonitor } from "composables/taskMonitor";
 import { copy as sendToClipboard } from "utils/clipboard";
 import { computed, onMounted, reactive, ref, watch } from "vue";
+import { RouterLink } from "vue-router";
 
 import { useHistoryStore } from "@/stores/historyStore";
 import { absPath } from "@/utils/redirect";
@@ -17,6 +18,7 @@ import { absPath } from "@/utils/redirect";
 import { exportToFileSource, getExportRecords, reimportHistoryFromRecord } from "./services";
 
 import ExportOptions from "./ExportOptions.vue";
+import ExportDOIForm from "components/Common/ExportDOIForm.vue";
 import ExportForm from "components/Common/ExportForm.vue";
 import ExportRecordDetails from "components/Common/ExportRecordDetails.vue";
 import ExportRecordTable from "components/Common/ExportRecordTable.vue";
@@ -29,6 +31,7 @@ const {
 } = useTaskMonitor();
 
 const { hasWritable: hasWritableFileSources } = useFileSources();
+const { hasWritable: hasWritableRDMFileSources } = useFileSources(true);
 
 const {
     isPreparing: isPreparingDownload,
@@ -228,6 +231,31 @@ function updateExportParams(newParams) {
                     </p>
                     <ExportForm what="history" :clear-input-after-export="true" @export="doExportToFileSource" />
                 </BTab>
+                <BTab
+                    v-if="hasWritableRDMFileSources"
+                    id="rdm-file-source-tab"
+                    title="to DOI repository"
+                    title-link-class="tab-export-to-doi-repo">
+                    <p>You can <b>publish your history</b> to one of the available DOI repositories here.</p>
+                    <p>
+                        Your history export archive needs to be uploaded to an existing record. You will need to create
+                        a <b>new record</b> on the repository or select an existing <b>draft record</b> and then export
+                        your history to it.
+                    </p>
+                    <BAlert show variant="info">
+                        You may need to setup your credentials for the selected repository in your
+                        <RouterLink to="/user/information" target="_blank">settings page</RouterLink> to be able to
+                        export. You can also define some default options for the export in those settings, like the
+                        public name you want to associate with your records or whether you want to publish them
+                        immediately or keep them as drafts after export.
+                    </BAlert>
+                    <ExportDOIForm
+                        what="history"
+                        :default-filename="historyName + ' (Galaxy History)'"
+                        :default-record-name="historyName"
+                        :clear-input-after-export="true"
+                        @export="doExportToFileSource" />
+                </BTab>
             </BTabs>
         </BCard>
 

From 6b54f38a6f581a605dc9ba41e10e3600f4a3d283 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 24 Jul 2023 18:37:30 +0200
Subject: [PATCH 16/41] Fix URL conversion between Invenio API / FS plugin API

---
 lib/galaxy/files/sources/invenio.py | 65 ++++++++++++++++-------------
 1 file changed, 36 insertions(+), 29 deletions(-)

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index d1765f0eafc7..69d0cc7fc9d0 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -7,7 +7,10 @@
     List,
     Optional,
 )
-from urllib.parse import urljoin
+from urllib.parse import (
+    quote,
+    urljoin,
+)
 
 import requests
 from typing_extensions import (
@@ -112,8 +115,14 @@ class InvenioRecord(TypedDict):
 class InvenioRDMFilesSource(RDMFilesSource):
     """A files source for Invenio turn-key research data management repository."""
 
+    # TODO: refactor the whole thing
+
     plugin_type = "inveniordm"
 
+    @property
+    def records_api_url(self) -> str:
+        return f"{self._repository_url}/api/records"
+
     def _list(
         self,
         path="/",
@@ -147,18 +156,30 @@ def _realize_to(
         user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
         opts: Optional[FilesSourceOptions] = None,
     ):
-        # source_path = '/api/records/pxpnk-7c133/Tester.rocrate.zip'
-        remote_path = urljoin(self.repository_url, source_path)
+        download_file_content_url = self._to_download_file_content_url(source_path)
+
         # TODO: user_context is always None here when called from a data fetch.
         # This prevents downloading files that require authentication even if the user provided a token.
         headers = self._get_request_headers(user_context)
-        req = urllib.request.Request(remote_path, headers=headers)
+        req = urllib.request.Request(download_file_content_url, headers=headers)
         with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT, context=SSL_CONTEXT) as page:
             f = open(native_path, "wb")
             return stream_to_open_named_file(
                 page, f.fileno(), native_path, source_encoding=get_charset_from_http_headers(page.headers)
             )
 
+    def _to_download_file_content_url(self, source_path: str) -> str:
+        # source_path can be:
+        # - '/{record_id}/{file_name}' when reimporting
+        # - '/{record_id}/files/{file_name}/content' when downloading a existing file
+        # We need to return a fully qualified url like
+        # 'https://<repository_url>/api/records/{record_id}/files/{file_name}/content' in both cases.
+        if source_path.endswith("/content"):
+            return f"{self.records_api_url}{source_path}"
+        record_id = source_path.split("/")[1]
+        file_name = source_path.split("/")[-1]
+        return urljoin(self.repository_url, f"/api/records/{record_id}/files/{quote(file_name)}/content")
+
     def _write_from(
         self,
         target_path: str,
@@ -167,25 +188,11 @@ def _write_from(
         opts: Optional[FilesSourceOptions] = None,
     ):
         filename = os.path.basename(target_path)
-        dirname = os.path.dirname(target_path)
-        record_id = dirname.replace("/api/records/", "")
-        use_existing_record = len(record_id) > 5
-
-        # TODO: if we create the record here, then the target_path of the export will not have the record id and it will not be possible to import it back.
-        # We need to create the record before the export and then use the record id in the target_path.
-
-        if use_existing_record:
-            draft_record = self._get_draft_record(record_id, user_context=user_context)
-        else:
-            record_title = f"{filename} (exported by Galaxy)"
-            draft_record = self._create_draft_record(title=record_title, user_context=user_context)
-        try:
-            self._upload_file_to_draft_record(draft_record, filename, native_path, user_context=user_context)
-            self._publish_draft_record(draft_record, user_context=user_context)
-        except Exception:
-            if not use_existing_record:
-                self._delete_draft_record(draft_record, user_context)
-            raise
+        record_id = os.path.dirname(target_path)
+
+        draft_record = self._get_draft_record(record_id, user_context=user_context)
+        self._upload_file_to_draft_record(draft_record, filename, native_path, user_context=user_context)
+        self._publish_draft_record(draft_record, user_context=user_context)
 
     def _list_records(self, write_intent: bool, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
         if write_intent:
@@ -194,7 +201,7 @@ def _list_records(self, write_intent: bool, user_context: Optional[ProvidesUserF
 
     def _list_all_records(self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
         # TODO: This is limited to 25 records by default. Add pagination support?
-        request_url = urljoin(self.repository_url, "api/records")
+        request_url = self.records_api_url
         response_data = self._get_response(user_context, request_url)
         return self._get_records_from_response(response_data)
 
@@ -208,7 +215,7 @@ def _list_writeable_records(self, user_context: Optional[ProvidesUserFileSources
     def _list_record_files(
         self, path: str, write_intent: bool, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
     ):
-        request_url = urljoin(self.repository_url, f"{path}{'/draft' if write_intent else '' }/files")
+        request_url = f"{self.records_api_url}{path}{'/draft' if write_intent else '' }/files"
         response_data = self._get_response(user_context, request_url)
         return self._get_record_files_from_response(path, response_data)
 
@@ -268,10 +275,10 @@ def _get_record_files_from_response(self, path: str, response: dict):
         return rval
 
     def _to_plugin_uri(self, uri: str) -> str:
-        return uri.replace(self.repository_url, self.get_uri_root())
+        return uri.replace(self.records_api_url, self.get_uri_root())
 
     def _get_draft_record(self, record_id: str, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
-        request_url = urljoin(self.repository_url, f"api/records/{record_id}/draft")
+        request_url = f"{self.records_api_url}{record_id}/draft"
         draft_record = self._get_response(user_context, request_url)
         return draft_record
 
@@ -301,7 +308,7 @@ def _create_draft_record(
                 "Cannot create record without authentication token. Please set your personal access token in your Galaxy preferences."
             )
 
-        create_record_url = urljoin(self.repository_url, "api/records")
+        create_record_url = self.records_api_url
         response = requests.post(create_record_url, json=create_record_request, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 201)
         record = response.json()
@@ -345,7 +352,7 @@ def _upload_file_to_draft_record(
     def _publish_draft_record(
         self, record: InvenioRecord, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
     ):
-        publish_record_url = urljoin(self.repository_url, f"api/records/{record['id']}/draft/actions/publish")
+        publish_record_url = f"{self.records_api_url}/{record['id']}/draft/actions/publish"
         headers = self._get_request_headers(user_context)
         response = requests.post(publish_record_url, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 202)

From cfa908ca7afe1916f2f8a841df9e562bf14f31f4 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 25 Jul 2023 16:34:30 +0200
Subject: [PATCH 17/41] Fix title display of record

v-localize will remove spaces between tags for some reason.
---
 client/src/components/Common/ExportDOIForm.vue | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Common/ExportDOIForm.vue b/client/src/components/Common/ExportDOIForm.vue
index d16b05a6b6db..3b72eedb652f 100644
--- a/client/src/components/Common/ExportDOIForm.vue
+++ b/client/src/components/Common/ExportDOIForm.vue
@@ -83,8 +83,9 @@ function clearInputs() {
         <div v-if="exportChoice === 'new'">
             <div v-if="newEntry">
                 <BCard>
-                    <p v-localize>
-                        A new draft record with name <b>{{ newEntry.name }}</b> has been created in the repository.
+                    <p>
+                        <b>{{ newEntry.name }}</b>
+                        <span v-localize> draft record has been created in the repository.</span>
                     </p>
                     <p v-if="newEntry.external_link">
                         You can preview the record in the repository and further edit its metadata at

From f5c03952fbe0e459cc4cbaa0ea04e2d14df2804d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20L=C3=B3pez?=
 <46503462+davelopez@users.noreply.github.com>
Date: Wed, 26 Jul 2023 16:54:58 +0200
Subject: [PATCH 18/41] Fix wording in API doc

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 lib/galaxy/webapps/galaxy/api/remote_files.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index ce930ebd0e11..856d70018d46 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -67,7 +67,7 @@
     title="Write Intent",
     description=(
         "Whether the query is made with the intention of writing to the source."
-        " If set to True, only entries that can be written to will be accessible."
+        " If set to True, only entries that can be written to will be returned."
     ),
 )
 

From 87909d629bb2420389e8e33efa2771002b2d0ece Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 28 Jul 2023 13:53:03 +0200
Subject: [PATCH 19/41] Add TypedDicts to represent Directories and Files

+ Docstring
---
 lib/galaxy/files/sources/__init__.py | 29 ++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index 863dfb03e3d5..8dcdef0fa547 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -10,6 +10,7 @@
 )
 
 from typing_extensions import (
+    Literal,
     NotRequired,
     TypedDict,
 )
@@ -68,17 +69,40 @@ class FilesSourceOptions:
 
 
 class EntryData(TypedDict):
+    """Provides data to create a new entry in a file source."""
+
     name: str
     # May contain additional properties depending on the file source
 
 
 class Entry(TypedDict):
+    """Represents the result of creating a new entry in a file source."""
+
     name: str
     uri: str
     # May contain additional properties depending on the file source
     external_link: NotRequired[str]
 
 
+class RemoteEntry(TypedDict):
+    name: str
+    uri: str
+    path: str
+
+
+TDirectoryClass = TypedDict("TDirectoryClass", {"class": Literal["Directory"]})
+TFileClass = TypedDict("TFileClass", {"class": Literal["File"]})
+
+
+class RemoteDirectory(RemoteEntry, TDirectoryClass):
+    pass
+
+
+class RemoteFile(RemoteEntry, TFileClass):
+    size: int
+    ctime: str
+
+
 class SingleFileSource(metaclass=abc.ABCMeta):
     """
     Represents a protocol handler for a single remote file that can be read by or written to by Galaxy.
@@ -320,6 +344,11 @@ def create_entry(
     def _create_entry(
         self, entry_data: EntryData, user_context=None, opts: Optional[FilesSourceOptions] = None
     ) -> Entry:
+        """Create a new entry (directory) in the file source.
+
+        The file source must be writeable.
+        This function can be overridden by subclasses to provide a way of creating entries in the file source.
+        """
         raise NotImplementedError()
 
     def write_from(self, target_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):

From 55c05c6954b776ead3e65024affd3ca42c589a8e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 28 Jul 2023 14:22:00 +0200
Subject: [PATCH 20/41] Add RDMRepositoryInteractor interface + refactor

---
 lib/galaxy/files/sources/_rdm.py    | 120 +++++++++++-
 lib/galaxy/files/sources/invenio.py | 286 +++++++++++++---------------
 2 files changed, 243 insertions(+), 163 deletions(-)

diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index 9479982be50a..9e00950255ab 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -1,6 +1,8 @@
 import logging
 from typing import (
     cast,
+    List,
+    NamedTuple,
     Optional,
 )
 
@@ -10,15 +12,110 @@
 from galaxy.files.sources import (
     BaseFilesSource,
     FilesSourceProperties,
+    RemoteDirectory,
+    RemoteFile,
 )
 
 log = logging.getLogger(__name__)
 
+OptionalUserContext = Optional[ProvidesUserFileSourcesUserContext]
+
 
 class RDMFilesSourceProperties(FilesSourceProperties):
     url: str
 
 
+class RecordFilename(NamedTuple):
+    record_id: str
+    filename: str
+
+
+class RDMRepositoryInteractor:
+    """Base class for interacting with an external RDM repository.
+
+    This class is not intended to be used directly, but rather to be subclassed
+    by file sources that interact with RDM repositories.
+    """
+
+    def __init__(self, repository_url: str, plugin: BaseFilesSource):
+        self._repository_url = repository_url
+        self._plugin = plugin
+
+    @property
+    def plugin(self) -> BaseFilesSource:
+        """Returns the plugin associated with this repository interactor."""
+        return self._plugin
+
+    @property
+    def repository_url(self) -> str:
+        """Returns the base URL of the repository.
+
+        Example: https://zenodo.org
+        """
+        return self._repository_url
+
+    def to_plugin_uri(self, record_id: str, filename: Optional[str] = None) -> str:
+        """Creates a valid plugin URI to reference the given record_id.
+
+        If a filename is provided, the URI will reference the specific file in the record."""
+        raise NotImplementedError()
+
+    def get_records(self, write_intent: bool, user_context: OptionalUserContext = None) -> List[RemoteDirectory]:
+        """Returns the list of records in the repository."""
+        raise NotImplementedError()
+
+    def get_files_in_record(
+        self, record_id: str, write_intent: bool, user_context: OptionalUserContext = None
+    ) -> List[RemoteFile]:
+        """Returns the list of files contained in the given record."""
+        raise NotImplementedError()
+
+    def create_draft_record(self, title: str, user_context: OptionalUserContext = None):
+        """Creates a draft record (directory) in the repository with basic metadata.
+
+        The metadata is usually just the title of the record and the user that created it.
+        Some plugins might also provide additional metadata defaults in the user settings."""
+        raise NotImplementedError()
+
+    def upload_file_to_draft_record(
+        self,
+        record_id: str,
+        filename: str,
+        file_path: str,
+        user_context: OptionalUserContext = None,
+    ) -> None:
+        """Uploads a file with the provided filename (from file_path) to a draft record with the given record_id.
+
+        The draft record must have been created in advance with the `create_draft_record` method.
+        The file must exist in the file system at the given file_path.
+        The user_context might be required to authenticate the user in the repository.
+        """
+        raise NotImplementedError()
+
+    def download_file_from_record(
+        self,
+        record_id: str,
+        filename: str,
+        file_path: str,
+        user_context: OptionalUserContext = None,
+    ) -> None:
+        """Downloads a file with the provided filename from the record with the given record_id.
+
+        The file will be downloaded to the file system at the given file_path.
+        The user_context might be required to authenticate the user in the repository if the
+        file is not publicly available.
+        """
+        raise NotImplementedError()
+
+    def publish_draft_record(self, record_id: str, user_context: OptionalUserContext = None) -> None:
+        """Publishes the draft record with the given record_id.
+
+        The draft record must have been created in advance with the `create_draft_record` method.
+        The user_context might be required to authenticate the user in the repository.
+        """
+        raise NotImplementedError()
+
+
 class RDMFilesSource(BaseFilesSource):
     """Base class for Research Data Management (RDM) file sources.
 
@@ -46,16 +143,27 @@ def __init__(self, **kwd: Unpack[FilesSourceProperties]):
             raise Exception("URL for RDM repository must be provided in configuration")
         self._repository_url = base_url
         self._props = props
+        self._repository_interactor = self.get_repository_interactor(base_url)
 
     @property
-    def repository_url(self) -> str:
-        return self._repository_url
+    def repository(self) -> RDMRepositoryInteractor:
+        return self._repository_interactor
+
+    def get_repository_interactor(self, repository_url: str) -> RDMRepositoryInteractor:
+        """Returns an interactor compatible with the given repository URL.
+
+        This must be implemented by subclasses."""
+        raise NotImplementedError()
+
+    def parse_path(self, source_path: str) -> RecordFilename:
+        # source_path has always the format: '/{record_id}/{file_name}'
+        record_id = source_path.split("/")[1]
+        filename = source_path.split("/")[-1]
+        return RecordFilename(record_id=record_id, filename=filename)
 
-    def _serialization_props(
-        self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
-    ) -> RDMFilesSourceProperties:
+    def _serialization_props(self, user_context: OptionalUserContext = None) -> RDMFilesSourceProperties:
         effective_props = {}
         for key, val in self._props.items():
             effective_props[key] = self._evaluate_prop(val, user_context=user_context)
-        effective_props["url"] = self.repository_url
+        effective_props["url"] = self._repository_url
         return cast(RDMFilesSourceProperties, effective_props)
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 69d0cc7fc9d0..28be0d97da40 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -1,16 +1,12 @@
 import datetime
 import json
-import os
 import ssl
 import urllib.request
 from typing import (
     List,
     Optional,
 )
-from urllib.parse import (
-    quote,
-    urljoin,
-)
+from urllib.parse import quote
 
 import requests
 from typing_extensions import (
@@ -18,13 +14,18 @@
     TypedDict,
 )
 
-from galaxy.files import ProvidesUserFileSourcesUserContext
 from galaxy.files.sources import (
     Entry,
     EntryData,
     FilesSourceOptions,
+    RemoteDirectory,
+    RemoteFile,
+)
+from galaxy.files.sources._rdm import (
+    OptionalUserContext,
+    RDMFilesSource,
+    RDMRepositoryInteractor,
 )
-from galaxy.files.sources._rdm import RDMFilesSource
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     get_charset_from_http_headers,
@@ -115,36 +116,34 @@ class InvenioRecord(TypedDict):
 class InvenioRDMFilesSource(RDMFilesSource):
     """A files source for Invenio turn-key research data management repository."""
 
-    # TODO: refactor the whole thing
-
     plugin_type = "inveniordm"
 
-    @property
-    def records_api_url(self) -> str:
-        return f"{self._repository_url}/api/records"
+    def get_repository_interactor(self, repository_url: str) -> RDMRepositoryInteractor:
+        return InvenioRepositoryInteractor(repository_url, self)
 
     def _list(
         self,
         path="/",
         recursive=True,
-        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        user_context: OptionalUserContext = None,
         opts: Optional[FilesSourceOptions] = None,
     ):
         write_intent = opts and opts.write_intent or False
         is_root_path = path == "/"
         if is_root_path:
-            return self._list_records(write_intent, user_context)
-        return self._list_record_files(path, write_intent, user_context)
+            return self.repository.get_records(write_intent, user_context)
+        record_id, _ = self.parse_path(path)
+        return self.repository.get_files_in_record(record_id, write_intent, user_context)
 
     def _create_entry(
         self,
         entry_data: EntryData,
-        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        user_context: OptionalUserContext = None,
         opts: Optional[FilesSourceOptions] = None,
     ) -> Entry:
-        record = self._create_draft_record(entry_data["name"], user_context=user_context)
+        record = self.repository.create_draft_record(entry_data["name"], user_context=user_context)
         return {
-            "uri": self._to_plugin_uri(record["links"]["record"]),
+            "uri": self.repository.to_plugin_uri(record["id"]),
             "name": record["metadata"]["title"],
             "external_link": record["links"]["self_html"],
         }
@@ -153,141 +152,53 @@ def _realize_to(
         self,
         source_path: str,
         native_path: str,
-        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        user_context: OptionalUserContext = None,
         opts: Optional[FilesSourceOptions] = None,
     ):
-        download_file_content_url = self._to_download_file_content_url(source_path)
-
         # TODO: user_context is always None here when called from a data fetch.
         # This prevents downloading files that require authentication even if the user provided a token.
-        headers = self._get_request_headers(user_context)
-        req = urllib.request.Request(download_file_content_url, headers=headers)
-        with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT, context=SSL_CONTEXT) as page:
-            f = open(native_path, "wb")
-            return stream_to_open_named_file(
-                page, f.fileno(), native_path, source_encoding=get_charset_from_http_headers(page.headers)
-            )
 
-    def _to_download_file_content_url(self, source_path: str) -> str:
-        # source_path can be:
-        # - '/{record_id}/{file_name}' when reimporting
-        # - '/{record_id}/files/{file_name}/content' when downloading a existing file
-        # We need to return a fully qualified url like
-        # 'https://<repository_url>/api/records/{record_id}/files/{file_name}/content' in both cases.
-        if source_path.endswith("/content"):
-            return f"{self.records_api_url}{source_path}"
-        record_id = source_path.split("/")[1]
-        file_name = source_path.split("/")[-1]
-        return urljoin(self.repository_url, f"/api/records/{record_id}/files/{quote(file_name)}/content")
+        record_id, filename = self.parse_path(source_path)
+        self.repository.download_file_from_record(record_id, filename, native_path, user_context=user_context)
 
     def _write_from(
         self,
         target_path: str,
         native_path: str,
-        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        user_context: OptionalUserContext = None,
         opts: Optional[FilesSourceOptions] = None,
     ):
-        filename = os.path.basename(target_path)
-        record_id = os.path.dirname(target_path)
+        record_id, filename = self.parse_path(target_path)
+        self.repository.upload_file_to_draft_record(record_id, filename, native_path, user_context=user_context)
+        self.repository.publish_draft_record(record_id, user_context=user_context)
 
-        draft_record = self._get_draft_record(record_id, user_context=user_context)
-        self._upload_file_to_draft_record(draft_record, filename, native_path, user_context=user_context)
-        self._publish_draft_record(draft_record, user_context=user_context)
 
-    def _list_records(self, write_intent: bool, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
-        if write_intent:
-            return self._list_writeable_records(user_context)
-        return self._list_all_records(user_context)
+class InvenioRepositoryInteractor(RDMRepositoryInteractor):
+    @property
+    def records_url(self) -> str:
+        return f"{self.repository_url}/api/records"
 
-    def _list_all_records(self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
-        # TODO: This is limited to 25 records by default. Add pagination support?
-        request_url = self.records_api_url
-        response_data = self._get_response(user_context, request_url)
-        return self._get_records_from_response(response_data)
+    def to_plugin_uri(self, record_id: str, filename: Optional[str] = None) -> str:
+        return f"{self.plugin.get_uri_root()}/{record_id}{f'/{filename}' if filename else ''}"
 
-    def _list_writeable_records(self, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
+    def get_records(self, write_intent: bool, user_context: OptionalUserContext = None) -> List[RemoteDirectory]:
+        # Only draft records owned by the user can be written to.
+        request_url = f"{self.repository_url}/api/user/records?is_published=false" if write_intent else self.records_url
         # TODO: This is limited to 25 records by default. Add pagination support?
-        # Only draft records can be written to.
-        request_url = urljoin(self.repository_url, "api/user/records?is_published=false")
         response_data = self._get_response(user_context, request_url)
         return self._get_records_from_response(response_data)
 
-    def _list_record_files(
-        self, path: str, write_intent: bool, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
-    ):
-        request_url = f"{self.records_api_url}{path}{'/draft' if write_intent else '' }/files"
+    def get_files_in_record(
+        self, record_id: str, write_intent: bool, user_context: OptionalUserContext = None
+    ) -> List[RemoteFile]:
+        request_url = f"{self.records_url}/{record_id}{'/draft' if write_intent else ''}/files"
         response_data = self._get_response(user_context, request_url)
-        return self._get_record_files_from_response(path, response_data)
-
-    def _get_response(self, user_context: Optional[ProvidesUserFileSourcesUserContext], request_url: str) -> dict:
-        headers = self._get_request_headers(user_context)
-        response = requests.get(request_url, headers=headers, verify=VERIFY)
-        self._ensure_response_has_expected_status_code(response, 200)
-        return response.json()
-
-    def _get_request_headers(self, user_context: Optional[ProvidesUserFileSourcesUserContext]):
-        vault = user_context.user_vault if user_context else None
-        token = vault.read_secret(f"preferences/{self.id}/token") if vault else None
-        headers = {"Authorization": f"Bearer {token}"} if token else {}
-        return headers
-
-    def _get_records_from_response(self, response: dict):
-        records = response["hits"]["hits"]
-        return self._get_records_as_directories(records)
-
-    def _get_records_as_directories(self, records):
-        rval = []
-        for record in records:
-            uri = self._to_plugin_uri(record["links"]["self"])
-            # TODO: define model for Directory and File
-            rval.append(
-                {
-                    "class": "Directory",
-                    "name": record["metadata"]["title"],
-                    "ctime": record["created"],
-                    "uri": uri,
-                    "path": f"/{record['id']}",
-                }
-            )
-
-        return rval
+        return self._get_record_files_from_response(record_id, response_data)
 
-    def _get_record_files_from_response(self, path: str, response: dict):
-        files_enabled = response.get("enabled", False)
-        if not files_enabled:
-            return []
-        entries = response["entries"]
-        rval = []
-        for entry in entries:
-            if entry.get("status") == "completed":
-                uri = self._to_plugin_uri(entry["links"]["content"])
-                path = self._to_plugin_uri(entry["links"]["self"])
-                rval.append(
-                    {
-                        "class": "File",
-                        "name": entry["key"],
-                        "size": entry["size"],
-                        "ctime": entry["created"],
-                        "uri": uri,
-                        "path": path,
-                    }
-                )
-        return rval
-
-    def _to_plugin_uri(self, uri: str) -> str:
-        return uri.replace(self.records_api_url, self.get_uri_root())
-
-    def _get_draft_record(self, record_id: str, user_context: Optional[ProvidesUserFileSourcesUserContext] = None):
-        request_url = f"{self.records_api_url}{record_id}/draft"
-        draft_record = self._get_response(user_context, request_url)
-        return draft_record
-
-    def _create_draft_record(
-        self, title: str, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
-    ) -> InvenioRecord:
+    def create_draft_record(self, title: str, user_context: OptionalUserContext = None) -> RemoteDirectory:
         today = datetime.date.today().isoformat()
         creator = self._get_creator_from_user_context(user_context)
-        should_publish = self._get_public_records_user_setting_enabled_status(user_context)
+        should_publish = bool(self.get_user_preference_by_key("public_records", user_context))
         access = "public" if should_publish else "restricted"
         create_record_request = {
             "access": {"record": access, "files": access},
@@ -308,27 +219,19 @@ def _create_draft_record(
                 "Cannot create record without authentication token. Please set your personal access token in your Galaxy preferences."
             )
 
-        create_record_url = self.records_api_url
-        response = requests.post(create_record_url, json=create_record_request, headers=headers, verify=VERIFY)
+        response = requests.post(self.records_url, json=create_record_request, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 201)
         record = response.json()
         return record
 
-    def _delete_draft_record(
-        self, record: InvenioRecord, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
-    ):
-        delete_record_url = record["links"]["self"]
-        headers = self._get_request_headers(user_context)
-        response = requests.delete(delete_record_url, headers=headers, verify=VERIFY)
-        self._ensure_response_has_expected_status_code(response, 204)
-
-    def _upload_file_to_draft_record(
+    def upload_file_to_draft_record(
         self,
-        record: InvenioRecord,
+        record_id: str,
         filename: str,
-        native_path: str,
-        user_context: Optional[ProvidesUserFileSourcesUserContext] = None,
+        file_path: str,
+        user_context: OptionalUserContext = None,
     ):
+        record = self._get_draft_record(record_id, user_context=user_context)
         upload_file_url = record["links"]["files"]
         headers = self._get_request_headers(user_context)
 
@@ -341,7 +244,7 @@ def _upload_file_to_draft_record(
         file_entry = next(entry for entry in entries if entry["key"] == filename)
         upload_file_content_url = file_entry["links"]["content"]
         commit_file_upload_url = file_entry["links"]["commit"]
-        with open(native_path, "rb") as file:
+        with open(file_path, "rb") as file:
             response = requests.put(upload_file_content_url, data=file, headers=headers, verify=VERIFY)
             self._ensure_response_has_expected_status_code(response, 200)
 
@@ -349,17 +252,74 @@ def _upload_file_to_draft_record(
         response = requests.post(commit_file_upload_url, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 200)
 
-    def _publish_draft_record(
-        self, record: InvenioRecord, user_context: Optional[ProvidesUserFileSourcesUserContext] = None
+    def download_file_from_record(
+        self,
+        record_id: str,
+        filename: str,
+        file_path: str,
+        user_context: OptionalUserContext = None,
     ):
-        publish_record_url = f"{self.records_api_url}/{record['id']}/draft/actions/publish"
+        download_file_content_url = f"{self.records_url}/{record_id}/files/{quote(filename)}/content"
+
+        headers = self._get_request_headers(user_context)
+        req = urllib.request.Request(download_file_content_url, headers=headers)
+        with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT, context=SSL_CONTEXT) as page:
+            f = open(file_path, "wb")
+            return stream_to_open_named_file(
+                page, f.fileno(), file_path, source_encoding=get_charset_from_http_headers(page.headers)
+            )
+
+    def publish_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
+        publish_record_url = f"{self.records_url}/{record_id}/draft/actions/publish"
         headers = self._get_request_headers(user_context)
         response = requests.post(publish_record_url, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 202)
 
-    def _get_creator_from_user_context(self, user_context: Optional[ProvidesUserFileSourcesUserContext]):
-        preferences = user_context.preferences if user_context else None
-        public_name = preferences.get(f"{self.id}|public_name", None) if preferences else None
+    def _get_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
+        request_url = f"{self.records_url}/{record_id}/draft"
+        draft_record = self._get_response(user_context, request_url)
+        return draft_record
+
+    def _get_records_from_response(self, response: dict) -> List[RemoteDirectory]:
+        records = response["hits"]["hits"]
+        rval: List[RemoteDirectory] = []
+        for record in records:
+            uri = self.to_plugin_uri(record_id=record["id"])
+            path = self.plugin.to_relative_path(uri)
+            rval.append(
+                {
+                    "class": "Directory",
+                    "name": record["metadata"]["title"],
+                    "uri": uri,
+                    "path": path,
+                }
+            )
+        return rval
+
+    def _get_record_files_from_response(self, record_id: str, response: dict) -> List[RemoteFile]:
+        files_enabled = response.get("enabled", False)
+        if not files_enabled:
+            return []
+        entries = response["entries"]
+        rval: List[RemoteFile] = []
+        for entry in entries:
+            if entry.get("status") == "completed":
+                uri = self.to_plugin_uri(record_id=record_id, filename=entry["key"])
+                path = self.plugin.to_relative_path(uri)
+                rval.append(
+                    {
+                        "class": "File",
+                        "name": entry["key"],
+                        "size": entry["size"],
+                        "ctime": entry["created"],
+                        "uri": uri,
+                        "path": path,
+                    }
+                )
+        return rval
+
+    def _get_creator_from_user_context(self, user_context: OptionalUserContext):
+        public_name = self.get_user_preference_by_key("public_name", user_context)
         family_name = "Galaxy User"
         given_name = "Anonymous"
         if public_name:
@@ -371,14 +331,26 @@ def _get_creator_from_user_context(self, user_context: Optional[ProvidesUserFile
                 given_name = public_name
         return {"person_or_org": {"family_name": family_name, "given_name": given_name, "type": "personal"}}
 
-    def _get_public_records_user_setting_enabled_status(
-        self, user_context: Optional[ProvidesUserFileSourcesUserContext]
-    ) -> bool:
+    def get_user_preference_by_key(self, key: str, user_context: OptionalUserContext):
         preferences = user_context.preferences if user_context else None
-        public_records = preferences.get(f"{self.id}|public_records", None) if preferences else None
-        if public_records:
-            return True
-        return False
+        value = preferences.get(f"{self.plugin.id}|{key}", None) if preferences else None
+        return value
+
+    def _get_response(self, user_context: OptionalUserContext, request_url: str) -> dict:
+        headers = self._get_request_headers(user_context)
+        response = requests.get(request_url, headers=headers, verify=VERIFY)
+        self._ensure_response_has_expected_status_code(response, 200)
+        return response.json()
+
+    def _get_request_headers(self, user_context: OptionalUserContext):
+        token = self.get_authorization_token(user_context)
+        headers = {"Authorization": f"Bearer {token}"} if token else {}
+        return headers
+
+    def get_authorization_token(self, user_context) -> str:
+        vault = user_context.user_vault if user_context else None
+        token = vault.read_secret(f"preferences/{self.plugin.id}/token") if vault else None
+        return token
 
     def _ensure_response_has_expected_status_code(self, response, expected_status_code: int):
         if response.status_code != expected_status_code:

From 9e645aff7b318b7deed8d915db213908bc283f09 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 28 Jul 2023 14:44:43 +0200
Subject: [PATCH 21/41] Rename write_intent to writeable

---
 client/src/components/FilesDialog/services.ts |  6 +++---
 client/src/schema/schema.ts                   |  8 ++++----
 lib/galaxy/files/sources/__init__.py          |  6 +++---
 lib/galaxy/files/sources/_rdm.py              | 15 +++++++++++----
 lib/galaxy/files/sources/invenio.py           | 15 ++++++++-------
 lib/galaxy/managers/remote_files.py           |  4 ++--
 lib/galaxy/webapps/galaxy/api/remote_files.py |  8 ++++----
 7 files changed, 35 insertions(+), 27 deletions(-)

diff --git a/client/src/components/FilesDialog/services.ts b/client/src/components/FilesDialog/services.ts
index 12ad338dc08d..7566689cc81e 100644
--- a/client/src/components/FilesDialog/services.ts
+++ b/client/src/components/FilesDialog/services.ts
@@ -25,11 +25,11 @@ const getRemoteFiles = fetcher.path("/api/remote_files").method("get").create();
  * Get the list of files and directories from the server for the given file source URI.
  * @param uri The file source URI to browse.
  * @param isRecursive Whether to recursively retrieve all files inside subdirectories.
- * @param writeIntent Whether to include only entries that can be written to.
+ * @param writeable Whether to return only entries that can be written to.
  * @returns The list of files and directories from the server for the given URI.
  */
-export async function browseRemoteFiles(uri: string, isRecursive = false, writeIntent = false): Promise<RemoteEntry[]> {
-    const { data } = await getRemoteFiles({ target: uri, recursive: isRecursive, write_intent: writeIntent });
+export async function browseRemoteFiles(uri: string, isRecursive = false, writeable = false): Promise<RemoteEntry[]> {
+    const { data } = await getRemoteFiles({ target: uri, recursive: isRecursive, writeable });
     return data as RemoteEntry[];
 }
 
diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index 6668bfebbff0..0466dd8d2565 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -11167,13 +11167,13 @@ export interface operations {
             /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
             /** @description Wether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
             /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
-            /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be accessible. */
+            /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be returned. */
             query?: {
                 target?: string;
                 format?: components["schemas"]["RemoteFilesFormat"];
                 recursive?: boolean;
                 disable?: components["schemas"]["RemoteFilesDisableMode"];
-                write_intent?: boolean;
+                writeable?: boolean;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
@@ -16128,13 +16128,13 @@ export interface operations {
             /** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
             /** @description Wether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
             /** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
-            /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be accessible. */
+            /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be returned. */
             query?: {
                 target?: string;
                 format?: components["schemas"]["RemoteFilesFormat"];
                 recursive?: boolean;
                 disable?: components["schemas"]["RemoteFilesDisableMode"];
-                write_intent?: boolean;
+                writeable?: boolean;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index 8dcdef0fa547..769907eef0b2 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -57,9 +57,9 @@ class FilesSourceOptions:
     """Options to control behavior of file source operations, such as realize_to, write_from and list."""
 
     # Indicates access to the FS operation with intent to write.
-    # A file source can be "writeable" but, for example, some directories (or elements) may be restricted or read-only
-    # so those should be skipped while browsing with write_intent=True.
-    write_intent: Optional[bool]
+    # Even if a file source is "writeable" some directories (or elements) may be restricted or read-only
+    # so those should be skipped while browsing with writeable=True.
+    writeable: Optional[bool]
 
     # Property overrides for values initially configured through the constructor. For example
     # the HTTPFilesSource passes in additional http_headers through these properties, which
diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index 9e00950255ab..ee2a0c7adb78 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -60,14 +60,21 @@ def to_plugin_uri(self, record_id: str, filename: Optional[str] = None) -> str:
         If a filename is provided, the URI will reference the specific file in the record."""
         raise NotImplementedError()
 
-    def get_records(self, write_intent: bool, user_context: OptionalUserContext = None) -> List[RemoteDirectory]:
-        """Returns the list of records in the repository."""
+    def get_records(self, writeable: bool, user_context: OptionalUserContext = None) -> List[RemoteDirectory]:
+        """Returns the list of records in the repository.
+
+        If writeable is True, only records that the user can write to will be returned.
+        The user_context might be required to authenticate the user in the repository.
+        """
         raise NotImplementedError()
 
     def get_files_in_record(
-        self, record_id: str, write_intent: bool, user_context: OptionalUserContext = None
+        self, record_id: str, writeable: bool, user_context: OptionalUserContext = None
     ) -> List[RemoteFile]:
-        """Returns the list of files contained in the given record."""
+        """Returns the list of files contained in the given record.
+
+        If writeable is True, we are signaling that the user intends to write to the record.
+        """
         raise NotImplementedError()
 
     def create_draft_record(self, title: str, user_context: OptionalUserContext = None):
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 28be0d97da40..d7debf620660 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -128,12 +128,12 @@ def _list(
         user_context: OptionalUserContext = None,
         opts: Optional[FilesSourceOptions] = None,
     ):
-        write_intent = opts and opts.write_intent or False
+        writeable = opts and opts.writeable or False
         is_root_path = path == "/"
         if is_root_path:
-            return self.repository.get_records(write_intent, user_context)
+            return self.repository.get_records(writeable, user_context)
         record_id, _ = self.parse_path(path)
-        return self.repository.get_files_in_record(record_id, write_intent, user_context)
+        return self.repository.get_files_in_record(record_id, writeable, user_context)
 
     def _create_entry(
         self,
@@ -181,17 +181,18 @@ def records_url(self) -> str:
     def to_plugin_uri(self, record_id: str, filename: Optional[str] = None) -> str:
         return f"{self.plugin.get_uri_root()}/{record_id}{f'/{filename}' if filename else ''}"
 
-    def get_records(self, write_intent: bool, user_context: OptionalUserContext = None) -> List[RemoteDirectory]:
+    def get_records(self, writeable: bool, user_context: OptionalUserContext = None) -> List[RemoteDirectory]:
         # Only draft records owned by the user can be written to.
-        request_url = f"{self.repository_url}/api/user/records?is_published=false" if write_intent else self.records_url
+        request_url = f"{self.repository_url}/api/user/records?is_published=false" if writeable else self.records_url
         # TODO: This is limited to 25 records by default. Add pagination support?
         response_data = self._get_response(user_context, request_url)
         return self._get_records_from_response(response_data)
 
     def get_files_in_record(
-        self, record_id: str, write_intent: bool, user_context: OptionalUserContext = None
+        self, record_id: str, writeable: bool, user_context: OptionalUserContext = None
     ) -> List[RemoteFile]:
-        request_url = f"{self.records_url}/{record_id}{'/draft' if write_intent else ''}/files"
+        conditionally_draft = "/draft" if writeable else ""
+        request_url = f"{self.records_url}/{record_id}{conditionally_draft}/files"
         response_data = self._get_response(user_context, request_url)
         return self._get_record_files_from_response(record_id, response_data)
 
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index 863c0494436c..8964661b9f13 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -44,7 +44,7 @@ def index(
         format: Optional[RemoteFilesFormat],
         recursive: Optional[bool],
         disable: Optional[RemoteFilesDisableMode],
-        write_intent: Optional[bool] = False,
+        writeable: Optional[bool] = False,
     ) -> AnyRemoteFilesListResponse:
         """Returns a list of remote files available to the user."""
 
@@ -81,7 +81,7 @@ def index(
         file_source = file_source_path.file_source
 
         opts = FilesSourceOptions()
-        opts.write_intent = write_intent or False
+        opts.writeable = writeable or False
         try:
             index = file_source.list(
                 file_source_path.path,
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 856d70018d46..6ef5b4df72d6 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -62,9 +62,9 @@
     ),
 )
 
-WriteIntentQueryParam: Optional[bool] = Query(
+WriteableQueryParam: Optional[bool] = Query(
     default=None,
-    title="Write Intent",
+    title="Writeable",
     description=(
         "Whether the query is made with the intention of writing to the source."
         " If set to True, only entries that can be written to will be returned."
@@ -110,10 +110,10 @@ async def index(
         format: Optional[RemoteFilesFormat] = FormatQueryParam,
         recursive: Optional[bool] = RecursiveQueryParam,
         disable: Optional[RemoteFilesDisableMode] = DisableModeQueryParam,
-        write_intent: Optional[bool] = WriteIntentQueryParam,
+        writeable: Optional[bool] = WriteableQueryParam,
     ) -> AnyRemoteFilesListResponse:
         """Lists all remote files available to the user from different sources."""
-        return self.manager.index(user_ctx, target, format, recursive, disable, write_intent=write_intent)
+        return self.manager.index(user_ctx, target, format, recursive, disable, writeable)
 
     @router.get(
         "/api/remote_files/plugins",

From f674acf69af833aa7c80a6e58cea722f46545a27 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 1 Aug 2023 13:53:54 +0200
Subject: [PATCH 22/41] Remove rdm_only parameter

---
 client/src/schema/schema.ts                   |  2 --
 lib/galaxy/files/__init__.py                  |  3 ---
 lib/galaxy/managers/remote_files.py           |  4 +---
 lib/galaxy/webapps/galaxy/api/remote_files.py | 11 +----------
 4 files changed, 2 insertions(+), 18 deletions(-)

diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index 0466dd8d2565..21e6d861505a 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -16196,10 +16196,8 @@ export interface operations {
          */
         parameters?: {
             /** @description Whether to return browsable filesources only. The default is `True`, which will omit filesourceslike `http` and `base64` that do not implement a list method. */
-            /** @description Whether to return only RDM compatible plugins. The default is `False`, which will return all plugins. */
             query?: {
                 browsable_only?: boolean;
-                rdm_only?: boolean;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
diff --git a/lib/galaxy/files/__init__.py b/lib/galaxy/files/__init__.py
index 97f8c4765054..88184c7862bc 100644
--- a/lib/galaxy/files/__init__.py
+++ b/lib/galaxy/files/__init__.py
@@ -165,14 +165,11 @@ def plugins_to_dict(
         for_serialization: bool = False,
         user_context: Optional["FileSourceDictifiable"] = None,
         browsable_only: Optional[bool] = False,
-        rdm_only: Optional[bool] = False,
     ) -> List[Dict[str, Any]]:
         rval = []
         for file_source in self._file_sources:
             if not file_source.user_has_access(user_context):
                 continue
-            if rdm_only and not getattr(file_source, "supports_rdm", False):
-                continue
             if browsable_only and not file_source.get_browsable():
                 continue
             el = file_source.to_dict(for_serialization=for_serialization, user_context=user_context)
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index 8964661b9f13..3075e6e55b8a 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -128,16 +128,14 @@ def index(
         return index
 
     def get_files_source_plugins(
-        self, user_context: ProvidesUserContext, browsable_only: Optional[bool] = True, rdm_only: Optional[bool] = False
+        self, user_context: ProvidesUserContext, browsable_only: Optional[bool] = True
     ) -> FilesSourcePluginList:
         """Display plugin information for each of the gxfiles:// URI targets available."""
         user_file_source_context = ProvidesUserFileSourcesUserContext(user_context)
         browsable_only = True if browsable_only is None else browsable_only
-        rdm_only = rdm_only or False
         plugins_dict = self._file_sources.plugins_to_dict(
             user_context=user_file_source_context,
             browsable_only=browsable_only,
-            rdm_only=rdm_only,
         )
         plugins = [FilesSourcePlugin(**plugin_dict) for plugin_dict in plugins_dict]
         return FilesSourcePluginList.construct(__root__=plugins)
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 6ef5b4df72d6..06566b663863 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -80,14 +80,6 @@
     ),
 )
 
-RDMOnlyQueryParam: Optional[bool] = Query(
-    default=False,
-    title="RDM only",
-    description=(
-        "Whether to return only RDM compatible plugins. The default is `False`, which will return all plugins."
-    ),
-)
-
 
 @router.cbv
 class FastAPIRemoteFiles:
@@ -124,10 +116,9 @@ async def plugins(
         self,
         user_ctx: ProvidesUserContext = DependsOnTrans,
         browsable_only: Optional[bool] = BrowsableQueryParam,
-        rdm_only: Optional[bool] = RDMOnlyQueryParam,
     ) -> FilesSourcePluginList:
         """Display plugin information for each of the gxfiles:// URI targets available."""
-        return self.manager.get_files_source_plugins(user_ctx, browsable_only, rdm_only)
+        return self.manager.get_files_source_plugins(user_ctx, browsable_only)
 
     @router.post(
         "/api/remote_files",

From 00d79e2d216e8d334be3ec89f987ed5e452839a7 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 1 Aug 2023 14:23:28 +0200
Subject: [PATCH 23/41] Fix FilesSourcePluginList schema

The common field `browsable` was missing and only when browsable is True we require the `uri_root`.

We can also drop the `Extra.allow` config in FilesSourcePlugin model because the specific fields for different file sources are not returned in the API response since `plugins_to_dict` is called with for_serialization=False by default.
---
 client/src/schema/schema.ts         | 73 ++++++++++++++++++++++++++---
 lib/galaxy/managers/remote_files.py | 16 +++----
 lib/galaxy/schema/remote_files.py   | 28 ++++++-----
 3 files changed, 89 insertions(+), 28 deletions(-)

diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index 21e6d861505a..ee9f9644a2f9 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -2212,6 +2212,63 @@ export interface components {
              */
             variant: components["schemas"]["NotificationVariant"];
         };
+        /**
+         * BrowsableFilesSourcePlugin
+         * @description Base model definition with common configuration used by all derived models.
+         */
+        BrowsableFilesSourcePlugin: {
+            /**
+             * Browsable
+             * @enum {boolean}
+             */
+            browsable: true;
+            /**
+             * Documentation
+             * @description Documentation or extended description for this plugin.
+             * @example Galaxy's library import directory
+             */
+            doc: string;
+            /**
+             * ID
+             * @description The `FilesSource` plugin identifier
+             * @example _import
+             */
+            id: string;
+            /**
+             * Label
+             * @description The display label for this plugin.
+             * @example Library Import Directory
+             */
+            label: string;
+            /**
+             * Requires groups
+             * @description Only users belonging to the groups specified here can access this files source.
+             */
+            requires_groups?: string;
+            /**
+             * Requires roles
+             * @description Only users with the roles specified here can access this files source.
+             */
+            requires_roles?: string;
+            /**
+             * Type
+             * @description The type of the plugin.
+             * @example gximport
+             */
+            type: string;
+            /**
+             * URI root
+             * @description The URI root used by this type of plugin.
+             * @example gximport://
+             */
+            uri_root: string;
+            /**
+             * Writeable
+             * @description Whether this files source plugin allows write access.
+             * @example false
+             */
+            writable: boolean;
+        };
         /**
          * BulkOperationItemError
          * @description Base model definition with common configuration used by all derived models.
@@ -4345,6 +4402,11 @@ export interface components {
          * @description Base model definition with common configuration used by all derived models.
          */
         FilesSourcePlugin: {
+            /**
+             * Browsable
+             * @description Whether this file source plugin can list items.
+             */
+            browsable: boolean;
             /**
              * Documentation
              * @description Documentation or extended description for this plugin.
@@ -4379,12 +4441,6 @@ export interface components {
              * @example gximport
              */
             type: string;
-            /**
-             * URI root
-             * @description The URI root used by this type of plugin.
-             * @example gximport://
-             */
-            uri_root: string;
             /**
              * Writeable
              * @description Whether this files source plugin allows write access.
@@ -4408,7 +4464,10 @@ export interface components {
          *   }
          * ]
          */
-        FilesSourcePluginList: components["schemas"]["FilesSourcePlugin"][];
+        FilesSourcePluginList: (
+            | components["schemas"]["BrowsableFilesSourcePlugin"]
+            | components["schemas"]["FilesSourcePlugin"]
+        )[];
         /**
          * FolderLibraryFolderItem
          * @description Base model definition with common configuration used by all derived models.
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index 3075e6e55b8a..fed33051fda9 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -1,7 +1,12 @@
 import hashlib
 import logging
 from operator import itemgetter
-from typing import Optional
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+)
 
 from galaxy import exceptions
 from galaxy.files import (
@@ -14,8 +19,6 @@
     AnyRemoteFilesListResponse,
     CreatedEntryResponse,
     CreateEntryPayload,
-    FilesSourcePlugin,
-    FilesSourcePluginList,
     RemoteFilesDisableMode,
     RemoteFilesFormat,
     RemoteFilesTarget,
@@ -127,9 +130,7 @@ def index(
 
         return index
 
-    def get_files_source_plugins(
-        self, user_context: ProvidesUserContext, browsable_only: Optional[bool] = True
-    ) -> FilesSourcePluginList:
+    def get_files_source_plugins(self, user_context: ProvidesUserContext, browsable_only: Optional[bool] = True):
         """Display plugin information for each of the gxfiles:// URI targets available."""
         user_file_source_context = ProvidesUserFileSourcesUserContext(user_context)
         browsable_only = True if browsable_only is None else browsable_only
@@ -137,8 +138,7 @@ def get_files_source_plugins(
             user_context=user_file_source_context,
             browsable_only=browsable_only,
         )
-        plugins = [FilesSourcePlugin(**plugin_dict) for plugin_dict in plugins_dict]
-        return FilesSourcePluginList.construct(__root__=plugins)
+        return plugins_dict
 
     @property
     def _file_sources(self) -> ConfiguredFileSources:
diff --git a/lib/galaxy/schema/remote_files.py b/lib/galaxy/schema/remote_files.py
index a408f076a9c8..100a61a3998f 100644
--- a/lib/galaxy/schema/remote_files.py
+++ b/lib/galaxy/schema/remote_files.py
@@ -7,7 +7,6 @@
 )
 
 from pydantic import (
-    Extra,
     Field,
     Required,
 )
@@ -49,12 +48,6 @@ class FilesSourcePlugin(Model):
         description="The type of the plugin.",
         example="gximport",
     )
-    uri_root: str = Field(
-        Required,
-        title="URI root",
-        description="The URI root used by this type of plugin.",
-        example="gximport://",
-    )
     label: str = Field(
         Required,
         title="Label",
@@ -67,6 +60,11 @@ class FilesSourcePlugin(Model):
         description="Documentation or extended description for this plugin.",
         example="Galaxy's library import directory",
     )
+    browsable: bool = Field(
+        Required,
+        title="Browsable",
+        description="Whether this file source plugin can list items.",
+    )
     writable: bool = Field(
         Required,
         title="Writeable",
@@ -84,15 +82,19 @@ class FilesSourcePlugin(Model):
         description="Only users belonging to the groups specified here can access this files source.",
     )
 
-    class Config:
-        # This allows additional fields (that are not validated)
-        # to be serialized/deserealized. This allows to have
-        # different fields depending on the plugin type
-        extra = Extra.allow
+
+class BrowsableFilesSourcePlugin(FilesSourcePlugin):
+    browsable: Literal[True]
+    uri_root: str = Field(
+        Required,
+        title="URI root",
+        description="The URI root used by this type of plugin.",
+        example="gximport://",
+    )
 
 
 class FilesSourcePluginList(Model):
-    __root__: List[FilesSourcePlugin] = Field(
+    __root__: List[Union[BrowsableFilesSourcePlugin, FilesSourcePlugin]] = Field(
         default=[],
         title="List of files source plugins",
         example=[

From 8876828c3fa523812b342d43d5deee8ac56e84bf Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 1 Aug 2023 15:50:23 +0200
Subject: [PATCH 24/41] Add PluginKind to file sources and allow filtering

---
 .../src/components/Common/ExportDOIForm.vue   |  8 +++--
 client/src/components/Common/ExportForm.vue   | 10 +++++-
 .../components/FilesDialog/FilesDialog.vue    | 27 +++++++-------
 .../src/components/FilesDialog/FilesInput.vue |  9 +++--
 client/src/components/FilesDialog/services.ts | 36 +++++++++++++++----
 .../src/components/FilesDialog/testingData.ts |  7 ++--
 .../History/Export/HistoryExport.vue          |  4 +--
 client/src/composables/fileSources.ts         | 14 +++++---
 client/src/schema/schema.ts                   | 10 ++++++
 lib/galaxy/files/__init__.py                  | 11 +++++-
 lib/galaxy/files/sources/__init__.py          | 36 +++++++++++++++++++
 lib/galaxy/files/sources/_rdm.py              |  5 ++-
 lib/galaxy/files/sources/base64.py            |  2 ++
 lib/galaxy/files/sources/drs.py               |  2 ++
 lib/galaxy/files/sources/galaxy.py            |  4 +++
 lib/galaxy/files/sources/http.py              |  2 ++
 lib/galaxy/managers/remote_files.py           | 19 +++++++---
 lib/galaxy/webapps/galaxy/api/remote_files.py | 32 +++++++++++++++--
 18 files changed, 193 insertions(+), 45 deletions(-)

diff --git a/client/src/components/Common/ExportDOIForm.vue b/client/src/components/Common/ExportDOIForm.vue
index 3b72eedb652f..10c14cc058a0 100644
--- a/client/src/components/Common/ExportDOIForm.vue
+++ b/client/src/components/Common/ExportDOIForm.vue
@@ -2,7 +2,7 @@
 import { BButton, BCard, BFormGroup, BFormInput, BFormRadio, BFormRadioGroup } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import { CreatedEntry, createRemoteEntry } from "@/components/FilesDialog/services";
+import { CreatedEntry, createRemoteEntry, FilterFileSourcesOptions } from "@/components/FilesDialog/services";
 import localize from "@/utils/localization";
 
 import ExternalLink from "@/components/ExternalLink.vue";
@@ -28,6 +28,8 @@ const emit = defineEmits<{
 
 type ExportChoice = "existing" | "new";
 
+const includeOnlyDOICompatible: FilterFileSourcesOptions = { include: ["rdm"] };
+
 const recordUri = ref<string>("");
 const sourceUri = ref<string>("");
 const fileName = ref<string>(props.defaultFilename);
@@ -115,7 +117,7 @@ function clearInputs() {
                         v-model="sourceUri"
                         mode="source"
                         :require-writable="true"
-                        :rdm-only="true" />
+                        :filter-options="includeOnlyDOICompatible" />
                 </BFormGroup>
                 <BFormGroup
                     id="fieldset-record-name"
@@ -148,7 +150,7 @@ function clearInputs() {
                     v-model="recordUri"
                     mode="directory"
                     :require-writable="true"
-                    :rdm-only="true" />
+                    :filter-options="includeOnlyDOICompatible" />
             </BFormGroup>
             <BButton
                 v-localize
diff --git a/client/src/components/Common/ExportForm.vue b/client/src/components/Common/ExportForm.vue
index 993b5c641a14..c3387dcd9991 100644
--- a/client/src/components/Common/ExportForm.vue
+++ b/client/src/components/Common/ExportForm.vue
@@ -2,6 +2,7 @@
 import { BButton, BCol, BFormGroup, BFormInput, BRow } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
+import { FilterFileSourcesOptions } from "@/components/FilesDialog/services";
 import localize from "@/utils/localization";
 
 import FilesInput from "@/components/FilesDialog/FilesInput.vue";
@@ -20,6 +21,8 @@ const emit = defineEmits<{
     (e: "export", directory: string, name: string): void;
 }>();
 
+const defaultExportFilterOptions: FilterFileSourcesOptions = { exclude: ["rdm"] };
+
 const directory = ref<string>("");
 const name = ref<string>("");
 
@@ -43,7 +46,12 @@ const doExport = () => {
 <template>
     <div class="export-to-remote-file">
         <BFormGroup id="fieldset-directory" label-for="directory" :description="directoryDescription" class="mt-3">
-            <FilesInput id="directory" v-model="directory" mode="directory" :require-writable="true" />
+            <FilesInput
+                id="directory"
+                v-model="directory"
+                mode="directory"
+                :require-writable="true"
+                :filter-options="defaultExportFilterOptions" />
         </BFormGroup>
         <BFormGroup id="fieldset-name" label-for="name" :description="nameDescription" class="mt-3">
             <BFormInput id="name" v-model="name" :placeholder="namePlaceholder" required />
diff --git a/client/src/components/FilesDialog/FilesDialog.vue b/client/src/components/FilesDialog/FilesDialog.vue
index 2a6e7a570881..d7b092c65434 100644
--- a/client/src/components/FilesDialog/FilesDialog.vue
+++ b/client/src/components/FilesDialog/FilesDialog.vue
@@ -12,7 +12,14 @@ import { useConfig } from "@/composables/config";
 import { errorMessageAsString } from "@/utils/simple-error";
 
 import { DirectoryRecord, Model, RecordItem } from "./model";
-import { browseRemoteFiles, FilesSourcePlugin, getFileSources, RemoteEntry } from "./services";
+import {
+    BrowsableFilesSourcePlugin,
+    browseRemoteFiles,
+    FileSourceBrowsingMode,
+    FilterFileSourcesOptions,
+    getFileSources,
+    RemoteEntry,
+} from "./services";
 
 import DataDialogSearch from "@/components/SelectionDialog/DataDialogSearch.vue";
 import DataDialogTable from "@/components/SelectionDialog/DataDialogTable.vue";
@@ -23,16 +30,12 @@ library.add(faCaretLeft);
 interface FilesDialogProps {
     /** Whether to allow multiple selections */
     multiple?: boolean;
-    /** The browsing mode:
-     * - `file` - allows to select files or directories contained in a source (default)
-     * - `directory` - allows to select directories (paths) only
-     * - `source` - allows to select a source plugin root and doesn't list its contents
-     */
-    mode?: "file" | "directory" | "source";
+    /** Browsing mode to define the selection behavior */
+    mode?: FileSourceBrowsingMode;
     /** Whether to show only writable sources */
     requireWritable?: boolean;
-    /** Whether to show only RDM sources */
-    rdmOnly?: boolean;
+    /** Options to filter the file sources */
+    filterOptions?: FilterFileSourcesOptions;
     /** Callback function to be called passing the results when selection is complete */
     callback?: (files: any) => void;
 }
@@ -41,7 +44,7 @@ const props = withDefaults(defineProps<FilesDialogProps>(), {
     multiple: false,
     mode: "file",
     requireWritable: false,
-    rdmOnly: false,
+    filterOptions: undefined,
     callback: () => {},
 });
 
@@ -215,7 +218,7 @@ function load(record?: DirectoryRecord) {
     undoShow.value = !urlTracker.value.atRoot();
     if (urlTracker.value.atRoot() || errorMessage.value) {
         errorMessage.value = undefined;
-        getFileSources(props.rdmOnly)
+        getFileSources(props.filterOptions)
             .then((results) => {
                 const convertedItems = results
                     .filter((item) => !props.requireWritable || item.writable)
@@ -277,7 +280,7 @@ function entryToRecord(entry: RemoteEntry): RecordItem {
     return result;
 }
 
-function fileSourcePluginToRecord(plugin: FilesSourcePlugin): RecordItem {
+function fileSourcePluginToRecord(plugin: BrowsableFilesSourcePlugin): RecordItem {
     const result = {
         id: plugin.id,
         label: plugin.label,
diff --git a/client/src/components/FilesDialog/FilesInput.vue b/client/src/components/FilesDialog/FilesInput.vue
index c7a0c88f680a..00ebedcd62e0 100644
--- a/client/src/components/FilesDialog/FilesInput.vue
+++ b/client/src/components/FilesDialog/FilesInput.vue
@@ -4,11 +4,13 @@ import { computed } from "vue";
 
 import { filesDialog } from "@/utils/data";
 
+import { FileSourceBrowsingMode, FilterFileSourcesOptions } from "./services";
+
 interface Props {
     value: string;
-    mode?: "file" | "directory";
+    mode?: FileSourceBrowsingMode;
     requireWritable?: boolean;
-    rdmOnly?: boolean;
+    filterOptions?: FilterFileSourcesOptions;
 }
 
 interface SelectableFile {
@@ -18,6 +20,7 @@ interface SelectableFile {
 const props = withDefaults(defineProps<Props>(), {
     mode: "file",
     requireWritable: false,
+    filterOptions: undefined,
 });
 
 const emit = defineEmits<{
@@ -37,7 +40,7 @@ const selectFile = () => {
     const dialogProps = {
         mode: props.mode,
         requireWritable: props.requireWritable,
-        rdmOnly: props.rdmOnly,
+        filterOptions: props.filterOptions,
     };
     filesDialog((selected: SelectableFile) => {
         currentValue.value = selected?.url;
diff --git a/client/src/components/FilesDialog/services.ts b/client/src/components/FilesDialog/services.ts
index 7566689cc81e..116429bc7f32 100644
--- a/client/src/components/FilesDialog/services.ts
+++ b/client/src/components/FilesDialog/services.ts
@@ -1,22 +1,46 @@
 import type { components } from "@/schema";
 import { fetcher } from "@/schema/fetcher";
 
-export type FilesSourcePlugin = components["schemas"]["FilesSourcePlugin"];
+/** The browsing mode:
+ * - `file` - allows to select files or directories contained in a source (default)
+ * - `directory` - allows to select directories (paths) only
+ * - `source` - allows to select a source plugin root and doesn't list its contents
+ */
+export type FileSourceBrowsingMode = "file" | "directory" | "source";
+export type BrowsableFilesSourcePlugin = components["schemas"]["BrowsableFilesSourcePlugin"];
 export type RemoteFile = components["schemas"]["RemoteFile"];
 export type RemoteDirectory = components["schemas"]["RemoteDirectory"];
 export type RemoteEntry = RemoteFile | RemoteDirectory;
 export type CreatedEntry = components["schemas"]["CreatedEntryResponse"];
+export type FileSourcePluginKind = components["schemas"]["PluginKind"];
+
+/** The options to filter the list of available file sources. */
+export interface FilterFileSourcesOptions {
+    /** The kinds of file sources to return, multiple kinds can be specified.
+     * If undefined, all file sources are returned.
+     */
+    include?: FileSourcePluginKind[];
+    /** The kind of file sources to exclude, multiple kinds can be specified.
+     * Excluded have precedence over included.
+     * If undefined, all file sources are returned.
+     */
+    exclude?: FileSourcePluginKind[];
+}
 
 const getRemoteFilesPlugins = fetcher.path("/api/remote_files/plugins").method("get").create();
 
 /**
  * Get the list of available file sources from the server that can be browsed.
- * @param rdm_only Whether to only include Research Data Management (RDM) specific file sources.
- * @returns The list of available file sources from the server.
+ * @param options The options to filter the file sources.
+ * @returns The list of available (browsable) file sources from the server.
  */
-export async function getFileSources(rdm_only = false): Promise<FilesSourcePlugin[]> {
-    const { data } = await getRemoteFilesPlugins({ browsable_only: true, rdm_only: rdm_only });
-    return data;
+export async function getFileSources(options: FilterFileSourcesOptions = {}): Promise<BrowsableFilesSourcePlugin[]> {
+    const { data } = await getRemoteFilesPlugins({
+        browsable_only: true,
+        include_kind: options.include,
+        exclude_kind: options.exclude,
+    });
+    return data as BrowsableFilesSourcePlugin[];
 }
 
 const getRemoteFiles = fetcher.path("/api/remote_files").method("get").create();
diff --git a/client/src/components/FilesDialog/testingData.ts b/client/src/components/FilesDialog/testingData.ts
index 90851131921b..df7ccafc86cb 100644
--- a/client/src/components/FilesDialog/testingData.ts
+++ b/client/src/components/FilesDialog/testingData.ts
@@ -1,4 +1,4 @@
-import { FilesSourcePlugin } from "./services";
+import { BrowsableFilesSourcePlugin } from "./services";
 
 export const ftpId = "_ftp";
 export const rootId = "pdb-gzip";
@@ -26,7 +26,7 @@ export interface RemoteFile extends RemoteEntry {
 
 export type RemoteFilesList = (RemoteDirectory | RemoteFile)[];
 
-export const rootResponse: FilesSourcePlugin[] = [
+export const rootResponse: BrowsableFilesSourcePlugin[] = [
     {
         id: "_ftp",
         type: "gxftp",
@@ -34,6 +34,7 @@ export const rootResponse: FilesSourcePlugin[] = [
         label: "FTP Directory",
         doc: "Galaxy User's FTP Directory",
         writable: true,
+        browsable: true,
     },
     {
         id: "pdb-gzip",
@@ -42,6 +43,7 @@ export const rootResponse: FilesSourcePlugin[] = [
         label: "PDB",
         doc: "Protein Data Bank (PDB)",
         writable: true,
+        browsable: true,
     },
     {
         id: "empty-dir",
@@ -50,6 +52,7 @@ export const rootResponse: FilesSourcePlugin[] = [
         label: "Empty Directory",
         doc: "Empty Directory",
         writable: true,
+        browsable: true,
     },
 ];
 
diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue
index 1262b53c32ec..15c25e9c9bba 100644
--- a/client/src/components/History/Export/HistoryExport.vue
+++ b/client/src/components/History/Export/HistoryExport.vue
@@ -30,8 +30,8 @@ const {
     hasFailed: taskHasFailed,
 } = useTaskMonitor();
 
-const { hasWritable: hasWritableFileSources } = useFileSources();
-const { hasWritable: hasWritableRDMFileSources } = useFileSources(true);
+const { hasWritable: hasWritableFileSources } = useFileSources({ exclude: ["rdm"] });
+const { hasWritable: hasWritableRDMFileSources } = useFileSources({ include: ["rdm"] });
 
 const {
     isPreparing: isPreparingDownload,
diff --git a/client/src/composables/fileSources.ts b/client/src/composables/fileSources.ts
index d2a378b19350..1ed12e79f05c 100644
--- a/client/src/composables/fileSources.ts
+++ b/client/src/composables/fileSources.ts
@@ -1,19 +1,23 @@
 import { onMounted, readonly, ref } from "vue";
 
-import { FilesSourcePlugin, getFileSources } from "@/components/FilesDialog/services";
+import {
+    BrowsableFilesSourcePlugin,
+    FilterFileSourcesOptions,
+    getFileSources,
+} from "@/components/FilesDialog/services";
 
 /**
  * Composable for accessing and working with file sources.
  *
- * @param rdmOnly Whether to only include Research Data Management (RDM) specific file sources.
+ * @param options - The options to filter the file sources.
  */
-export function useFileSources(rdmOnly = false) {
+export function useFileSources(options: FilterFileSourcesOptions = {}) {
     const isLoading = ref(true);
     const hasWritable = ref(false);
-    const fileSources = ref<FilesSourcePlugin[]>([]);
+    const fileSources = ref<BrowsableFilesSourcePlugin[]>([]);
 
     onMounted(async () => {
-        fileSources.value = await getFileSources(rdmOnly);
+        fileSources.value = await getFileSources(options);
         hasWritable.value = fileSources.value.some((fs) => fs.writable);
         isLoading.value = false;
     });
diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index ee9f9644a2f9..96924c2a576b 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -7819,6 +7819,12 @@ export interface components {
          * @enum {string}
          */
         PersonalNotificationCategory: "message" | "new_shared_item";
+        /**
+         * PluginKind
+         * @description Enum to distinguish between different kinds or categories of plugins.
+         * @enum {string}
+         */
+        PluginKind: "rfs" | "drs" | "rdm" | "stock";
         /**
          * PrepareStoreDownloadPayload
          * @description Base model definition with common configuration used by all derived models.
@@ -16255,8 +16261,12 @@ export interface operations {
          */
         parameters?: {
             /** @description Whether to return browsable filesources only. The default is `True`, which will omit filesourceslike `http` and `base64` that do not implement a list method. */
+            /** @description Whether to return **only** filesources of the specified kind. The default is `None`, which will return all filesources. Multiple values can be specified by repeating the parameter. */
+            /** @description Whether to exclude filesources of the specified kind from the list. The default is `None`, which will return all filesources. Multiple values can be specified by repeating the parameter. */
             query?: {
                 browsable_only?: boolean;
+                include_kind?: components["schemas"]["PluginKind"][];
+                exclude_kind?: components["schemas"]["PluginKind"][];
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
diff --git a/lib/galaxy/files/__init__.py b/lib/galaxy/files/__init__.py
index 88184c7862bc..ac575b6c20ca 100644
--- a/lib/galaxy/files/__init__.py
+++ b/lib/galaxy/files/__init__.py
@@ -11,7 +11,10 @@
 )
 
 from galaxy import exceptions
-from galaxy.files.sources import BaseFilesSource
+from galaxy.files.sources import (
+    BaseFilesSource,
+    PluginKind,
+)
 from galaxy.util import plugin_config
 from galaxy.util.dictifiable import Dictifiable
 
@@ -165,11 +168,17 @@ def plugins_to_dict(
         for_serialization: bool = False,
         user_context: Optional["FileSourceDictifiable"] = None,
         browsable_only: Optional[bool] = False,
+        include_kind: Optional[Set[PluginKind]] = None,
+        exclude_kind: Optional[Set[PluginKind]] = None,
     ) -> List[Dict[str, Any]]:
         rval = []
         for file_source in self._file_sources:
             if not file_source.user_has_access(user_context):
                 continue
+            if include_kind and file_source.plugin_kind not in include_kind:
+                continue
+            if exclude_kind and file_source.plugin_kind in exclude_kind:
+                continue
             if browsable_only and not file_source.get_browsable():
                 continue
             el = file_source.to_dict(for_serialization=for_serialization, user_context=user_context)
diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index 769907eef0b2..d649563bf3d0 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -1,6 +1,7 @@
 import abc
 import os
 import time
+from enum import Enum
 from typing import (
     Any,
     ClassVar,
@@ -32,6 +33,40 @@
     from galaxy.files import ConfiguredFileSourcesConfig
 
 
+class PluginKind(str, Enum):
+    """Enum to distinguish between different kinds or categories of plugins."""
+
+    rfs = "rfs"
+    """Remote File System
+
+    A remote file system is a file source that is backed by a remote file system
+    that is accessible via a URI. Examples include FTP, SFTP, S3, etc.
+    """
+
+    drs = "drs"
+    """Data Repository Service
+
+    A data repository service is a file source that is backed by a remote data
+    repository service implementing the (DRS) API which provides a generic interface
+    to data repositories so data consumers, including workflow systems,
+    can access data in a single, standard way regardless of where it's stored and how it's managed.
+    """
+
+    rdm = "rdm"
+    """Research Data Management
+
+    A research data management file source is a file source that is backed by a remote
+    research data management system that can provide DOIs. Examples include InvenioRDM, Zenodo, etc.
+    """
+
+    stock = "stock"
+    """Stock Plugin
+
+    A stock plugin is a file source that is shipped with Galaxy and covers common
+    use cases. Examples include the UserFTP, LibraryImport, UserLibraryImport, etc.
+    """
+
+
 class FilesSourceProperties(TypedDict):
     """Initial set of properties used to initialize a filesource.
 
@@ -234,6 +269,7 @@ def get_browsable(self) -> bool:
 
 class BaseFilesSource(FilesSource):
     plugin_type: ClassVar[str]
+    plugin_kind: ClassVar[PluginKind] = PluginKind.rfs  # Remote File Source by default, override in subclasses
 
     def get_browsable(self) -> bool:
         # Check whether the list method has been overridden
diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index ee2a0c7adb78..0df8c9552697 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -12,6 +12,7 @@
 from galaxy.files.sources import (
     BaseFilesSource,
     FilesSourceProperties,
+    PluginKind,
     RemoteDirectory,
     RemoteFile,
 )
@@ -139,9 +140,7 @@ class RDMFilesSource(BaseFilesSource):
 
     """
 
-    # This allows to filter out the RDM file sources from the list of available
-    # file sources.
-    supports_rdm = True
+    plugin_kind = PluginKind.rdm
 
     def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         props = self._parse_common_config_opts(kwd)
diff --git a/lib/galaxy/files/sources/base64.py b/lib/galaxy/files/sources/base64.py
index 1c7f16ab1985..98f48ef287ed 100644
--- a/lib/galaxy/files/sources/base64.py
+++ b/lib/galaxy/files/sources/base64.py
@@ -8,6 +8,7 @@
     BaseFilesSource,
     FilesSourceOptions,
     FilesSourceProperties,
+    PluginKind,
 )
 
 log = logging.getLogger(__name__)
@@ -15,6 +16,7 @@
 
 class Base64FilesSource(BaseFilesSource):
     plugin_type = "base64"
+    plugin_kind = PluginKind.stock
 
     def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         kwds: FilesSourceProperties = dict(
diff --git a/lib/galaxy/files/sources/drs.py b/lib/galaxy/files/sources/drs.py
index 6586ade4c306..9571e1f2a878 100644
--- a/lib/galaxy/files/sources/drs.py
+++ b/lib/galaxy/files/sources/drs.py
@@ -13,6 +13,7 @@
     BaseFilesSource,
     FilesSourceOptions,
     FilesSourceProperties,
+    PluginKind,
 )
 
 log = logging.getLogger(__name__)
@@ -26,6 +27,7 @@ class DRSFilesSourceProperties(FilesSourceProperties, total=False):
 
 class DRSFilesSource(BaseFilesSource):
     plugin_type = "drs"
+    plugin_kind = PluginKind.drs
 
     def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         kwds: FilesSourceProperties = dict(
diff --git a/lib/galaxy/files/sources/galaxy.py b/lib/galaxy/files/sources/galaxy.py
index ebbf9d303e4c..fa07f1efa356 100644
--- a/lib/galaxy/files/sources/galaxy.py
+++ b/lib/galaxy/files/sources/galaxy.py
@@ -7,6 +7,7 @@
 
 from typing_extensions import Unpack
 
+from galaxy.files.sources import PluginKind
 from .posix import (
     PosixFilesSource,
     PosixFilesSourceProperties,
@@ -15,6 +16,7 @@
 
 class UserFtpFilesSource(PosixFilesSource):
     plugin_type = "gxftp"
+    plugin_kind = PluginKind.stock
 
     def __init__(self, **kwd: Unpack[PosixFilesSourceProperties]):
         posix_kwds: PosixFilesSourceProperties = dict(
@@ -39,6 +41,7 @@ def get_scheme(self) -> str:
 
 class LibraryImportFilesSource(PosixFilesSource):
     plugin_type = "gximport"
+    plugin_kind = PluginKind.stock
 
     def __init__(self, **kwd: Unpack[PosixFilesSourceProperties]):
         posix_kwds: PosixFilesSourceProperties = dict(
@@ -59,6 +62,7 @@ def get_scheme(self) -> str:
 
 class UserLibraryImportFilesSource(PosixFilesSource):
     plugin_type = "gxuserimport"
+    plugin_kind = PluginKind.stock
 
     def __init__(self, **kwd: Unpack[PosixFilesSourceProperties]):
         posix_kwds: PosixFilesSourceProperties = dict(
diff --git a/lib/galaxy/files/sources/http.py b/lib/galaxy/files/sources/http.py
index 83ecd3b0b9e2..18d4002e97df 100644
--- a/lib/galaxy/files/sources/http.py
+++ b/lib/galaxy/files/sources/http.py
@@ -18,6 +18,7 @@
     BaseFilesSource,
     FilesSourceOptions,
     FilesSourceProperties,
+    PluginKind,
 )
 
 log = logging.getLogger(__name__)
@@ -30,6 +31,7 @@ class HTTPFilesSourceProperties(FilesSourceProperties, total=False):
 
 class HTTPFilesSource(BaseFilesSource):
     plugin_type = "http"
+    plugin_kind = PluginKind.stock
 
     def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         kwds: FilesSourceProperties = dict(
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index fed33051fda9..06980dac8580 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -2,10 +2,8 @@
 import logging
 from operator import itemgetter
 from typing import (
-    Any,
-    Dict,
-    List,
     Optional,
+    Set,
 )
 
 from galaxy import exceptions
@@ -13,7 +11,10 @@
     ConfiguredFileSources,
     ProvidesUserFileSourcesUserContext,
 )
-from galaxy.files.sources import FilesSourceOptions
+from galaxy.files.sources import (
+    FilesSourceOptions,
+    PluginKind,
+)
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.schema.remote_files import (
     AnyRemoteFilesListResponse,
@@ -130,13 +131,21 @@ def index(
 
         return index
 
-    def get_files_source_plugins(self, user_context: ProvidesUserContext, browsable_only: Optional[bool] = True):
+    def get_files_source_plugins(
+        self,
+        user_context: ProvidesUserContext,
+        browsable_only: Optional[bool] = True,
+        include_kind: Optional[Set[PluginKind]] = None,
+        exclude_kind: Optional[Set[PluginKind]] = None,
+    ):
         """Display plugin information for each of the gxfiles:// URI targets available."""
         user_file_source_context = ProvidesUserFileSourcesUserContext(user_context)
         browsable_only = True if browsable_only is None else browsable_only
         plugins_dict = self._file_sources.plugins_to_dict(
             user_context=user_file_source_context,
             browsable_only=browsable_only,
+            include_kind=include_kind,
+            exclude_kind=exclude_kind,
         )
         return plugins_dict
 
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 06566b663863..5c858f39879c 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -2,11 +2,16 @@
 API operations on remote files.
 """
 import logging
-from typing import Optional
+from typing import (
+    List,
+    Optional,
+)
 
 from fastapi import Body
 from fastapi.param_functions import Query
+from typing_extensions import Annotated
 
+from galaxy.files.sources import PluginKind
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.remote_files import RemoteFilesManager
 from galaxy.schema.remote_files import (
@@ -80,6 +85,22 @@
     ),
 )
 
+IncludeKindQueryParam = Query(
+    title="Include kind",
+    description=(
+        "Whether to return **only** filesources of the specified kind. The default is `None`, which will return"
+        " all filesources. Multiple values can be specified by repeating the parameter."
+    ),
+)
+
+ExcludeKindQueryParam = Query(
+    title="Exclude kind",
+    description=(
+        "Whether to exclude filesources of the specified kind from the list. The default is `None`, which will return"
+        " all filesources. Multiple values can be specified by repeating the parameter."
+    ),
+)
+
 
 @router.cbv
 class FastAPIRemoteFiles:
@@ -116,9 +137,16 @@ async def plugins(
         self,
         user_ctx: ProvidesUserContext = DependsOnTrans,
         browsable_only: Optional[bool] = BrowsableQueryParam,
+        include_kind: Annotated[Optional[List[PluginKind]], IncludeKindQueryParam] = None,
+        exclude_kind: Annotated[Optional[List[PluginKind]], ExcludeKindQueryParam] = None,
     ) -> FilesSourcePluginList:
         """Display plugin information for each of the gxfiles:// URI targets available."""
-        return self.manager.get_files_source_plugins(user_ctx, browsable_only)
+        return self.manager.get_files_source_plugins(
+            user_ctx,
+            browsable_only,
+            set(include_kind) if include_kind else None,
+            set(exclude_kind) if exclude_kind else None,
+        )
 
     @router.post(
         "/api/remote_files",

From eb030c15dbe92262e85638c3124b1f98636edaf0 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 1 Aug 2023 17:00:56 +0200
Subject: [PATCH 25/41] Do not publish records directly form Galaxy

It is safer to let the user decide when to publish the record. Galaxy should only deal with draft records with limited metadata.
---
 client/src/components/Common/ExportDOIForm.vue        |  3 ++-
 .../src/components/History/Export/HistoryExport.vue   |  8 ++++----
 .../sample/user_preferences_extra_conf.yml.sample     |  8 ++++----
 lib/galaxy/files/sources/_rdm.py                      |  8 --------
 lib/galaxy/files/sources/invenio.py                   | 11 ++---------
 5 files changed, 12 insertions(+), 26 deletions(-)

diff --git a/client/src/components/Common/ExportDOIForm.vue b/client/src/components/Common/ExportDOIForm.vue
index 10c14cc058a0..bf22358541d9 100644
--- a/client/src/components/Common/ExportDOIForm.vue
+++ b/client/src/components/Common/ExportDOIForm.vue
@@ -90,7 +90,8 @@ function clearInputs() {
                         <span v-localize> draft record has been created in the repository.</span>
                     </p>
                     <p v-if="newEntry.external_link">
-                        You can preview the record in the repository and further edit its metadata at
+                        You can preview the record in the repository, further edit its metadata and decide when to
+                        publish it at
                         <ExternalLink :href="newEntry.external_link">
                             <b>{{ newEntry.external_link }}</b>
                         </ExternalLink>
diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue
index 15c25e9c9bba..14721531e5ab 100644
--- a/client/src/components/History/Export/HistoryExport.vue
+++ b/client/src/components/History/Export/HistoryExport.vue
@@ -236,11 +236,11 @@ function updateExportParams(newParams) {
                     id="rdm-file-source-tab"
                     title="to DOI repository"
                     title-link-class="tab-export-to-doi-repo">
-                    <p>You can <b>publish your history</b> to one of the available DOI repositories here.</p>
+                    <p>You can <b>upload your history</b> to one of the available DOI repositories here.</p>
                     <p>
-                        Your history export archive needs to be uploaded to an existing record. You will need to create
-                        a <b>new record</b> on the repository or select an existing <b>draft record</b> and then export
-                        your history to it.
+                        Your history export archive needs to be uploaded to an existing <i>draft</i> record. You will
+                        need to create a <b>new record</b> on the repository or select an existing
+                        <b>draft record</b> and then export your history to it.
                     </p>
                     <BAlert show variant="info">
                         You may need to setup your credentials for the selected repository in your
diff --git a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
index 17c7fbf41572..51d5aa8b9aa4 100644
--- a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
+++ b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
@@ -96,18 +96,18 @@ preferences:
               required: False
 
     invenio:
-        description: Your Invenio RDM Account
+        description: Your Invenio RDM Integration Settings
         inputs:
             - name: token
-              label: Personal Token to publish records to Invenio RDM
+              label: Personal Token to upload files to Invenio RDM
               type: secret
               store: vault # Requires setting up vault_config_file in your galaxy.yml
               required: False
             - name: public_name
-              label: Public name to publish records (formatted as "Lastname, Firstname")
+              label: Creator name to associate with new records (formatted as "Last name, First name"). If left blank "Anonymous Galaxy User" will be used.
               type: text
               required: False
             - name: public_records
-              label: Whether to publish records (file exports) or make them restricted. Only public records can be imported back.
+              label: Whether to make draft records publicly available or restricted.
               type: boolean
               required: False
diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index 0df8c9552697..847072a193da 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -115,14 +115,6 @@ def download_file_from_record(
         """
         raise NotImplementedError()
 
-    def publish_draft_record(self, record_id: str, user_context: OptionalUserContext = None) -> None:
-        """Publishes the draft record with the given record_id.
-
-        The draft record must have been created in advance with the `create_draft_record` method.
-        The user_context might be required to authenticate the user in the repository.
-        """
-        raise NotImplementedError()
-
 
 class RDMFilesSource(BaseFilesSource):
     """Base class for Research Data Management (RDM) file sources.
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index d7debf620660..6cfad1f4ec7a 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -170,7 +170,6 @@ def _write_from(
     ):
         record_id, filename = self.parse_path(target_path)
         self.repository.upload_file_to_draft_record(record_id, filename, native_path, user_context=user_context)
-        self.repository.publish_draft_record(record_id, user_context=user_context)
 
 
 class InvenioRepositoryInteractor(RDMRepositoryInteractor):
@@ -199,8 +198,8 @@ def get_files_in_record(
     def create_draft_record(self, title: str, user_context: OptionalUserContext = None) -> RemoteDirectory:
         today = datetime.date.today().isoformat()
         creator = self._get_creator_from_user_context(user_context)
-        should_publish = bool(self.get_user_preference_by_key("public_records", user_context))
-        access = "public" if should_publish else "restricted"
+        public = bool(self.get_user_preference_by_key("public_records", user_context))
+        access = "public" if public else "restricted"
         create_record_request = {
             "access": {"record": access, "files": access},
             "files": {"enabled": True},
@@ -270,12 +269,6 @@ def download_file_from_record(
                 page, f.fileno(), file_path, source_encoding=get_charset_from_http_headers(page.headers)
             )
 
-    def publish_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
-        publish_record_url = f"{self.records_url}/{record_id}/draft/actions/publish"
-        headers = self._get_request_headers(user_context)
-        response = requests.post(publish_record_url, headers=headers, verify=VERIFY)
-        self._ensure_response_has_expected_status_code(response, 202)
-
     def _get_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
         request_url = f"{self.records_url}/{record_id}/draft"
         draft_record = self._get_response(user_context, request_url)

From eacf78dd8365209ce5b7a8c4499915b6310b4f3f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 2 Aug 2023 15:45:57 +0200
Subject: [PATCH 26/41] Handle authorization in tool execution context

---
 lib/galaxy/files/sources/_rdm.py    | 21 +++++++++++++++++++--
 lib/galaxy/files/sources/invenio.py |  7 +------
 2 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index 847072a193da..2d7f3f9b8bfe 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -8,6 +8,7 @@
 
 from typing_extensions import Unpack
 
+from galaxy.exceptions import AuthenticationRequired
 from galaxy.files import ProvidesUserFileSourcesUserContext
 from galaxy.files.sources import (
     BaseFilesSource,
@@ -24,6 +25,7 @@
 
 class RDMFilesSourceProperties(FilesSourceProperties):
     url: str
+    token: str
 
 
 class RecordFilename(NamedTuple):
@@ -38,12 +40,12 @@ class RDMRepositoryInteractor:
     by file sources that interact with RDM repositories.
     """
 
-    def __init__(self, repository_url: str, plugin: BaseFilesSource):
+    def __init__(self, repository_url: str, plugin: "RDMFilesSource"):
         self._repository_url = repository_url
         self._plugin = plugin
 
     @property
-    def plugin(self) -> BaseFilesSource:
+    def plugin(self) -> "RDMFilesSource":
         """Returns the plugin associated with this repository interactor."""
         return self._plugin
 
@@ -140,6 +142,7 @@ def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         if not base_url:
             raise Exception("URL for RDM repository must be provided in configuration")
         self._repository_url = base_url
+        self._token = props.get("token", None)
         self._props = props
         self._repository_interactor = self.get_repository_interactor(base_url)
 
@@ -147,6 +150,10 @@ def __init__(self, **kwd: Unpack[FilesSourceProperties]):
     def repository(self) -> RDMRepositoryInteractor:
         return self._repository_interactor
 
+    @property
+    def token(self) -> Optional[str]:
+        return self._token if self._token and not self._token.startswith("$") else None
+
     def get_repository_interactor(self, repository_url: str) -> RDMRepositoryInteractor:
         """Returns an interactor compatible with the given repository URL.
 
@@ -164,4 +171,14 @@ def _serialization_props(self, user_context: OptionalUserContext = None) -> RDMF
         for key, val in self._props.items():
             effective_props[key] = self._evaluate_prop(val, user_context=user_context)
         effective_props["url"] = self._repository_url
+        effective_props["token"] = self.get_authorization_token(user_context)
         return cast(RDMFilesSourceProperties, effective_props)
+
+    def get_authorization_token(self, user_context: OptionalUserContext) -> str:
+        token = self.token
+        if not token and user_context:
+            vault = user_context.user_vault if user_context else None
+            token = vault.read_secret(f"preferences/{self.id}/token") if vault else None
+        if token is None:
+            raise AuthenticationRequired(f"No authorization token provided in user's settings for '{self.label}'")
+        return token
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 6cfad1f4ec7a..a7fb9d51a8f4 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -337,15 +337,10 @@ def _get_response(self, user_context: OptionalUserContext, request_url: str) ->
         return response.json()
 
     def _get_request_headers(self, user_context: OptionalUserContext):
-        token = self.get_authorization_token(user_context)
+        token = self.plugin.get_authorization_token(user_context)
         headers = {"Authorization": f"Bearer {token}"} if token else {}
         return headers
 
-    def get_authorization_token(self, user_context) -> str:
-        vault = user_context.user_vault if user_context else None
-        token = vault.read_secret(f"preferences/{self.plugin.id}/token") if vault else None
-        return token
-
     def _ensure_response_has_expected_status_code(self, response, expected_status_code: int):
         if response.status_code != expected_status_code:
             error_message = self._get_response_error_message(response)

From 5e99c9dd9d7291bd9214745703a9fc95500ab438 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 3 Aug 2023 10:55:56 +0200
Subject: [PATCH 27/41] Validate source_path format on parse

---
 lib/galaxy/files/sources/_rdm.py    | 20 +++++++++++++++-----
 lib/galaxy/files/sources/invenio.py |  2 +-
 2 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index 2d7f3f9b8bfe..7a98474cef91 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -160,11 +160,21 @@ def get_repository_interactor(self, repository_url: str) -> RDMRepositoryInterac
         This must be implemented by subclasses."""
         raise NotImplementedError()
 
-    def parse_path(self, source_path: str) -> RecordFilename:
-        # source_path has always the format: '/{record_id}/{file_name}'
-        record_id = source_path.split("/")[1]
-        filename = source_path.split("/")[-1]
-        return RecordFilename(record_id=record_id, filename=filename)
+    def parse_path(self, source_path: str, record_id_only: bool = False) -> RecordFilename:
+        if not source_path.startswith("/"):
+            raise ValueError(f"Invalid source path: '{source_path}'. Must start with '/'")
+        parts = source_path[1:].split("/", 2)
+        if record_id_only:
+            if len(parts) != 1:
+                raise ValueError(f"Invalid source path: '{source_path}'. Must have the format '/<record_id>'.")
+            return RecordFilename(record_id=parts[0], filename="")
+        if len(parts) != 2:
+            raise ValueError(f"Invalid source path: '{source_path}'. Must have the format '/<record_id>/<file_name>'.")
+        record_id, file_name = parts
+        return RecordFilename(record_id=record_id, filename=file_name)
+
+    def get_record_id_from_path(self, source_path: str) -> str:
+        return self.parse_path(source_path, record_id_only=True).record_id
 
     def _serialization_props(self, user_context: OptionalUserContext = None) -> RDMFilesSourceProperties:
         effective_props = {}
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index a7fb9d51a8f4..10e07677d3af 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -132,7 +132,7 @@ def _list(
         is_root_path = path == "/"
         if is_root_path:
             return self.repository.get_records(writeable, user_context)
-        record_id, _ = self.parse_path(path)
+        record_id = self.get_record_id_from_path(path)
         return self.repository.get_files_in_record(record_id, writeable, user_context)
 
     def _create_entry(

From cdb15c67c441ac277399740a0d0b96561009e79b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 12 Aug 2023 15:32:31 +0200
Subject: [PATCH 28/41] Refactor FilesDialog unit tests

---
 .../FilesDialog/FilesDialog.test.ts           | 38 ++++++++-----------
 1 file changed, 15 insertions(+), 23 deletions(-)

diff --git a/client/src/components/FilesDialog/FilesDialog.test.ts b/client/src/components/FilesDialog/FilesDialog.test.ts
index d45ca9d99d07..9318e275b9fd 100644
--- a/client/src/components/FilesDialog/FilesDialog.test.ts
+++ b/client/src/components/FilesDialog/FilesDialog.test.ts
@@ -1,5 +1,4 @@
 import { createLocalVue, shallowMount, Wrapper } from "@vue/test-utils";
-import BootstrapVue, { BButton } from "bootstrap-vue";
 import flushPromises from "flush-promises";
 
 import { selectionStates } from "@/components/SelectionDialog/selectionStates";
@@ -39,10 +38,7 @@ jest.mock("@/composables/config", () => ({
 interface RemoteFilesParams {
     target: string;
     recursive: boolean;
-}
-
-interface RemoteFilesResponse {
-    data?: RemoteFilesList;
+    writeable?: boolean;
 }
 
 interface RowElement extends BaseRecordItem, Element {
@@ -50,40 +46,36 @@ interface RowElement extends BaseRecordItem, Element {
 }
 
 function paramsToKey(params: RemoteFilesParams) {
+    params.writeable = false;
     return JSON.stringify(params);
 }
 
-const mockedOkApiRoutesMap = new Map<string, RemoteFilesResponse>([
-    [paramsToKey({ target: "gxfiles://pdb-gzip", recursive: false }), { data: pdbResponse }],
-    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1", recursive: false }), { data: directory1Response }],
-    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1", recursive: true }), { data: directory1RecursiveResponse }],
-    [paramsToKey({ target: "gxfiles://pdb-gzip/directory2", recursive: true }), { data: directory2RecursiveResponse }],
-    [
-        paramsToKey({ target: "gxfiles://pdb-gzip/directory1/subdirectory1", recursive: false }),
-        { data: subsubdirectoryResponse },
-    ],
+const mockedOkApiRoutesMap = new Map<string, RemoteFilesList>([
+    [paramsToKey({ target: "gxfiles://pdb-gzip", recursive: false }), pdbResponse],
+    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1", recursive: false }), directory1Response],
+    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1", recursive: true }), directory1RecursiveResponse],
+    [paramsToKey({ target: "gxfiles://pdb-gzip/directory2", recursive: true }), directory2RecursiveResponse],
+    [paramsToKey({ target: "gxfiles://pdb-gzip/directory1/subdirectory1", recursive: false }), subsubdirectoryResponse],
 ]);
 
-const mockedErrorApiRoutesMap = new Map<string, RemoteFilesResponse>([
-    [paramsToKey({ target: "gxfiles://empty-dir", recursive: false }), {}],
+const mockedErrorApiRoutesMap = new Map<string, RemoteFilesList>([
+    [paramsToKey({ target: "gxfiles://empty-dir", recursive: false }), []],
 ]);
 
-function getMockResponse(param: RemoteFilesParams) {
+function getMockedBrowseResponse(param: RemoteFilesParams) {
     const responseKey = paramsToKey(param);
     if (mockedErrorApiRoutesMap.has(responseKey)) {
         throw Error(someErrorText);
     }
-    return mockedOkApiRoutesMap.get(responseKey);
+    const result = mockedOkApiRoutesMap.get(responseKey);
+    return { data: result };
 }
 
 const initComponent = async (props: { multiple: boolean; mode?: string }) => {
     const localVue = createLocalVue();
 
-    localVue.use(BootstrapVue);
-    localVue.component("BBtnStub", BButton);
-
     mockFetcher.path("/api/remote_files/plugins").method("get").mock({ data: rootResponse });
-    mockFetcher.path("/api/remote_files").method("get").mock(getMockResponse);
+    mockFetcher.path("/api/remote_files").method("get").mock(getMockedBrowseResponse);
 
     const wrapper = shallowMount(FilesDialog, {
         localVue,
@@ -365,7 +357,7 @@ class Utils {
     }
 
     getRenderedRows(): RowElement[] {
-        return this.getTable().vm.items as RowElement[];
+        return this.getTable().props("items") as RowElement[];
     }
 
     expectAllRenderedItemsSelected() {

From 38798fc5e665e642f0bfdbefabad0172a5edd5a4 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sat, 12 Aug 2023 15:34:39 +0200
Subject: [PATCH 29/41] Fix typescript error in HistoryExport unit tests

---
 client/src/components/History/Export/HistoryExport.test.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/Export/HistoryExport.test.ts b/client/src/components/History/Export/HistoryExport.test.ts
index 968e4e77dfc1..712446f67b6e 100644
--- a/client/src/components/History/Export/HistoryExport.test.ts
+++ b/client/src/components/History/Export/HistoryExport.test.ts
@@ -37,10 +37,10 @@ const REMOTE_FILES_API_RESPONSE: FilesSourcePluginList = [
     {
         id: "test-posix-source",
         type: "posix",
-        uri_root: "gxfiles://test-posix-source",
         label: "TestSource",
         doc: "For testing",
         writable: true,
+        browsable: true,
         requires_roles: undefined,
         requires_groups: undefined,
     },

From 6c8bbe412718dc72bdb86a51ecd31b4525275b26 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 14 Aug 2023 12:27:59 +0200
Subject: [PATCH 30/41] Temporarily raise limit of records to 100

Until general pagination support is added for Remote File Sources.
---
 lib/galaxy/files/sources/invenio.py | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 10e07677d3af..621061952041 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -177,14 +177,23 @@ class InvenioRepositoryInteractor(RDMRepositoryInteractor):
     def records_url(self) -> str:
         return f"{self.repository_url}/api/records"
 
+    @property
+    def user_records_url(self) -> str:
+        return f"{self.repository_url}/api/user/records"
+
     def to_plugin_uri(self, record_id: str, filename: Optional[str] = None) -> str:
         return f"{self.plugin.get_uri_root()}/{record_id}{f'/{filename}' if filename else ''}"
 
     def get_records(self, writeable: bool, user_context: OptionalUserContext = None) -> List[RemoteDirectory]:
-        # Only draft records owned by the user can be written to.
-        request_url = f"{self.repository_url}/api/user/records?is_published=false" if writeable else self.records_url
-        # TODO: This is limited to 25 records by default. Add pagination support?
-        response_data = self._get_response(user_context, request_url)
+        params = {}
+        request_url = self.records_url
+        if writeable:
+            # Only draft records owned by the user can be written to.
+            params["is_published"] = "false"
+            request_url = self.user_records_url
+        # TODO: Add pagination support to FileSources. This is limited to 100 records by default for now.
+        params["size"] = 100
+        response_data = self._get_response(user_context, request_url, params=params)
         return self._get_records_from_response(response_data)
 
     def get_files_in_record(
@@ -330,9 +339,9 @@ def get_user_preference_by_key(self, key: str, user_context: OptionalUserContext
         value = preferences.get(f"{self.plugin.id}|{key}", None) if preferences else None
         return value
 
-    def _get_response(self, user_context: OptionalUserContext, request_url: str) -> dict:
+    def _get_response(self, user_context: OptionalUserContext, request_url: str, params: dict = None) -> dict:
         headers = self._get_request_headers(user_context)
-        response = requests.get(request_url, headers=headers, verify=VERIFY)
+        response = requests.get(request_url, params=params, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 200)
         return response.json()
 

From 1c9f1b4e191cae207883861999617f8b60b0b445 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 14 Aug 2023 14:42:05 +0200
Subject: [PATCH 31/41] Allow downloading files from draft and published
 records

---
 lib/galaxy/files/sources/invenio.py | 31 +++++++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 621061952041..f85aeae48091 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -3,6 +3,8 @@
 import ssl
 import urllib.request
 from typing import (
+    Any,
+    Dict,
     List,
     Optional,
 )
@@ -185,7 +187,7 @@ def to_plugin_uri(self, record_id: str, filename: Optional[str] = None) -> str:
         return f"{self.plugin.get_uri_root()}/{record_id}{f'/{filename}' if filename else ''}"
 
     def get_records(self, writeable: bool, user_context: OptionalUserContext = None) -> List[RemoteDirectory]:
-        params = {}
+        params: Dict[str, Any] = {}
         request_url = self.records_url
         if writeable:
             # Only draft records owned by the user can be written to.
@@ -268,8 +270,7 @@ def download_file_from_record(
         file_path: str,
         user_context: OptionalUserContext = None,
     ):
-        download_file_content_url = f"{self.records_url}/{record_id}/files/{quote(filename)}/content"
-
+        download_file_content_url = self._get_download_file_url(record_id, filename, user_context)
         headers = self._get_request_headers(user_context)
         req = urllib.request.Request(download_file_content_url, headers=headers)
         with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT, context=SSL_CONTEXT) as page:
@@ -278,6 +279,26 @@ def download_file_from_record(
                 page, f.fileno(), file_path, source_encoding=get_charset_from_http_headers(page.headers)
             )
 
+    def _get_download_file_url(self, record_id: str, filename: str, user_context: OptionalUserContext = None):
+        """Get the URL to download a file from a record.
+
+        This method is used to download files from both published and draft records that are accessible by the user.
+        """
+        is_draft_record = self._is_draft_record(record_id, user_context)
+        download_file_content_url = f"{self.records_url}/{record_id}/files/{quote(filename)}/content"
+        if is_draft_record:
+            download_file_content_url = download_file_content_url.replace("/files/", "/draft/files/")
+        return download_file_content_url
+
+    def _is_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
+        try:
+            self._get_draft_record(record_id, user_context)
+            return True
+        except Exception as e:
+            if "404" in str(e):
+                return False
+            raise e
+
     def _get_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
         request_url = f"{self.records_url}/{record_id}/draft"
         draft_record = self._get_response(user_context, request_url)
@@ -339,7 +360,9 @@ def get_user_preference_by_key(self, key: str, user_context: OptionalUserContext
         value = preferences.get(f"{self.plugin.id}|{key}", None) if preferences else None
         return value
 
-    def _get_response(self, user_context: OptionalUserContext, request_url: str, params: dict = None) -> dict:
+    def _get_response(
+        self, user_context: OptionalUserContext, request_url: str, params: Optional[Dict[str, Any]] = None
+    ) -> dict:
         headers = self._get_request_headers(user_context)
         response = requests.get(request_url, params=params, headers=headers, verify=VERIFY)
         self._ensure_response_has_expected_status_code(response, 200)

From 01415a6913f199d2cd7517f6cec979f5f0518b20 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 14 Aug 2023 15:11:31 +0200
Subject: [PATCH 32/41] Refactor Ok button disabled condition

---
 client/src/components/FilesDialog/FilesDialog.vue | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/client/src/components/FilesDialog/FilesDialog.vue b/client/src/components/FilesDialog/FilesDialog.vue
index d7b092c65434..f96306b674ca 100644
--- a/client/src/components/FilesDialog/FilesDialog.vue
+++ b/client/src/components/FilesDialog/FilesDialog.vue
@@ -70,6 +70,9 @@ const selectAllIcon = ref(selectionStates.unselected);
 const urlTracker = ref(new UrlTracker(""));
 
 const fileMode = computed(() => props.mode == "file");
+const okButtonDisabled = computed(
+    () => (fileMode.value && !hasValue.value) || isBusy.value || (!fileMode.value && urlTracker.value.atRoot())
+);
 
 /** Collects selected datasets in value array **/
 function clicked(record: RecordItem) {
@@ -392,7 +395,7 @@ onMounted(() => {
                 size="sm"
                 class="float-right ml-1 file-dialog-modal-ok"
                 variant="primary"
-                :disabled="(fileMode && !hasValue) || isBusy || (!fileMode && urlTracker.atRoot())"
+                :disabled="okButtonDisabled"
                 @click="onOk">
                 {{ fileMode ? "Ok" : "Select this folder" }}
             </BButton>

From 9987e0db0cb89ca02591e375be05031821a4d6c3 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 14 Aug 2023 15:41:32 +0200
Subject: [PATCH 33/41] Provide detailed error messages when invalid path

---
 lib/galaxy/files/sources/_rdm.py | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index 7a98474cef91..77600ab1f195 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -161,15 +161,29 @@ def get_repository_interactor(self, repository_url: str) -> RDMRepositoryInterac
         raise NotImplementedError()
 
     def parse_path(self, source_path: str, record_id_only: bool = False) -> RecordFilename:
+        """Parses the given source path and returns the record_id and filename.
+
+        The source path must have the format '/<record_id>/<file_name>'.
+        If record_id_only is True, the source path must have the format '/<record_id>' and an
+        empty filename will be returned.
+        """
+
+        def get_error_msg(details: str) -> str:
+            return f"Invalid source path: '{source_path}'. Expected format: '{expected_format}'. {details}"
+
+        expected_format = "/<record_id>"
         if not source_path.startswith("/"):
-            raise ValueError(f"Invalid source path: '{source_path}'. Must start with '/'")
+            raise ValueError(get_error_msg("Must start with '/'."))
         parts = source_path[1:].split("/", 2)
         if record_id_only:
             if len(parts) != 1:
-                raise ValueError(f"Invalid source path: '{source_path}'. Must have the format '/<record_id>'.")
+                raise ValueError(get_error_msg("Please provide the record_id only."))
             return RecordFilename(record_id=parts[0], filename="")
-        if len(parts) != 2:
-            raise ValueError(f"Invalid source path: '{source_path}'. Must have the format '/<record_id>/<file_name>'.")
+        expected_format = "/<record_id>/<file_name>"
+        if len(parts) < 2:
+            raise ValueError(get_error_msg("Please provide both the record_id and file_name."))
+        if len(parts) > 2:
+            raise ValueError(get_error_msg("Too many parts. Please provide the record_id and file_name only."))
         record_id, file_name = parts
         return RecordFilename(record_id=record_id, filename=file_name)
 

From 3e7fcfb72407658995517c7b33b691b6b11ae685 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 14 Aug 2023 16:54:59 +0200
Subject: [PATCH 34/41] Improve prefix to avoid collisions

When exporting a history archive to a remote source.
---
 .../Archiving/HistoryArchiveExportSelector.vue  | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue b/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
index 367de3b344f0..acad61d33d50 100644
--- a/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
+++ b/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
@@ -99,16 +99,19 @@ async function onCreateExportRecord() {
     isExportDialogOpen.value = true;
 }
 
-async function doExportToFileSource(exportDirectory: string, fileName: string) {
-    isExportingRecord.value = true;
-    isExportDialogOpen.value = false;
-
+async function doExportToFileSourceWithPrefix(exportDirectory: string, fileName: string) {
     // Avoid name collisions if multiple different histories are exported to the
     // same destination with the same name
-    const prefixedFileName = `${props.history.id}_${fileName}`;
+    const fileNameCompatibleUpdateTime = props.history.update_time.replace(/:/g, "-");
+    const prefixedFileName = `${fileNameCompatibleUpdateTime}_${fileName}`;
+    doExportToFileSource(exportDirectory, prefixedFileName);
+}
 
+async function doExportToFileSource(exportDirectory: string, fileName: string) {
+    isExportingRecord.value = true;
+    isExportDialogOpen.value = false;
     try {
-        await exportToFileSource(props.history.id, exportDirectory, prefixedFileName, DEFAULT_EXPORT_PARAMS);
+        await exportToFileSource(props.history.id, exportDirectory, fileName, DEFAULT_EXPORT_PARAMS);
     } catch (error) {
         exportErrorMessage.value = "The history export request failed. Please try again later.";
     }
@@ -196,7 +199,7 @@ function onArchiveHistoryWithExport() {
         </BButton>
 
         <BModal v-model="isExportDialogOpen" title="Export history to permanent storage" size="lg" hide-footer>
-            <ExportToFileSourceForm what="history" @export="doExportToFileSource" />
+            <ExportToFileSourceForm what="history" @export="doExportToFileSourceWithPrefix" />
         </BModal>
     </div>
 </template>

From b793678a7086d34877140ab22553492f1ac616d7 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 14 Aug 2023 16:58:42 +0200
Subject: [PATCH 35/41] Integrate on History Archive Export Selector

---
 .../HistoryArchiveExportSelector.vue          | 36 ++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue b/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
index acad61d33d50..b3d372fa1125 100644
--- a/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
+++ b/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
@@ -1,6 +1,7 @@
 <script setup lang="ts">
 import { BAlert, BButton, BFormCheckbox, BModal } from "bootstrap-vue";
 import { computed, onMounted, ref, watch } from "vue";
+import { RouterLink } from "vue-router";
 
 import type { ExportRecord } from "@/components/Common/models/exportRecordModel";
 import { exportToFileSource, getExportRecords } from "@/components/History/Export/services";
@@ -9,6 +10,7 @@ import { useTaskMonitor } from "@/composables/taskMonitor";
 import type { HistorySummary } from "@/stores/historyStore";
 
 import ExportRecordCard from "./ExportRecordCard.vue";
+import ExportToDOIRepositoryForm from "@/components/Common/ExportDOIForm.vue";
 import ExportToFileSourceForm from "@/components/Common/ExportForm.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
@@ -36,6 +38,10 @@ const isExportDialogOpen = ref(false);
 const isDeleteContentsConfirmed = ref(false);
 const exportErrorMessage = ref<string | null>(null);
 
+const historyName = computed(() => {
+    return props.history.name;
+});
+
 const mostUpToDateExport = computed(() => {
     return existingExports.value.find(
         (exportRecord) => exportRecord.isPermanent && (exportRecord.isUpToDate || exportRecord.isPreparing)
@@ -199,7 +205,35 @@ function onArchiveHistoryWithExport() {
         </BButton>
 
         <BModal v-model="isExportDialogOpen" title="Export history to permanent storage" size="lg" hide-footer>
-            <ExportToFileSourceForm what="history" @export="doExportToFileSourceWithPrefix" />
+            <BTabs card vertical lazy class="export-option-tabs">
+                <BTab id="to-remote-file-tab" title="To Remote File Source" active>
+                    <p>
+                        <b>Exporting to a remote file source</b> will create a compressed archive of the history
+                        contents, copy it to a remote location (e.g. an FTP server) and create an export record with
+                        this information that will be associated with the archived history. You will be able to recreate
+                        the history later by importing it from the export record.
+                    </p>
+                    <ExportToFileSourceForm what="history" @export="doExportToFileSourceWithPrefix" />
+                </BTab>
+                <BTab id="to-rdm-repository-tab" title="To RDM Repository">
+                    <p>
+                        <b>Exporting to a RDM repository</b> (e.g. Invenio RDM or Zenodo RDM) will require to create or
+                        select an existing record in the repository where the history archive will be uploaded. The
+                        export record will be associated with the archived history and you will be able to recreate the
+                        history later by importing it from the export record.
+                    </p>
+                    <p>
+                        You may need to setup your credentials for the selected repository in your
+                        <RouterLink to="/user/information" target="_blank">settings page</RouterLink> to be able to
+                        export.
+                    </p>
+                    <ExportToDOIRepositoryForm
+                        what="history"
+                        :default-filename="historyName + ' (Galaxy History)'"
+                        :default-record-name="historyName"
+                        @export="doExportToFileSource" />
+                </BTab>
+            </BTabs>
         </BModal>
     </div>
 </template>

From e757e4d0f39ea0c518852fa44b1720f21ebb1d3b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 14 Aug 2023 17:12:17 +0200
Subject: [PATCH 36/41] Rename DOI to RDM for consistency

---
 .../{ExportDOIForm.vue => ExportRDMForm.vue}  |  8 +++----
 .../HistoryArchiveExportSelector.vue          |  4 ++--
 .../History/Export/HistoryExport.vue          | 21 +++++++++++--------
 3 files changed, 18 insertions(+), 15 deletions(-)
 rename client/src/components/Common/{ExportDOIForm.vue => ExportRDMForm.vue} (96%)

diff --git a/client/src/components/Common/ExportDOIForm.vue b/client/src/components/Common/ExportRDMForm.vue
similarity index 96%
rename from client/src/components/Common/ExportDOIForm.vue
rename to client/src/components/Common/ExportRDMForm.vue
index bf22358541d9..105f7f947f4f 100644
--- a/client/src/components/Common/ExportDOIForm.vue
+++ b/client/src/components/Common/ExportRDMForm.vue
@@ -28,7 +28,7 @@ const emit = defineEmits<{
 
 type ExportChoice = "existing" | "new";
 
-const includeOnlyDOICompatible: FilterFileSourcesOptions = { include: ["rdm"] };
+const includeOnlyRDMCompatible: FilterFileSourcesOptions = { include: ["rdm"] };
 
 const recordUri = ref<string>("");
 const sourceUri = ref<string>("");
@@ -72,7 +72,7 @@ function clearInputs() {
 </script>
 
 <template>
-    <div class="export-to-doi-repository">
+    <div class="export-to-rdm-repository">
         <BFormGroup id="fieldset-name" label-for="name" :description="nameDescription" class="mt-3">
             <BFormInput id="name" v-model="fileName" :placeholder="namePlaceholder" required />
         </BFormGroup>
@@ -118,7 +118,7 @@ function clearInputs() {
                         v-model="sourceUri"
                         mode="source"
                         :require-writable="true"
-                        :filter-options="includeOnlyDOICompatible" />
+                        :filter-options="includeOnlyRDMCompatible" />
                 </BFormGroup>
                 <BFormGroup
                     id="fieldset-record-name"
@@ -151,7 +151,7 @@ function clearInputs() {
                     v-model="recordUri"
                     mode="directory"
                     :require-writable="true"
-                    :filter-options="includeOnlyDOICompatible" />
+                    :filter-options="includeOnlyRDMCompatible" />
             </BFormGroup>
             <BButton
                 v-localize
diff --git a/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue b/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
index b3d372fa1125..7cb655854395 100644
--- a/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
+++ b/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
@@ -10,8 +10,8 @@ import { useTaskMonitor } from "@/composables/taskMonitor";
 import type { HistorySummary } from "@/stores/historyStore";
 
 import ExportRecordCard from "./ExportRecordCard.vue";
-import ExportToDOIRepositoryForm from "@/components/Common/ExportDOIForm.vue";
 import ExportToFileSourceForm from "@/components/Common/ExportForm.vue";
+import ExportToRDMRepositoryForm from "@/components/Common/ExportRDMForm.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
 const {
@@ -227,7 +227,7 @@ function onArchiveHistoryWithExport() {
                         <RouterLink to="/user/information" target="_blank">settings page</RouterLink> to be able to
                         export.
                     </p>
-                    <ExportToDOIRepositoryForm
+                    <ExportToRDMRepositoryForm
                         what="history"
                         :default-filename="historyName + ' (Galaxy History)'"
                         :default-record-name="historyName"
diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue
index 14721531e5ab..941b87c03bbd 100644
--- a/client/src/components/History/Export/HistoryExport.vue
+++ b/client/src/components/History/Export/HistoryExport.vue
@@ -18,10 +18,10 @@ import { absPath } from "@/utils/redirect";
 import { exportToFileSource, getExportRecords, reimportHistoryFromRecord } from "./services";
 
 import ExportOptions from "./ExportOptions.vue";
-import ExportDOIForm from "components/Common/ExportDOIForm.vue";
-import ExportForm from "components/Common/ExportForm.vue";
-import ExportRecordDetails from "components/Common/ExportRecordDetails.vue";
-import ExportRecordTable from "components/Common/ExportRecordTable.vue";
+import ExportToFileSourceForm from "@/components/Common/ExportForm.vue";
+import ExportToRDMRepositoryForm from "@/components/Common/ExportRDMForm.vue";
+import ExportRecordDetails from "@/components/Common/ExportRecordDetails.vue";
+import ExportRecordTable from "@/components/Common/ExportRecordTable.vue";
 
 const {
     isRunning: isExportTaskRunning,
@@ -229,14 +229,17 @@ function updateExportParams(newParams) {
                         one of the available remote file sources here. You will be able to re-import it later as long as
                         it remains available on the remote server.
                     </p>
-                    <ExportForm what="history" :clear-input-after-export="true" @export="doExportToFileSource" />
+                    <ExportToFileSourceForm
+                        what="history"
+                        :clear-input-after-export="true"
+                        @export="doExportToFileSource" />
                 </BTab>
                 <BTab
                     v-if="hasWritableRDMFileSources"
                     id="rdm-file-source-tab"
-                    title="to DOI repository"
-                    title-link-class="tab-export-to-doi-repo">
-                    <p>You can <b>upload your history</b> to one of the available DOI repositories here.</p>
+                    title="to RDM repository"
+                    title-link-class="tab-export-to-rdm-repo">
+                    <p>You can <b>upload your history</b> to one of the available RDM repositories here.</p>
                     <p>
                         Your history export archive needs to be uploaded to an existing <i>draft</i> record. You will
                         need to create a <b>new record</b> on the repository or select an existing
@@ -249,7 +252,7 @@ function updateExportParams(newParams) {
                         public name you want to associate with your records or whether you want to publish them
                         immediately or keep them as drafts after export.
                     </BAlert>
-                    <ExportDOIForm
+                    <ExportToRDMRepositoryForm
                         what="history"
                         :default-filename="historyName + ' (Galaxy History)'"
                         :default-record-name="historyName"

From 06c140b487fb0c46ae85c065eb90cff21bb18a69 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:15:05 +0200
Subject: [PATCH 37/41] Handle errors creating new records

---
 client/src/components/Common/ExportRDMForm.vue | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/client/src/components/Common/ExportRDMForm.vue b/client/src/components/Common/ExportRDMForm.vue
index 105f7f947f4f..370561b1cf43 100644
--- a/client/src/components/Common/ExportRDMForm.vue
+++ b/client/src/components/Common/ExportRDMForm.vue
@@ -3,11 +3,15 @@ import { BButton, BCard, BFormGroup, BFormInput, BFormRadio, BFormRadioGroup } f
 import { computed, ref } from "vue";
 
 import { CreatedEntry, createRemoteEntry, FilterFileSourcesOptions } from "@/components/FilesDialog/services";
+import { useToast } from "@/composables/toast";
 import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import ExternalLink from "@/components/ExternalLink.vue";
 import FilesInput from "@/components/FilesDialog/FilesInput.vue";
 
+const toast = useToast();
+
 interface Props {
     what?: string;
     clearInputAfterExport?: boolean;
@@ -58,9 +62,12 @@ function doExport() {
 }
 
 async function doCreateRecord() {
-    //TODO: handle errors
-    newEntry.value = await createRemoteEntry(sourceUri.value, recordName.value);
-    recordUri.value = newEntry.value.uri;
+    try {
+        newEntry.value = await createRemoteEntry(sourceUri.value, recordName.value);
+        recordUri.value = newEntry.value.uri;
+    } catch (e) {
+        toast.error(errorMessageAsString(e));
+    }
 }
 
 function clearInputs() {

From 3350337d1e52a308a6e5f12346bd43061452d552 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 15 Aug 2023 12:20:33 +0200
Subject: [PATCH 38/41] Add external link to Invenio RDM

---
 .../Archiving/HistoryArchiveExportSelector.vue        | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue b/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
index 7cb655854395..4e7219d5f31e 100644
--- a/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
+++ b/client/src/components/History/Archiving/HistoryArchiveExportSelector.vue
@@ -12,6 +12,7 @@ import type { HistorySummary } from "@/stores/historyStore";
 import ExportRecordCard from "./ExportRecordCard.vue";
 import ExportToFileSourceForm from "@/components/Common/ExportForm.vue";
 import ExportToRDMRepositoryForm from "@/components/Common/ExportRDMForm.vue";
+import ExternalLink from "@/components/ExternalLink.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
 const {
@@ -217,10 +218,12 @@ function onArchiveHistoryWithExport() {
                 </BTab>
                 <BTab id="to-rdm-repository-tab" title="To RDM Repository">
                     <p>
-                        <b>Exporting to a RDM repository</b> (e.g. Invenio RDM or Zenodo RDM) will require to create or
-                        select an existing record in the repository where the history archive will be uploaded. The
-                        export record will be associated with the archived history and you will be able to recreate the
-                        history later by importing it from the export record.
+                        <b>Exporting to a RDM repository</b> (e.g. any
+                        <ExternalLink href="https://inveniosoftware.org/products/rdm/"> Invenio RDM </ExternalLink>
+                        compatible repository) will require to create or select an existing record in the repository
+                        where the history archive will be uploaded. The export record will be associated with the
+                        archived history and you will be able to recreate the history later by importing it from the
+                        export record.
                     </p>
                     <p>
                         You may need to setup your credentials for the selected repository in your

From e9926036c34c89befad88df3738f17e2816dab22 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 15 Aug 2023 15:16:15 +0200
Subject: [PATCH 39/41] Add unit tests for ExportRDMForm component

---
 .../components/Common/ExportRDMForm.test.ts   | 139 ++++++++++++++++++
 .../src/components/Common/ExportRDMForm.vue   |  24 ++-
 2 files changed, 155 insertions(+), 8 deletions(-)
 create mode 100644 client/src/components/Common/ExportRDMForm.test.ts

diff --git a/client/src/components/Common/ExportRDMForm.test.ts b/client/src/components/Common/ExportRDMForm.test.ts
new file mode 100644
index 000000000000..7f19404d7ab1
--- /dev/null
+++ b/client/src/components/Common/ExportRDMForm.test.ts
@@ -0,0 +1,139 @@
+import { getLocalVue } from "@tests/jest/helpers";
+import { mount, Wrapper } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+
+import { mockFetcher } from "@/schema/__mocks__";
+
+import { CreatedEntry } from "../FilesDialog/services";
+
+import ExportRDMForm from "./ExportRDMForm.vue";
+import FilesInput from "@/components/FilesDialog/FilesInput.vue";
+
+jest.mock("@/schema");
+
+const localVue = getLocalVue(true);
+
+const CREATE_RECORD_BTN = "#create-record-button";
+const EXPORT_TO_NEW_RECORD_BTN = "#export-button-new-record";
+const EXPORT_TO_EXISTING_RECORD_BTN = "#export-button-existing-record";
+
+const FAKE_RDM_SOURCE_URI = "gxfiles://test-uri";
+const FAKE_RDM_EXISTING_RECORD_URI = "gxfiles://test-uri/test-record";
+const FAKE_RECORD_NAME = "test record name";
+const FAKE_ENTRY: CreatedEntry = {
+    uri: FAKE_RDM_SOURCE_URI,
+    name: FAKE_RECORD_NAME,
+    external_link: "http://example.com",
+};
+
+async function initWrapper() {
+    mockFetcher.path("/api/remote_files").method("post").mock({ data: FAKE_ENTRY });
+
+    const wrapper = mount(ExportRDMForm, {
+        propsData: {},
+        localVue,
+    });
+    await flushPromises();
+    return wrapper;
+}
+
+describe("ExportRDMForm", () => {
+    let wrapper: Wrapper<Vue>;
+
+    beforeEach(async () => {
+        wrapper = await initWrapper();
+    });
+
+    describe("Export to new record", () => {
+        beforeEach(async () => {
+            await selectExportChoice("new");
+        });
+
+        it("enables the create new record button when the required fields are filled in", async () => {
+            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeTruthy();
+
+            await setRecordNameInput(FAKE_RECORD_NAME);
+            await setRDMSourceInput(FAKE_RDM_SOURCE_URI);
+
+            expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeFalsy();
+        });
+
+        it("displays the export to this record button when the create new record button is clicked", async () => {
+            expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeFalsy();
+
+            await setRecordNameInput(FAKE_RECORD_NAME);
+            await setRDMSourceInput(FAKE_RDM_SOURCE_URI);
+            await clickCreateNewRecordButton();
+
+            expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeTruthy();
+        });
+
+        it("emits an export event when the export to new record button is clicked", async () => {
+            await setFileNameInput("test file name");
+            await setRecordNameInput(FAKE_RECORD_NAME);
+            await setRDMSourceInput(FAKE_RDM_SOURCE_URI);
+            await clickCreateNewRecordButton();
+
+            await wrapper.find(EXPORT_TO_NEW_RECORD_BTN).trigger("click");
+            expect(wrapper.emitted("export")).toBeTruthy();
+        });
+    });
+
+    describe("Export to existing record", () => {
+        beforeEach(async () => {
+            await selectExportChoice("existing");
+        });
+
+        it("enables the export to existing record button when the required fields are filled in", async () => {
+            expect(wrapper.find(EXPORT_TO_EXISTING_RECORD_BTN).attributes("disabled")).toBeTruthy();
+
+            await setFileNameInput("test file name");
+            await setRDMDirectoryInput(FAKE_RDM_EXISTING_RECORD_URI);
+
+            expect(wrapper.find(EXPORT_TO_EXISTING_RECORD_BTN).attributes("disabled")).toBeFalsy();
+        });
+
+        it("emits an export event when the export to existing record button is clicked", async () => {
+            await setFileNameInput("test file name");
+            await setRDMDirectoryInput(FAKE_RDM_EXISTING_RECORD_URI);
+            await wrapper.find(EXPORT_TO_EXISTING_RECORD_BTN).trigger("click");
+            expect(wrapper.emitted("export")).toBeTruthy();
+        });
+    });
+
+    async function selectExportChoice(choice: string) {
+        const exportChoice = wrapper.find(`#radio-${choice}`);
+        await exportChoice.setChecked(true);
+    }
+
+    async function setRDMSourceInput(newValue: string) {
+        const component = wrapper.findComponent(FilesInput);
+        expect(component.attributes("placeholder")).toContain("source");
+        component.vm.$emit("input", newValue);
+        await flushPromises();
+    }
+
+    async function setRDMDirectoryInput(newValue: string) {
+        const component = wrapper.findComponent(FilesInput);
+        expect(component.attributes("placeholder")).toContain("directory");
+        component.vm.$emit("input", newValue);
+        await flushPromises();
+    }
+
+    async function setRecordNameInput(newValue: string) {
+        const recordNameInput = wrapper.find("#record-name-input");
+        await recordNameInput.setValue(newValue);
+    }
+
+    async function setFileNameInput(newValue: string) {
+        const recordNameInput = wrapper.find("#file-name-input");
+        await recordNameInput.setValue(newValue);
+    }
+
+    async function clickCreateNewRecordButton() {
+        const createRecordButton = wrapper.find(CREATE_RECORD_BTN);
+        expect(createRecordButton.attributes("disabled")).toBeFalsy();
+        await createRecordButton.trigger("click");
+        await flushPromises();
+    }
+});
diff --git a/client/src/components/Common/ExportRDMForm.vue b/client/src/components/Common/ExportRDMForm.vue
index 370561b1cf43..81a75640ca80 100644
--- a/client/src/components/Common/ExportRDMForm.vue
+++ b/client/src/components/Common/ExportRDMForm.vue
@@ -81,12 +81,14 @@ function clearInputs() {
 <template>
     <div class="export-to-rdm-repository">
         <BFormGroup id="fieldset-name" label-for="name" :description="nameDescription" class="mt-3">
-            <BFormInput id="name" v-model="fileName" :placeholder="namePlaceholder" required />
+            <BFormInput id="file-name-input" v-model="fileName" :placeholder="namePlaceholder" required />
         </BFormGroup>
 
         <BFormRadioGroup v-model="exportChoice" class="export-radio-group">
-            <BFormRadio v-localize name="exportChoice" value="new"> Export to new record </BFormRadio>
-            <BFormRadio v-localize name="exportChoice" value="existing"> Export to existing draft record </BFormRadio>
+            <BFormRadio id="radio-new" v-localize name="exportChoice" value="new"> Export to new record </BFormRadio>
+            <BFormRadio id="radio-existing" v-localize name="exportChoice" value="existing">
+                Export to existing draft record
+            </BFormRadio>
         </BFormRadioGroup>
 
         <div v-if="exportChoice === 'new'">
@@ -105,6 +107,7 @@ function clearInputs() {
                     </p>
                     <p v-localize>Please use the button below to upload the exported {{ props.what }} to the record.</p>
                     <BButton
+                        id="export-button-new-record"
                         v-localize
                         class="export-button"
                         variant="primary"
@@ -116,12 +119,12 @@ function clearInputs() {
             </div>
             <div v-else>
                 <BFormGroup
-                    id="fieldset-record"
+                    id="fieldset-record-new"
                     label-for="source-selector"
                     :description="repositoryRecordDescription"
                     class="mt-3">
                     <FilesInput
-                        id="repository-selector"
+                        id="source-selector"
                         v-model="sourceUri"
                         mode="source"
                         :require-writable="true"
@@ -132,14 +135,18 @@ function clearInputs() {
                     label-for="record-name"
                     :description="recordNameDescription"
                     class="mt-3">
-                    <BFormInput id="record-name" v-model="recordName" :placeholder="recordNamePlaceholder" required />
+                    <BFormInput
+                        id="record-name-input"
+                        v-model="recordName"
+                        :placeholder="recordNamePlaceholder"
+                        required />
                 </BFormGroup>
                 <p v-localize>
                     You need to create the new record in a repository before exporting the {{ props.what }} to it.
                 </p>
                 <BButton
+                    id="create-record-button"
                     v-localize
-                    class="export-button"
                     variant="primary"
                     :disabled="!canCreateRecord"
                     @click.prevent="doCreateRecord">
@@ -149,7 +156,7 @@ function clearInputs() {
         </div>
         <div v-else>
             <BFormGroup
-                id="fieldset-record"
+                id="fieldset-record-existing"
                 label-for="existing-record-selector"
                 :description="repositoryRecordDescription"
                 class="mt-3">
@@ -161,6 +168,7 @@ function clearInputs() {
                     :filter-options="includeOnlyRDMCompatible" />
             </BFormGroup>
             <BButton
+                id="export-button-existing-record"
                 v-localize
                 class="export-button"
                 variant="primary"

From 7d7cb604e801e423a6a6a5e9a4fbb68c81c3f710 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 15 Aug 2023 18:54:38 +0200
Subject: [PATCH 40/41] Drop testing parameters to skip SSL verification

---
 lib/galaxy/files/sources/invenio.py | 20 ++++++--------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index f85aeae48091..ee11124581bd 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -1,6 +1,5 @@
 import datetime
 import json
-import ssl
 import urllib.request
 from typing import (
     Any,
@@ -34,13 +33,6 @@
     stream_to_open_named_file,
 )
 
-# TODO: Remove this block. Ignoring SSL errors for testing purposes.
-VERIFY = False
-SSL_CONTEXT = ssl.create_default_context()
-SSL_CONTEXT.check_hostname = False
-SSL_CONTEXT.verify_mode = ssl.CERT_NONE
-
-
 AccessStatus = Literal["public", "restricted"]
 
 
@@ -230,7 +222,7 @@ def create_draft_record(self, title: str, user_context: OptionalUserContext = No
                 "Cannot create record without authentication token. Please set your personal access token in your Galaxy preferences."
             )
 
-        response = requests.post(self.records_url, json=create_record_request, headers=headers, verify=VERIFY)
+        response = requests.post(self.records_url, json=create_record_request, headers=headers)
         self._ensure_response_has_expected_status_code(response, 201)
         record = response.json()
         return record
@@ -247,7 +239,7 @@ def upload_file_to_draft_record(
         headers = self._get_request_headers(user_context)
 
         # Add file metadata entry
-        response = requests.post(upload_file_url, json=[{"key": filename}], headers=headers, verify=VERIFY)
+        response = requests.post(upload_file_url, json=[{"key": filename}], headers=headers)
         self._ensure_response_has_expected_status_code(response, 201)
 
         # Upload file content
@@ -256,11 +248,11 @@ def upload_file_to_draft_record(
         upload_file_content_url = file_entry["links"]["content"]
         commit_file_upload_url = file_entry["links"]["commit"]
         with open(file_path, "rb") as file:
-            response = requests.put(upload_file_content_url, data=file, headers=headers, verify=VERIFY)
+            response = requests.put(upload_file_content_url, data=file, headers=headers)
             self._ensure_response_has_expected_status_code(response, 200)
 
         # Commit file upload
-        response = requests.post(commit_file_upload_url, headers=headers, verify=VERIFY)
+        response = requests.post(commit_file_upload_url, headers=headers)
         self._ensure_response_has_expected_status_code(response, 200)
 
     def download_file_from_record(
@@ -273,7 +265,7 @@ def download_file_from_record(
         download_file_content_url = self._get_download_file_url(record_id, filename, user_context)
         headers = self._get_request_headers(user_context)
         req = urllib.request.Request(download_file_content_url, headers=headers)
-        with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT, context=SSL_CONTEXT) as page:
+        with urllib.request.urlopen(req, timeout=DEFAULT_SOCKET_TIMEOUT) as page:
             f = open(file_path, "wb")
             return stream_to_open_named_file(
                 page, f.fileno(), file_path, source_encoding=get_charset_from_http_headers(page.headers)
@@ -364,7 +356,7 @@ def _get_response(
         self, user_context: OptionalUserContext, request_url: str, params: Optional[Dict[str, Any]] = None
     ) -> dict:
         headers = self._get_request_headers(user_context)
-        response = requests.get(request_url, params=params, headers=headers, verify=VERIFY)
+        response = requests.get(request_url, params=params, headers=headers)
         self._ensure_response_has_expected_status_code(response, 200)
         return response.json()
 

From 343f8745bb96ef2c721e16f0c567ad68475b5c57 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 16 Aug 2023 11:58:57 +0200
Subject: [PATCH 41/41] Refactor draft record check

---
 lib/galaxy/files/sources/invenio.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index ee11124581bd..aa502924478e 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -283,16 +283,16 @@ def _get_download_file_url(self, record_id: str, filename: str, user_context: Op
         return download_file_content_url
 
     def _is_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
-        try:
-            self._get_draft_record(record_id, user_context)
-            return True
-        except Exception as e:
-            if "404" in str(e):
-                return False
-            raise e
+        request_url = self._get_draft_record_url(record_id)
+        headers = self._get_request_headers(user_context)
+        response = requests.get(request_url, headers=headers)
+        return response.status_code == 200
+
+    def _get_draft_record_url(self, record_id: str):
+        return f"{self.records_url}/{record_id}/draft"
 
     def _get_draft_record(self, record_id: str, user_context: OptionalUserContext = None):
-        request_url = f"{self.records_url}/{record_id}/draft"
+        request_url = self._get_draft_record_url(record_id)
         draft_record = self._get_response(user_context, request_url)
         return draft_record