From 24facf52f4436275dc1e8b85e69dd047649b32d7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 11 Sep 2023 15:47:15 -0400
Subject: [PATCH] Implement instance URLs in Galaxy markdown.

---
 .../Markdown/Elements/InstanceUrl.vue         |  31 ++++++
 .../Markdown/MarkdownContainer.test.js        |   7 ++
 .../components/Markdown/MarkdownContainer.vue |  38 +++++++
 .../components/Markdown/MarkdownToolBox.vue   |  43 ++++++++
 .../components/PageDisplay/PageDisplay.vue    |   4 +-
 lib/galaxy/config/__init__.py                 |   2 +
 lib/galaxy/config/config_manage.py            |   2 +
 lib/galaxy/config/schemas/config_schema.yml   |  53 +++++++---
 lib/galaxy/managers/configuration.py          |   4 +
 lib/galaxy/managers/markdown_parse.py         |   7 ++
 lib/galaxy/managers/markdown_util.py          | 100 ++++++++++++++++++
 lib/galaxy/webapps/galaxy/api/drs.py          |   4 +-
 12 files changed, 275 insertions(+), 20 deletions(-)
 create mode 100644 client/src/components/Markdown/Elements/InstanceUrl.vue

diff --git a/client/src/components/Markdown/Elements/InstanceUrl.vue b/client/src/components/Markdown/Elements/InstanceUrl.vue
new file mode 100644
index 000000000000..a7f52d957354
--- /dev/null
+++ b/client/src/components/Markdown/Elements/InstanceUrl.vue
@@ -0,0 +1,31 @@
+<script setup lang="ts">
+import { computed } from "vue";
+
+import ExternalLink from "@/components/ExternalLink.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
+
+interface InstanceUrlProps {
+    href?: string;
+    title?: string;
+    loading: boolean;
+}
+
+const props = withDefaults(defineProps<InstanceUrlProps>(), {
+    href: null,
+    title: null,
+});
+
+const effectiveTitle = computed(() => {
+    return props.title ? props.title : props.href;
+});
+</script>
+
+<template>
+    <p>
+        <LoadingSpan v-if="props.loading" message="Loading instance configuration"> </LoadingSpan>
+        <ExternalLink v-else-if="props.href" :href="props.href">
+            {{ effectiveTitle }}
+        </ExternalLink>
+        <i v-else> Configuration value unset, please contact Galaxy admin. </i>
+    </p>
+</template>
diff --git a/client/src/components/Markdown/MarkdownContainer.test.js b/client/src/components/Markdown/MarkdownContainer.test.js
index 484e92c97e94..a40f1d810176 100644
--- a/client/src/components/Markdown/MarkdownContainer.test.js
+++ b/client/src/components/Markdown/MarkdownContainer.test.js
@@ -11,6 +11,13 @@ import MountTarget from "./MarkdownContainer.vue";
 jest.mock("utils/redirect");
 withPrefix.mockImplementation((url) => url);
 
+jest.mock("@/composables/config", () => ({
+    useConfig: jest.fn(() => ({
+        config: {},
+        isConfigLoaded: true,
+    })),
+}));
+
 const localVue = getLocalVue();
 const axiosMock = new MockAdapter(axios);
 
diff --git a/client/src/components/Markdown/MarkdownContainer.vue b/client/src/components/Markdown/MarkdownContainer.vue
index 9ece148b02b6..5e0be545dd5a 100644
--- a/client/src/components/Markdown/MarkdownContainer.vue
+++ b/client/src/components/Markdown/MarkdownContainer.vue
@@ -1,6 +1,8 @@
 <script setup>
 import { computed, ref } from "vue";
 
+import { useConfig } from "@/composables/config";
+
 import HistoryDatasetAsImage from "./Elements/HistoryDatasetAsImage.vue";
 import HistoryDatasetCollectionDisplay from "./Elements/HistoryDatasetCollection/CollectionDisplay.vue";
 import HistoryDatasetDetails from "./Elements/HistoryDatasetDetails.vue";
@@ -8,6 +10,7 @@ import HistoryDatasetDisplay from "./Elements/HistoryDatasetDisplay.vue";
 import HistoryDatasetIndex from "./Elements/HistoryDatasetIndex.vue";
 import HistoryDatasetLink from "./Elements/HistoryDatasetLink.vue";
 import HistoryLink from "./Elements/HistoryLink.vue";
+import InstanceUrl from "./Elements/InstanceUrl.vue";
 import InvocationTime from "./Elements/InvocationTime.vue";
 import JobMetrics from "./Elements/JobMetrics.vue";
 import JobParameters from "./Elements/JobParameters.vue";
@@ -15,6 +18,8 @@ import ToolStd from "./Elements/ToolStd.vue";
 import Visualization from "./Elements/Visualization.vue";
 import WorkflowDisplay from "./Elements/Workflow/WorkflowDisplay.vue";
 
+const { config, isConfigLoaded } = useConfig();
+
 const toggle = ref(false);
 const props = defineProps({
     name: {
@@ -75,6 +80,39 @@ const isVisible = computed(() => !isCollapsible.value || toggle.value);
             <div v-else-if="name == 'generate_time'" class="galaxy-time">
                 <pre><code>{{ time }}</code></pre>
             </div>
+            <InstanceUrl
+                v-else-if="name == 'instance_citation_link'"
+                :href="config.citation_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl v-else-if="name == 'instance_terms_link'" :href="config.terms_url" :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_support_link'"
+                :href="config.support_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_help_link'"
+                :href="config.helpsite_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_resources_link'"
+                :href="config.instance_resource_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_access_link'"
+                :href="config.instance_access_url"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
+            <InstanceUrl
+                v-else-if="name == 'instance_organization_link'"
+                :href="config.ga4gh_service_organization_url"
+                :title="config.ga4gh_service_organization_name"
+                :loading="!isConfigLoaded">
+            </InstanceUrl>
             <HistoryLink v-else-if="name == 'history_link'" :args="args" :histories="histories" />
             <HistoryDatasetAsImage v-else-if="name == 'history_dataset_as_image'" :args="args" />
             <HistoryDatasetLink v-else-if="name == 'history_dataset_link'" :args="args" />
diff --git a/client/src/components/Markdown/MarkdownToolBox.vue b/client/src/components/Markdown/MarkdownToolBox.vue
index 19b3caa3bcee..f363d8159abe 100644
--- a/client/src/components/Markdown/MarkdownToolBox.vue
+++ b/client/src/components/Markdown/MarkdownToolBox.vue
@@ -19,6 +19,7 @@
                     :expanded="true"
                     @onClick="onClick" />
                 <ToolSection v-else :category="workflowSection" :expanded="true" @onClick="onClick" />
+                <ToolSection :category="linksSection" :expanded="false" @onClick="onClick" />
                 <ToolSection :category="otherSection" :expanded="true" @onClick="onClick" />
                 <ToolSection
                     v-if="hasVisualizations"
@@ -232,6 +233,48 @@ export default {
                     },
                 ],
             },
+            linksSection: {
+                title: "Galaxy Instance Links",
+                name: "links",
+                elems: [
+                    {
+                        id: "instance_access_link",
+                        name: "Access",
+                        description: "(link used to access this Galaxy)",
+                    },
+                    {
+                        id: "instance_resources_link",
+                        name: "Resources",
+                        description: "(link for more information about this Galaxy)",
+                    },
+                    {
+                        id: "instance_help_link",
+                        name: "Help",
+                        description: "(link for finding help content for this Galaxy)",
+                    },
+                    {
+                        id: "instance_support_link",
+                        name: "Support",
+                        description: "(link for support for this Galaxy)",
+                    },
+                    {
+                        id: "instance_citation_link",
+                        name: "Citation",
+                        description: "(link describing how cite this Galaxy instance)",
+                    },
+                    {
+                        id: "instance_terms_link",
+                        name: "Terms and Conditions",
+                        description: "(link describing how terms and conditions for using this Galaxy instance)",
+                    },
+                    {
+                        id: "instance_organization_link",
+                        name: "Organization",
+                        description: "(link describing organization that runs this Galaxy instance)",
+                    },
+                ],
+            },
+
             visualizationSection: {
                 title: "Visualizations",
                 name: "visualizations",
diff --git a/client/src/components/PageDisplay/PageDisplay.vue b/client/src/components/PageDisplay/PageDisplay.vue
index 6b7fb048ee26..f3b18494ab16 100644
--- a/client/src/components/PageDisplay/PageDisplay.vue
+++ b/client/src/components/PageDisplay/PageDisplay.vue
@@ -11,7 +11,7 @@
                     @onEdit="onEdit" />
                 <PageHtml v-else :page="page" />
             </div>
-            <b-alert v-else variant="info" show>Unsupported page format.</b-alert>
+            <LoadingSpan v-else message="Loading Galaxy configuration" />
         </template>
     </PublishedItem>
 </template>
@@ -23,10 +23,12 @@ import { urlData } from "@/utils/url";
 
 import PageHtml from "./PageHtml.vue";
 import PublishedItem from "@/components/Common/PublishedItem.vue";
+import LoadingSpan from "@/components/LoadingSpan.vue";
 import Markdown from "@/components/Markdown/Markdown.vue";
 
 export default {
     components: {
+        LoadingSpan,
         Markdown,
         PageHtml,
         PublishedItem,
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index e6a381a64da3..f8db25623a06 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -637,6 +637,8 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         "fetch_url_whitelist": "fetch_url_allowlist",
         "containers_resolvers_config_file": "container_resolvers_config_file",
         "activation_email": "email_from",
+        "ga4gh_service_organization_name": "organization_name",
+        "ga4gh_service_organization_url": "organization_url",
     }
 
     deprecated_options = list(renamed_options.keys()) + [
diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py
index ef21f95b3339..5f91bc0d386c 100644
--- a/lib/galaxy/config/config_manage.py
+++ b/lib/galaxy/config/config_manage.py
@@ -203,6 +203,8 @@ def lint(self, args, app_desc, key, value) -> None:
     "legacy_eager_objectstore_initialization": _DeprecatedAndDroppedAction(),
     "enable_openid": _DeprecatedAndDroppedAction(),
     "openid_consumer_cache_path": _DeprecatedAndDroppedAction(),
+    "ga4gh_service_organization_name": _RenameAction("organization_name"),
+    "ga4gh_service_organization_url": _RenameAction("organization_url"),
 }
 
 
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index e2f2c7320acf..52d5b3965f60 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -1180,11 +1180,20 @@ mapping:
         type: str
         required: false
         desc: |
-          URL of the support resource for the galaxy instance.  Used in activation
-          emails.
+          URL of the support resource for the galaxy instance.  Used outside of web contexts
+          such as in activation emails and in Galaxy markdown report generation.
 
           Example value 'https://galaxyproject.org/'
 
+      instance_access_url:
+        type: str
+        required: false
+        desc: |
+          URL used to access this Galaxy server. Used outside of web contexts
+          such as in Galaxy markdown report generation.
+
+          Example value 'https://usegalaxy.org'
+
       email_domain_blocklist_file:
         type: str
         required: false
@@ -2931,45 +2940,55 @@ mapping:
           a real admin user account via API.
           You should probably not set this on a production server.
 
-      ga4gh_service_id:
+      organization_name:
         type: str
         required: false
         desc: |
-          Service ID for GA4GH services (exposed via the service-info endpoint for the Galaxy DRS API).
-          If unset, one will be generated using the URL the target API requests are made against.
+          The name of the organization that operates this Galaxy instance. Serves as the
+          default for the GA4GH service organization name and can be exposed through Galaxy
+          markdown for reports and such. For instance, "Not Evil Corporation".
+
+          For GA4GH APIs, this is exposed via the service-info endpoint for the Galaxy DRS API.
+          If unset, one will be generated using ga4gh_service_id (but only in the context
+          of GA4GH APIs).
 
           For more information on GA4GH service definitions - check out
           https://github.com/ga4gh-discovery/ga4gh-service-registry
           and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
 
-          This value should likely reflect your service's URL. For instance for usegalaxy.org
-          this value should be org.usegalaxy. Particular Galaxy implementations will treat this
-          value as a prefix and append the service type to this ID. For instance for the DRS
-          service "id" (available via the DRS API) for the above configuration value would be
-          org.usegalaxy.drs.
-
-      ga4gh_service_organization_name:
+      organization_url:
         type: str
         required: false
         desc: |
-          Service name for host organization (exposed via the service-info endpoint for the Galaxy DRS API).
-          If unset, one will be generated using ga4gh_service_id.
+          The URL of the organization that operates this Galaxy instance. Serves as the
+          default for the GA4GH service organization name and can be exposed through Galaxy
+          markdown for reports and such. For instance, "notevilcorp.com".
+
+          For GA4GH APIs, this is exposed via the service-info endpoint for the Galaxy DRS API.
+          If unset, one will be generated using ga4gh_service_id (but only in the context
+          of GA4GH APIs).
 
           For more information on GA4GH service definitions - check out
           https://github.com/ga4gh-discovery/ga4gh-service-registry
           and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
 
-      ga4gh_service_organization_url:
+      ga4gh_service_id:
         type: str
-        required: False
+        required: false
         desc: |
-          Organization URL for host organization (exposed via the service-info endpoint for the Galaxy DRS API).
+          Service ID for GA4GH services (exposed via the service-info endpoint for the Galaxy DRS API).
           If unset, one will be generated using the URL the target API requests are made against.
 
           For more information on GA4GH service definitions - check out
           https://github.com/ga4gh-discovery/ga4gh-service-registry
           and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
 
+          This value should likely reflect your service's URL. For instance for usegalaxy.org
+          this value should be org.usegalaxy. Particular Galaxy implementations will treat this
+          value as a prefix and append the service type to this ID. For instance for the DRS
+          service "id" (available via the DRS API) for the above configuration value would be
+          org.usegalaxy.drs.
+
       ga4gh_service_environment:
         type: str
         required: False
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index 2f5f4b8700f5..c3ea10c0b4d6 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -213,6 +213,10 @@ def _config_is_truthy(item, key, **context):
             "tool_training_recommendations_link": _use_config,
             "tool_training_recommendations_api_url": _use_config,
             "enable_notification_system": _use_config,
+            "instance_resource_url": _use_config,
+            "instance_access_url": _use_config,
+            "organization_name": _use_config,
+            "organization_url": _use_config,
         }
 
 
diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py
index ca486283f844..ff47b5cf488c 100644
--- a/lib/galaxy/managers/markdown_parse.py
+++ b/lib/galaxy/managers/markdown_parse.py
@@ -44,6 +44,13 @@ class DynamicArguments:
     "tool_stdout": ["step", "job_id"],
     "generate_galaxy_version": [],
     "generate_time": [],
+    "instance_access_link": [],
+    "instance_resources_link": [],
+    "instance_help_link": [],
+    "instance_support_link": [],
+    "instance_citation_link": [],
+    "instance_terms_link": [],
+    "instance_organization_link": [],
     "visualization": DYNAMIC_ARGUMENTS,
     # Invocation Flavored Markdown
     "invocation_time": ["invocation_id"],
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index 4e5219251ccc..0c222a3c914a 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -174,6 +174,28 @@ def _remap(container, line):
                 rval = self.handle_generate_galaxy_version(line, version)
             elif container == "generate_time":
                 rval = self.handle_generate_time(line, now())
+            elif container == "instance_access_link":
+                url = trans.app.config.instance_access_url
+                rval = self.handle_instance_access_link(line, url)
+            elif container == "instance_resources_link":
+                url = trans.app.config.instance_resource_url
+                rval = self.handle_instance_resources_link(line, url)
+            elif container == "instance_help_link":
+                url = trans.app.config.helpsite_url
+                rval = self.handle_instance_help_link(line, url)
+            elif container == "instance_support_link":
+                url = trans.app.config.support_url
+                rval = self.handle_instance_support_link(line, url)
+            elif container == "instance_citation_link":
+                url = trans.app.config.citation_url
+                rval = self.handle_instance_citation_link(line, url)
+            elif container == "instance_terms_link":
+                url = trans.app.config.terms_url
+                rval = self.handle_instance_terms_link(line, url)
+            elif container == "instance_organization_link":
+                title = trans.app.config.organization_name
+                url = trans.app.config.organization_url
+                rval = self.handle_instance_organization_link(line, title, url)
             elif container == "invocation_time":
                 invocation = workflow_manager.get_invocation(trans, object_id)
                 rval = self.handle_invocation_time(line, invocation)
@@ -270,6 +292,34 @@ def handle_generate_galaxy_version(self, line, galaxy_version):
     def handle_generate_time(self, line, date):
         pass
 
+    @abc.abstractmethod
+    def handle_instance_access_link(self, line, url):
+        pass
+
+    @abc.abstractmethod
+    def handle_instance_resources_link(self, line, url):
+        pass
+
+    @abc.abstractmethod
+    def handle_instance_help_link(self, line, url):
+        pass
+
+    @abc.abstractmethod
+    def handle_instance_support_link(self, line, url):
+        pass
+
+    @abc.abstractmethod
+    def handle_instance_citation_link(self, line, url):
+        pass
+
+    @abc.abstractmethod
+    def handle_instance_terms_link(self, line, url):
+        pass
+
+    @abc.abstractmethod
+    def handle_instance_organization_link(self, line, title, url):
+        pass
+
     @abc.abstractmethod
     def handle_invocation_time(self, line, date):
         pass
@@ -346,6 +396,27 @@ def handle_generate_galaxy_version(self, line, generate_version):
     def handle_generate_time(self, line, generate_time):
         pass
 
+    def handle_instance_access_link(self, line, url):
+        pass
+
+    def handle_instance_resources_link(self, line, url):
+        pass
+
+    def handle_instance_help_link(self, line, url):
+        pass
+
+    def handle_instance_support_link(self, line, url):
+        pass
+
+    def handle_instance_citation_link(self, line, url):
+        pass
+
+    def handle_instance_terms_link(self, line, url):
+        pass
+
+    def handle_instance_organization_link(self, line, title, url):
+        pass
+
     def handle_invocation_time(self, line, invocation):
         self.ensure_rendering_data_for("invocations", invocation)["create_time"] = invocation.create_time.isoformat()
 
@@ -546,6 +617,35 @@ def handle_generate_time(self, line, generate_time):
         content = literal_via_fence(generate_time.isoformat())
         return (content, True)
 
+    def handle_instance_access_link(self, line, url):
+        return self._handle_link(url)
+
+    def handle_instance_resources_link(self, line, url):
+        return self._handle_link(url)
+
+    def handle_instance_help_link(self, line, url):
+        return self._handle_link(url)
+
+    def handle_instance_support_link(self, line, url):
+        return self._handle_link(url)
+
+    def handle_instance_citation_link(self, line, url):
+        return self._handle_link(url)
+
+    def handle_instance_terms_link(self, line, url):
+        return self._handle_link(url)
+
+    def handle_instance_organization_link(self, line, title, url):
+        return self._handle_link(url, title)
+
+    def _handle_link(self, url, title=None):
+        if not url:
+            content = "*Not configured, please contact Galaxy admin*"
+            return (content, True)
+        elif not title:
+            title = url
+        return (f"[{title}]({url})", True)
+
     def handle_invocation_time(self, line, invocation):
         content = literal_via_fence(invocation.create_time.isoformat())
         return (content, True)
diff --git a/lib/galaxy/webapps/galaxy/api/drs.py b/lib/galaxy/webapps/galaxy/api/drs.py
index 70ec82384960..b5960ee49f4f 100644
--- a/lib/galaxy/webapps/galaxy/api/drs.py
+++ b/lib/galaxy/webapps/galaxy/api/drs.py
@@ -51,8 +51,8 @@ def service_info(self, request: Request) -> Service:
         default_organization_id = ".".join(reversed(hostname.split(".")))
         config = self.config
         organization_id = config.ga4gh_service_id or default_organization_id
-        organization_name = config.ga4gh_service_organization_name or organization_id
-        organization_url = config.ga4gh_service_organization_url or f"{components.scheme}://{components.netloc}"
+        organization_name = config.organization_name or organization_id
+        organization_url = config.organization_url or f"{components.scheme}://{components.netloc}"
 
         organization = ServiceOrganization(
             url=organization_url,