From c5734906799c6b4286490ddaae8f4e65fbdf1165 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 30 Oct 2024 11:09:25 +0000 Subject: [PATCH] Update documentation --- _autosummary/one.api.html | 10 ++++-- _modules/one/api.html | 55 ++++++++++++++++------------- _modules/one/params.html | 13 +++++-- _modules/one/remote/aws.html | 2 +- _modules/one/tests/test_one.html | 5 +++ _modules/one/tests/test_params.html | 12 +++++-- searchindex.js | 2 +- 7 files changed, 67 insertions(+), 32 deletions(-) diff --git a/_autosummary/one.api.html b/_autosummary/one.api.html index 841eeb03..a37c58fa 100644 --- a/_autosummary/one.api.html +++ b/_autosummary/one.api.html @@ -412,7 +412,7 @@
-list_datasets(eid=None, filename=None, collection=None, revision=None, qc=QC.FAIL, ignore_qc_not_set=False, details=False, query_type=None, default_revisions_only=False) → ndarray | DataFrame[source]
+list_datasets(eid=None, filename=None, collection=None, revision=None, qc=QC.FAIL, ignore_qc_not_set=False, details=False, query_type=None, default_revisions_only=False, keep_eid_index=False) → ndarray | DataFrame[source]

Given an eid, return the datasets for those sessions.

If no eid is provided, a list of all datasets is returned. When details is false, a sorted array of unique datasets is returned (their relative paths).

@@ -436,6 +436,9 @@

  • query_type (str) – Query cache (‘local’) or Alyx database (‘remote’).

  • default_revisions_only (bool) – When true, only matching datasets that are considered default revisions are returned. If no ‘default_revision’ column is present, and ALFError is raised.

    • +

  • keep_eid_index (bool) – If details is true, this determines whether the returned data frame contains the eid +in the index. When false (default) the returned data frame index is the dataset id +only, otherwise the index is a MultIndex with levels (eid, id).

    • Returns:
    @@ -948,7 +951,7 @@
    -list_datasets(eid=None, filename=None, collection=None, revision=None, qc=QC.FAIL, ignore_qc_not_set=False, details=False, query_type=None, default_revisions_only=False) → ndarray | DataFrame[source]
    +list_datasets(eid=None, filename=None, collection=None, revision=None, qc=QC.FAIL, ignore_qc_not_set=False, details=False, query_type=None, default_revisions_only=False, keep_eid_index=False) → ndarray | DataFrame[source]

    Given an eid, return the datasets for those sessions.

    If no eid is provided, a list of all datasets is returned. When details is false, a sorted array of unique datasets is returned (their relative paths).

    @@ -972,6 +975,9 @@

  • query_type (str) – Query cache (‘local’) or Alyx database (‘remote’).

  • default_revisions_only (bool) – When true, only matching datasets that are considered default revisions are returned. If no ‘default_revision’ column is present, and ALFError is raised.

    • +

  • keep_eid_index (bool) – If details is true, this determines whether the returned data frame contains the eid +in the index. When false (default) the returned data frame index is the dataset id +only, otherwise the index is a MultIndex with levels (eid, id).

    • Returns:
    diff --git a/_modules/one/api.html b/_modules/one/api.html index e3f331bd..4f8dc93e 100644 --- a/_modules/one/api.html +++ b/_modules/one/api.html @@ -847,7 +847,8 @@

    Source code for one.api

         @util.refresh
     def list_datasets(
             self, eid=None, filename=None, collection=None, revision=None, qc=QC.FAIL,
-            ignore_qc_not_set=False, details=False, query_type=None, default_revisions_only=False
+            ignore_qc_not_set=False, details=False, query_type=None, default_revisions_only=False,
+            keep_eid_index=False
     ) -> Union[np.ndarray, pd.DataFrame]:
         """
         Given an eid, return the datasets for those sessions.
@@ -883,6 +884,10 @@ 
    Source code for one.api
             default_revisions_only : bool
             When true, only matching datasets that are considered default revisions are returned.
             If no 'default_revision' column is present, and ALFError is raised.
+        keep_eid_index : bool
+            If details is true, this determines whether the returned data frame contains the eid
+            in the index. When false (default) the returned data frame index is the dataset id
+            only, otherwise the index is a MultIndex with levels (eid, id).
 
         Returns
         -------
@@ -933,8 +938,15 @@ 
    Source code for one.api
                 return datasets.iloc[0:0]  # Return empty
 
         datasets = util.filter_datasets(datasets, **filter_args)
-        # Return only the relative path
-        return datasets if details else datasets['rel_path'].sort_values().values.tolist()
    
+        if details:
+            if keep_eid_index and datasets.index.nlevels == 1:
+                # Reinstate eid index
+                datasets = pd.concat({str(eid): datasets}, names=['eid'])
+            # Return the full data frame
+            return datasets
+        else:
+            # Return only the relative path
+            return datasets['rel_path'].sort_values().values.tolist()
    
 
 
 
    
@@ -1144,7 +1156,8 @@ 
    Source code for one.api
             >>> load_object(eid, 'spikes', attribute=['times*', 'clusters'])
         """
         query_type = query_type or self.mode
-        datasets = self.list_datasets(eid, details=True, query_type=query_type)
+        datasets = self.list_datasets(
+            eid, details=True, query_type=query_type, keep_eid_index=True)
 
         if len(datasets) == 0:
             raise alferr.ALFObjectNotFound(obj)
@@ -1166,9 +1179,6 @@ 
    Source code for one.api
     
         # For those that don't exist, download them
         offline = None if query_type == 'auto' else self.mode == 'local'
-        if datasets.index.nlevels == 1:
-            # Reinstate eid index
-            datasets = pd.concat({str(eid): datasets}, names=['eid'])
         files = self._check_filesystem(datasets, offline=offline, check_hash=check_hash)
         files = [x for x in files if x]
         if not files:
@@ -1259,7 +1269,8 @@ 
    Source code for one.api
                 wildcards/regular expressions must not be used. To use wildcards, pass the collection
             and revision as separate keyword arguments.
         """
-        datasets = self.list_datasets(eid, details=True, query_type=query_type or self.mode)
+        datasets = self.list_datasets(
+            eid, details=True, query_type=query_type or self.mode, keep_eid_index=True)
         # If only two parts and wildcards are on, append ext wildcard
         if self.wildcards and isinstance(dataset, str) and len(dataset.split('.')) == 2:
             dataset += '.*'
@@ -1276,9 +1287,6 @@ 
    Source code for one.api
                                             wildcards=self.wildcards, assert_unique=assert_unique)
         if len(datasets) == 0:
             raise alferr.ALFObjectNotFound(f'Dataset "{dataset}" not found')
-        if datasets.index.nlevels == 1:
-            # Reinstate eid index
-            datasets = pd.concat({str(eid): datasets}, names=['eid'])
 
         # Check files exist / download remote files
         offline = None if query_type == 'auto' else self.mode == 'local'
@@ -1421,7 +1429,8 @@ 
    Source code for one.api
     
         # Short circuit
         query_type = query_type or self.mode
-        all_datasets = self.list_datasets(eid, details=True, query_type=query_type)
+        all_datasets = self.list_datasets(
+            eid, details=True, query_type=query_type, keep_eid_index=True)
         if len(all_datasets) == 0:
             if assert_present:
                 raise alferr.ALFObjectNotFound(f'No datasets found for session {eid}')
@@ -1453,9 +1462,6 @@ 
    Source code for one.api
                       for x, y, z in zip(datasets, collections, revisions)]
         present = [len(x) == 1 for x in slices]
         present_datasets = pd.concat(slices)
-        if present_datasets.index.nlevels == 1:
-            # Reinstate eid index
-            present_datasets = pd.concat({str(eid): present_datasets}, names=['eid'])
 
         # Check if user is blindly downloading all data and warn of non-default revisions
         if 'default_revision' in present_datasets and \
@@ -1619,8 +1625,8 @@ 
    Source code for one.api
                 No datasets match the object, attribute or revision filters for this collection.
         """
         query_type = query_type or self.mode
-        datasets = self.list_datasets(eid, details=True, collection=collection,
-                                      query_type=query_type)
+        datasets = self.list_datasets(
+            eid, details=True, collection=collection, query_type=query_type, keep_eid_index=True)
 
         if len(datasets) == 0:
             raise alferr.ALFError(f'{collection} not found for session {eid}')
@@ -1633,9 +1639,6 @@ 
    Source code for one.api
             if len(datasets) == 0:
             raise alferr.ALFObjectNotFound(object or '')
         parts = [alfiles.rel_path_parts(x) for x in datasets.rel_path]
-        if datasets.index.nlevels == 1:
-            # Reinstate eid index
-            datasets = pd.concat({str(eid): datasets}, names=['eid'])
 
         # For those that don't exist, download them
         offline = None if query_type == 'auto' else self.mode == 'local'
@@ -2006,16 +2009,19 @@ 
    Source code for one.api
         @util.refresh
     def list_datasets(
             self, eid=None, filename=None, collection=None, revision=None, qc=QC.FAIL,
-            ignore_qc_not_set=False, details=False, query_type=None, default_revisions_only=False
+            ignore_qc_not_set=False, details=False, query_type=None, default_revisions_only=False,
+            keep_eid_index=False
     ) -> Union[np.ndarray, pd.DataFrame]:
         filters = dict(
             collection=collection, filename=filename, revision=revision, qc=qc,
             ignore_qc_not_set=ignore_qc_not_set, default_revisions_only=default_revisions_only)
         if (query_type or self.mode) != 'remote':
-            return super().list_datasets(eid, details=details, query_type=query_type, **filters)
+            return super().list_datasets(eid, details=details, keep_eid_index=keep_eid_index,
+                                         query_type=query_type, **filters)
         elif not eid:
             warnings.warn('Unable to list all remote datasets')
-            return super().list_datasets(eid, details=details, query_type=query_type, **filters)
+            return super().list_datasets(eid, details=details, keep_eid_index=keep_eid_index,
+                                         query_type=query_type, **filters)
         eid = self.to_eid(eid)  # Ensure we have a UUID str list
         if not eid:
             return self._cache['datasets'].iloc[0:0] if details else []  # Return empty
@@ -2563,8 +2569,9 @@ 
    Source code for one.api
                 assert record['relative_path'].endswith(dset['rel_path']), \
                 f'Relative path for dataset {uuid} does not match Alyx record'
             source_path = PurePosixPath(record['data_repository_path'], record['relative_path'])
+            local_path = self.cache_dir.joinpath(alfiles.get_alf_path(source_path))
+            # Add UUIDs to filenames, if required
             source_path = alfiles.add_uuid_string(source_path, uuid)
-            local_path = self.cache_dir.joinpath(record['relative_path'])
             if keep_uuid is True or (keep_uuid is None and self.uuid_filenames is True):
                 local_path = alfiles.add_uuid_string(local_path, uuid)
             local_path.parent.mkdir(exist_ok=True, parents=True)
diff --git a/_modules/one/params.html b/_modules/one/params.html
index aa5b467a..f0562aab 100644
--- a/_modules/one/params.html
+++ b/_modules/one/params.html
@@ -236,6 +236,7 @@ 
    Source code for one.params
         if not silent:
         prompt = 'Param %s, current value is ["%s"]:'
         par = iopar.as_dict(par_default)
+        quotes = '"\'`'
         # Iterate through non-password pars
         for k in filter(lambda k: 'PWD' not in k, par.keys()):
             cpar = _get_current_par(k, par_current)
@@ -249,10 +250,18 @@ 
    Source code for one.params
                     url_parsed = urlsplit(par[k])
                 if not (url_parsed.netloc and re.match('https?', url_parsed.scheme)):
                     raise ValueError(f'{k} must be valid HTTP URL')
-                if k == 'ALYX_URL':
-                    client = par[k]
             else:
                 par[k] = input(prompt % (k, cpar)).strip() or cpar
+            # Check whether user erroneously entered quotation marks
+            # Prompting the user here (hopefully) corrects them before they input a password
+            # where the use of quotation marks may be legitimate
+            if par[k] and len(par[k]) >= 2 and par[k][0] in quotes and par[k][-1] in quotes:
+                warnings.warn('Do not use quotation marks with input answers', UserWarning)
+                ans = input('Strip quotation marks from response? [Y/n]:').strip() or 'y'
+                if ans.lower()[0] == 'y':
+                    par[k] = par[k].strip(quotes)
+            if k == 'ALYX_URL':
+                client = par[k]
 
         cpar = _get_current_par('HTTP_DATA_SERVER_PWD', par_current)
         prompt = f'Enter the FlatIron HTTP password for {par["HTTP_DATA_SERVER_LOGIN"]} '\
diff --git a/_modules/one/remote/aws.html b/_modules/one/remote/aws.html
index a190bb21..0b7e9783 100644
--- a/_modules/one/remote/aws.html
+++ b/_modules/one/remote/aws.html
@@ -384,7 +384,7 @@ 
    Source code for one.remote.aws
                 _logger.debug(f"{destination} exists and match size -- skipping")
             return destination
         with tqdm(total=filesize, unit='B',
-                  unit_scale=True, desc=str(destination)) as t:
+                  unit_scale=True, desc=f'(S3) {destination}') as t:
             file_object.download_file(Filename=str(destination), Callback=_callback_hook(t))
     except (NoCredentialsError, PartialCredentialsError) as ex:
         raise ex  # Credentials need updating in Alyx # pragma: no cover
diff --git a/_modules/one/tests/test_one.html b/_modules/one/tests/test_one.html
index 97fa2f1d..22c4a34f 100644
--- a/_modules/one/tests/test_one.html
+++ b/_modules/one/tests/test_one.html
@@ -536,6 +536,11 @@ 
    Source code for one.tests.test_one
             self.assertEqual(27, len(dsets))
         self.assertEqual(1, dsets.index.nlevels, 'details data frame should be without eid index')
 
+        # Test keep_eid_index parameter
+        dsets = self.one.list_datasets('KS005/2019-04-02/001', details=True, keep_eid_index=True)
+        self.assertEqual(27, len(dsets))
+        self.assertEqual(2, dsets.index.nlevels, 'details data frame should be with eid index')
+
         # Test filters
         filename = {'attribute': ['times', 'intervals'], 'extension': 'npy'}
         dsets = self.one.list_datasets('ZFM-01935/2021-02-05/001', filename)
diff --git a/_modules/one/tests/test_params.html b/_modules/one/tests/test_params.html
index 5d75c12d..b8b3a9ed 100644
--- a/_modules/one/tests/test_params.html
+++ b/_modules/one/tests/test_params.html
@@ -171,8 +171,16 @@ 
    Source code for one.tests.test_params
             # Check verification prompt
         resp_map = {'ALYX_LOGIN': 'mistake', 'settings correct?': 'N'}
         with mock.patch('one.params.input', new=partial(self._mock_input, **resp_map)):
-            cache = one.params.setup()
-            self.assertNotEqual(cache.ALYX_LOGIN, 'mistake')
+            one.params.setup()
+            par = one.params.get(self.url, silent=True)
+            self.assertNotEqual(par.ALYX_LOGIN, 'mistake')
+
+        # Check prompt when quotation marks used
+        resp_map = {'ALYX_LOGIN': '"foo"', 'Strip quotation marks': 'y', 'settings correct?': 'Y'}
+        with mock.patch('one.params.input', new=partial(self._mock_input, **resp_map)):
+            self.assertWarnsRegex(UserWarning, 'quotation marks', one.params.setup)
+            par = one.params.get(self.url, silent=True)
+            self.assertEqual(par.ALYX_LOGIN, 'foo', 'failed to strip quotes from user input')
 
         # Check that raises ValueError when bad URL provided
         self.url = 'ftp://foo.bar.org'
diff --git a/searchindex.js b/searchindex.js
index 9cacc063..ecbed16c 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1. Installation": [[65, "installation"]], "2. Setup": [[65, "setup"]], "3. Post setup": [[65, "post-setup"]], "4. Update": [[65, "update"]], "ALF": [[52, null]], "ALF path": [[48, "alf-path"]], "ALyx Filenames (ALF)": [[48, null]], "API Reference": [[49, null]], "Accessing other Alyx tables": [[57, "Accessing-other-Alyx-tables"]], "Advanced loading": [[59, "Advanced-loading"]], "Advanced searching": [[62, "Advanced-searching"]], "Checking the cache": [[54, "Checking-the-cache"]], "Collections": [[48, "collections"], [59, "Collections"]], "Collections and revisions": [[66, "collections-and-revisions"]], "Combining with load methods": [[58, "Combining-with-load-methods"]], "Committing code to GitHub repo": [[50, "committing-code-to-github-repo"]], "Connect to IBL Public database": [[65, "connect-to-ibl-public-database"]], "Connecting to specific database (relevant for IBL users)": [[65, "connecting-to-specific-database-relevant-for-ibl-users"]], "Contributing to code": [[50, "contributing-to-code"]], "Contributing to documentation": [[50, null]], "Dataset name": [[48, "dataset-name"]], "Dataset type": [[48, "dataset-type"]], "Dataset types": [[55, "Dataset-types"]], "Datasets": [[55, "Datasets"], [66, "datasets"]], "Datasets and their types": [[55, null]], "Detailed Index": [[51, null]], "Difference between remote mode search terms": [[62, "Difference-between-remote-mode-search-terms"]], "Difference between search term behaviours": [[62, "Difference-between-search-term-behaviours"]], "Download only": [[59, "Download-only"]], "Downloading example data": [[54, "Downloading-example-data"]], "Example": [[63, "Example"]], "Example queries": [[64, "Example-queries"]], "Experiment IDs": [[56, null], [66, "experiment-ids"]], "Exploring the REST endpoints": [[64, "Exploring-the-REST-endpoints"]], "Extension": [[48, "extension"]], "Extra": [[48, "extra"]], "FAQ": [[0, null]], "Field lookup reference": [[64, "Field-lookup-reference"]], "Filtering attributes": [[59, "Filtering-attributes"]], "Filtering lists": [[58, "Filtering-lists"]], "For data sharers": [[66, "for-data-sharers"]], "Generating the cache": [[54, "Generating-the-cache"]], "Glossary": [[48, "glossary"]], "Gotchas": [[62, "Gotchas"]], "How do I change my download (a.k.a. cache) directory?": [[0, "how-do-i-change-my-download-a-k-a-cache-directory"]], "How do I check which version of ONE I\u2019m using within Python?": [[0, "how-do-i-check-which-version-of-one-i-m-using-within-python"]], "How do I download the datasets cache for a specific IBL paper release?": [[0, "how-do-i-download-the-datasets-cache-for-a-specific-ibl-paper-release"]], "How do I get information about a session from an experiment ID?": [[0, "how-do-i-get-information-about-a-session-from-an-experiment-id"]], "How do I load cache tables from a different location?": [[0, "how-do-i-load-cache-tables-from-a-different-location"]], "How do I load datasets that pass quality control": [[0, "how-do-i-load-datasets-that-pass-quality-control"]], "How do I log out, or temporarily log in as someone else?": [[0, "how-do-i-log-out-or-temporarily-log-in-as-someone-else"]], "How do I release my own data with the ONE API?": [[0, "how-do-i-release-my-own-data-with-the-one-api"]], "How do I search for sessions with the exact subject name (excluding partial matches)?": [[0, "how-do-i-search-for-sessions-with-the-exact-subject-name-excluding-partial-matches"]], "How do I use ONE in a read-only environment?": [[0, "how-do-i-use-one-in-a-read-only-environment"]], "How do I use ONE without connecting to my database?": [[0, "how-do-i-use-one-without-connecting-to-my-database"]], "How do check who I\u2019m logged in as?": [[0, "how-do-check-who-i-m-logged-in-as"]], "How the ONE API works": [[66, "how-the-one-api-works"]], "How to set up and save": [[63, "How-to-set-up-and-save"]], "I made a mistake during setup and now can\u2019t call setup, how do I fix it?": [[0, "i-made-a-mistake-during-setup-and-now-can-t-call-setup-how-do-i-fix-it"]], "Introduction to ONE (Open Neurophysiology Environment)": [[66, null]], "JSON field lookups": [[64, "JSON-field-lookups"]], "Listing Alyx Filenames": [[53, null]], "Listing aggregate datasets": [[58, "Listing-aggregate-datasets"]], "Listing data": [[66, "listing-data"]], "Listing with ONE": [[58, null]], "Load spike times from a probe UUID": [[59, "Load-spike-times-from-a-probe-UUID"]], "Loading aggregate datasets": [[59, "Loading-aggregate-datasets"]], "Loading collections": [[59, "Loading-collections"]], "Loading data": [[66, "loading-data"]], "Loading with ONE": [[59, null]], "Loading with file name parts": [[59, "Loading-with-file-name-parts"]], "Loading with relative paths": [[59, "Loading-with-relative-paths"]], "Loading with timeseries": [[59, "Loading-with-timeseries"]], "Looking up fields": [[64, "Looking-up-fields"]], "Misc": [[52, null]], "More regex examples": [[59, "More-regex-examples"]], "Namespace": [[48, "namespace"]], "ONE API modes": [[60, null]], "ONE Quick Start": [[61, null]], "ONE REST queries": [[57, null]], "ONE installation and setup": [[65, null]], "Online vs Offline": [[60, "Online-vs-Offline"]], "Optional components": [[48, "optional-components"]], "Query modes": [[60, "Query-modes"]], "REST caching": [[60, "REST-caching"]], "Recording data access": [[63, null]], "Refreshing the cache tables": [[60, "Refreshing-the-cache-tables"]], "Regex systems between modes": [[62, "Regex-systems-between-modes"]], "Related field lookups": [[64, "Related-field-lookups"]], "Relations": [[48, "relations"]], "Relative path": [[48, "relative-path"]], "Releasing (developers only)": [[50, "releasing-developers-only"]], "Releasing data with ONE": [[54, null]], "Revisions": [[48, "revisions"], [59, "Revisions"]], "Running locally": [[50, "running-locally"]], "Searching data with a release tag": [[62, "Searching-data-with-a-release-tag"]], "Searching for experiments": [[66, "searching-for-experiments"]], "Searching insertions": [[62, "Searching-insertions"]], "Searching with ONE": [[62, null]], "Searching with one.alyx.rest": [[57, "Searching-with-one.alyx.rest"]], "Session path": [[48, "session-path"]], "Setup": [[24, "setup"]], "Structure": [[50, "structure"]], "Summary": [[60, "Summary"]], "Summary of methods": [[19, "summary-of-methods"]], "The dataset, datasets and dataset_types remote arguments": [[62, "The-dataset,-datasets-and-dataset_types-remote-arguments"]], "Timescale": [[48, "timescale"]], "Useful Alyx REST queries": [[64, null]], "Using ONE to access data": [[52, null]], "Using ONE to share data": [[52, null]], "Using ONE with Alyx": [[52, null]], "Using local folder structure": [[65, "using-local-folder-structure"]], "Validating your data": [[54, "Validating-your-data"]], "Welcome to ONE\u2019s documentation!": [[52, null]], "What to do if I am seeing a certificate error?": [[0, "what-to-do-if-i-am-seeing-a-certificate-error"]], "Why are my recent data missing from my cache but present on Alyx?": [[0, "why-are-my-recent-data-missing-from-my-cache-but-present-on-alyx"]], "Why are my search results inconsistent and/or seem to change?": [[0, "why-are-my-search-results-inconsistent-and-or-seem-to-change"]], "Why does the search return a LazyID object?": [[0, "why-does-the-search-return-a-lazyid-object"]], "contained_by": [[64, "contained_by"]], "contains": [[64, "contains"], [64, "contains-1"]], "convert session dicts to eids": [[64, "convert-session-dicts-to-eids"]], "date": [[64, "date"]], "day": [[64, "day"]], "endswith": [[64, "endswith"]], "exact": [[64, "exact"]], "gt": [[64, "gt"]], "gte": [[64, "gte"]], "has_any_keys": [[64, "has_any_keys"]], "has_key": [[64, "has_key"]], "has_keys": [[64, "has_keys"]], "hour": [[64, "hour"]], "icontains": [[64, "icontains"]], "iendswith": [[64, "iendswith"]], "iexact": [[64, "iexact"]], "in": [[64, "in"]], "iregex": [[64, "iregex"]], "isnull": [[64, "isnull"]], "iso_week_day": [[64, "iso_week_day"]], "iso_year": [[64, "iso_year"]], "istartswith": [[64, "istartswith"]], "list ephys sessions that have errored tasks": 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"one.api.One.list_collections", false]], "list_datasets() (one method)": [[14, "one.api.One.list_datasets", false]], "list_datasets() (onealyx method)": [[14, "one.api.OneAlyx.list_datasets", false]], "list_endpoints() (alyxclient method)": [[47, "one.webclient.AlyxClient.list_endpoints", false]], "list_revisions() (one method)": [[14, "one.api.One.list_revisions", false]], "list_subjects() (one method)": [[14, "one.api.One.list_subjects", false]], "listable() (in module one.util)": [[45, "one.util.Listable", false]], "load_aggregate() (onealyx method)": [[14, "one.api.OneAlyx.load_aggregate", false]], "load_cache() (one method)": [[14, "one.api.One.load_cache", false]], "load_cache() (onealyx method)": [[14, "one.api.OneAlyx.load_cache", false]], "load_client_params() (in module one.remote.base)": [[22, "one.remote.base.load_client_params", false]], "load_collection() (one method)": [[14, "one.api.One.load_collection", false]], "load_dataset() (one method)": [[14, "one.api.One.load_dataset", false]], "load_dataset_from_id() (one method)": [[14, "one.api.One.load_dataset_from_id", false]], "load_datasets() (one method)": [[14, "one.api.One.load_datasets", false]], "load_file_content() (in module one.alf.io)": [[6, "one.alf.io.load_file_content", false]], "load_object() (in module one.alf.io)": [[6, "one.alf.io.load_object", false]], "load_object() (one method)": [[14, "one.api.One.load_object", false]], "login() (globus method)": [[24, "one.remote.globus.Globus.login", false]], "logout() (alyxclient method)": [[47, "one.webclient.AlyxClient.logout", false]], "logout() (globus method)": [[24, "one.remote.globus.Globus.logout", false]], "ls() (globus method)": [[24, "one.remote.globus.Globus.ls", false]], "make_parquet_db() (in module one.alf.cache)": [[3, "one.alf.cache.make_parquet_db", false]], "module": [[1, "module-one", false], [2, "module-one.alf", false], [3, "module-one.alf.cache", false], [4, "module-one.alf.exceptions", false], [5, "module-one.alf.files", false], [6, "module-one.alf.io", false], [7, "module-one.alf.spec", false], [14, "module-one.api", false], [16, "module-one.converters", false], [17, "module-one.params", false], [19, "module-one.registration", false], [20, "module-one.remote", false], [21, "module-one.remote.aws", false], [22, "module-one.remote.base", false], [24, "module-one.remote.globus", false], [28, "module-one.tests", false], [29, "module-one.tests.alf", false], [30, "module-one.tests.alf.test_alf_files", false], [31, "module-one.tests.alf.test_alf_io", false], [32, "module-one.tests.alf.test_alf_spec", false], [33, "module-one.tests.alf.test_cache", false], [34, "module-one.tests.remote", false], [35, "module-one.tests.remote.test_aws", false], [36, "module-one.tests.remote.test_base", false], [37, "module-one.tests.remote.test_globus", false], [38, "module-one.tests.test_alyxclient", false], [39, "module-one.tests.test_alyxrest", false], [40, "module-one.tests.test_converters", false], [41, "module-one.tests.test_one", false], [42, "module-one.tests.test_params", false], [43, "module-one.tests.test_registration", false], [44, "module-one.tests.util", false], [45, "module-one.util", false], [47, "module-one.webclient", false]], "mv() (globus method)": [[24, "one.remote.globus.Globus.mv", false]], "n_threads (in module one.api)": [[15, "one.api.N_THREADS", false]], "next_num_folder() (in module one.alf.io)": [[6, "one.alf.io.next_num_folder", false]], "no_cache() (in module one.webclient)": [[47, "one.webclient.no_cache", false]], "not_set (qc attribute)": [[7, "one.alf.spec.QC.NOT_SET", false]], "offline (one property)": [[14, "one.api.One.offline", false]], "one": [[1, "module-one", false]], "one (class in one.api)": [[14, "one.api.One", false]], "one (testonealyx attribute)": [[41, "one.tests.test_one.TestOneAlyx.one", false]], "one (testonedownload attribute)": [[41, "one.tests.test_one.TestOneDownload.one", false]], "one (testregistrationclient attribute)": [[43, "one.tests.test_registration.TestRegistrationClient.one", false]], "one() (in module one.api)": [[14, "one.api.ONE", false]], "one.alf": [[2, "module-one.alf", false]], "one.alf.cache": [[3, "module-one.alf.cache", false]], "one.alf.exceptions": [[4, "module-one.alf.exceptions", false]], "one.alf.files": [[5, "module-one.alf.files", false]], "one.alf.io": [[6, "module-one.alf.io", false]], "one.alf.spec": [[7, "module-one.alf.spec", false]], "one.api": [[14, "module-one.api", false]], "one.converters": [[16, "module-one.converters", false]], "one.params": [[17, "module-one.params", false]], "one.registration": [[19, "module-one.registration", false]], "one.remote": [[20, "module-one.remote", false]], "one.remote.aws": [[21, "module-one.remote.aws", false]], "one.remote.base": [[22, "module-one.remote.base", false]], "one.remote.globus": [[24, "module-one.remote.globus", false]], "one.tests": [[28, "module-one.tests", false]], "one.tests.alf": [[29, "module-one.tests.alf", false]], "one.tests.alf.test_alf_files": [[30, "module-one.tests.alf.test_alf_files", false]], "one.tests.alf.test_alf_io": [[31, "module-one.tests.alf.test_alf_io", false]], "one.tests.alf.test_alf_spec": [[32, "module-one.tests.alf.test_alf_spec", false]], "one.tests.alf.test_cache": [[33, "module-one.tests.alf.test_cache", false]], "one.tests.remote": [[34, "module-one.tests.remote", false]], "one.tests.remote.test_aws": [[35, "module-one.tests.remote.test_aws", false]], "one.tests.remote.test_base": [[36, "module-one.tests.remote.test_base", false]], "one.tests.remote.test_globus": [[37, "module-one.tests.remote.test_globus", false]], "one.tests.test_alyxclient": [[38, "module-one.tests.test_alyxclient", false]], "one.tests.test_alyxrest": [[39, "module-one.tests.test_alyxrest", false]], "one.tests.test_converters": [[40, "module-one.tests.test_converters", false]], "one.tests.test_one": [[41, "module-one.tests.test_one", false]], "one.tests.test_params": [[42, "module-one.tests.test_params", false]], "one.tests.test_registration": [[43, "module-one.tests.test_registration", false]], "one.tests.util": [[44, "module-one.tests.util", false]], "one.util": [[45, "module-one.util", false]], "one.webclient": [[47, "module-one.webclient", false]], "one_path_from_dataset() (in module one.converters)": [[16, "one.converters.one_path_from_dataset", false]], "onealyx (class in one.api)": [[14, "one.api.OneAlyx", false]], "padded_sequence() (in module one.alf.files)": [[5, "one.alf.files.padded_sequence", false]], "parse_id() (in module one.util)": [[45, "one.util.parse_id", false]], "parse_values() (in module one.converters)": [[16, "one.converters.parse_values", false]], "pass (qc attribute)": [[7, "one.alf.spec.QC.PASS", false]], "patch() (alyxclient method)": [[47, "one.webclient.AlyxClient.patch", false]], "patch_cache() (in module one.util)": [[45, "one.util.patch_cache", false]], "path2eid() (conversionmixin method)": [[16, "one.converters.ConversionMixin.path2eid", false]], "path2eid() (onealyx method)": [[14, "one.api.OneAlyx.path2eid", false]], "path2record() (conversionmixin method)": [[16, "one.converters.ConversionMixin.path2record", false]], "path2ref() (conversionmixin static method)": [[16, "one.converters.ConversionMixin.path2ref", false]], "path2url() (conversionmixin method)": [[16, "one.converters.ConversionMixin.path2url", false]], "path2url() (onealyx method)": [[14, "one.api.OneAlyx.path2url", false]], "path_from_dataset() (in module one.converters)": [[16, "one.converters.path_from_dataset", false]], "path_from_filerecord() (in module one.converters)": [[16, "one.converters.path_from_filerecord", false]], "path_mock (testbase attribute)": [[36, "one.tests.remote.test_base.TestBase.path_mock", false]], "path_mock (testglobus attribute)": [[37, "one.tests.remote.test_globus.TestGlobus.path_mock", false]], "path_pattern() (in module one.alf.spec)": [[7, "one.alf.spec.path_pattern", false]], "pid2eid() (onealyx method)": [[14, "one.api.OneAlyx.pid2eid", false]], "post() (alyxclient method)": [[47, "one.webclient.AlyxClient.post", false]], "prepare_files() (registrationclient method)": [[19, "one.registration.RegistrationClient.prepare_files", false]], "print_endpoint_info() (alyxclient method)": [[47, "one.webclient.AlyxClient.print_endpoint_info", false]], "put() (alyxclient method)": [[47, "one.webclient.AlyxClient.put", false]], "qc (class in one.alf.spec)": [[7, "one.alf.spec.QC", false]], "qc_type (in module one.util)": [[45, "one.util.QC_TYPE", false], [46, "one.util.QC_TYPE", false]], "read_ts() (in module one.alf.io)": [[6, "one.alf.io.read_ts", false]], "readablealf() (in module one.alf.spec)": [[7, "one.alf.spec.readableALF", false]], "record2path() (conversionmixin method)": [[16, "one.converters.ConversionMixin.record2path", false]], "record2url() (conversionmixin method)": [[16, "one.converters.ConversionMixin.record2url", false]], "recurse() (in module one.converters)": [[16, "one.converters.recurse", false]], "ref2dict() (conversionmixin static method)": [[16, "one.converters.ConversionMixin.ref2dict", false]], "ref2eid() (conversionmixin method)": [[16, "one.converters.ConversionMixin.ref2eid", false]], "ref2path() (conversionmixin method)": [[16, "one.converters.ConversionMixin.ref2path", false]], "refresh() (in module one.util)": [[45, "one.util.refresh", false]], "refresh_cache() (one method)": [[14, "one.api.One.refresh_cache", false]], "regex() (in module one.alf.spec)": [[7, "one.alf.spec.regex", false]], "register_files() (registrationclient method)": [[19, "one.registration.RegistrationClient.register_files", false]], "register_session() (registrationclient method)": [[19, "one.registration.RegistrationClient.register_session", false]], "register_water_administration() (registrationclient method)": [[19, "one.registration.RegistrationClient.register_water_administration", false]], "register_weight() (registrationclient method)": [[19, "one.registration.RegistrationClient.register_weight", false]], "registrationclient (class in one.registration)": [[19, "one.registration.RegistrationClient", false]], "rel_path2url() (alyxclient method)": [[47, "one.webclient.AlyxClient.rel_path2url", false]], "rel_path_parts() (in module one.alf.files)": [[5, "one.alf.files.rel_path_parts", false]], "rel_path_spec (in module one.alf.spec)": [[7, "one.alf.spec.REL_PATH_SPEC", false], [11, "one.alf.spec.REL_PATH_SPEC", false]], "rel_ses_files (testsoneparquet attribute)": [[33, "one.tests.alf.test_cache.TestsONEParquet.rel_ses_files", false]], "rel_ses_path (testsoneparquet attribute)": [[33, "one.tests.alf.test_cache.TestsONEParquet.rel_ses_path", false]], "remove_empty_folders() (in module one.alf.io)": [[6, "one.alf.io.remove_empty_folders", false]], "remove_missing_datasets() (in module one.alf.cache)": [[3, "one.alf.cache.remove_missing_datasets", false]], "remove_uuid_file() (in module one.alf.io)": [[6, "one.alf.io.remove_uuid_file", false]], "remove_uuid_recursive() (in module one.alf.io)": [[6, "one.alf.io.remove_uuid_recursive", false]], "remove_uuid_string() (in module one.alf.files)": [[5, "one.alf.files.remove_uuid_string", false]], "repo (testaws attribute)": [[35, "one.tests.remote.test_aws.TestAWS.repo", false]], "repo_from_alyx() (downloadclient static method)": [[22, "one.remote.base.DownloadClient.repo_from_alyx", false]], "rest() (alyxclient method)": [[47, "one.webclient.AlyxClient.rest", false]], "rest_schemes (alyxclient property)": [[47, "one.webclient.AlyxClient.rest_schemes", false]], "revisions_datasets_table() (in module one.tests.util)": [[44, "one.tests.util.revisions_datasets_table", false]], "run_task() (globus method)": [[24, "one.remote.globus.Globus.run_task", false]], "s3_download_file() (in module one.remote.aws)": [[21, "one.remote.aws.s3_download_file", false]], "s3_download_folder() (in module one.remote.aws)": [[21, "one.remote.aws.s3_download_folder", false]], "save() (in module one.params)": [[17, "one.params.save", false]], "save_cache() (one method)": [[14, "one.api.One.save_cache", false]], "save_client_params() (in module one.remote.base)": [[22, "one.remote.base.save_client_params", false]], "save_loaded_ids() (one method)": [[14, "one.api.One.save_loaded_ids", false]], "save_metadata() (in module one.alf.io)": [[6, "one.alf.io.save_metadata", false]], "save_object_npy() (in module one.alf.io)": [[6, "one.alf.io.save_object_npy", false]], "search() (one method)": [[14, "one.api.One.search", false]], "search() (onealyx method)": [[14, "one.api.OneAlyx.search", false]], "search_insertions() (onealyx method)": [[14, "one.api.OneAlyx.search_insertions", false]], "search_terms() (one method)": [[14, "one.api.One.search_terms", false]], "search_terms() (onealyx method)": [[14, "one.api.OneAlyx.search_terms", false]], "ses2eid() (lazyid static method)": [[45, "one.util.LazyId.ses2eid", false]], "ses2records() (in module one.util)": [[45, "one.util.ses2records", false]], "ses_info (testsoneparquet attribute)": [[33, "one.tests.alf.test_cache.TestsONEParquet.ses_info", false]], "session_path (testalffolders attribute)": [[31, "one.tests.alf.test_alf_io.TestALFFolders.session_path", false]], "session_path_parts() (in module one.alf.files)": [[5, "one.alf.files.session_path_parts", false]], "session_record2path() (in module one.converters)": [[16, "one.converters.session_record2path", false]], "session_spec (in module one.alf.spec)": [[7, "one.alf.spec.SESSION_SPEC", false], [12, "one.alf.spec.SESSION_SPEC", false]], "set_up_env() (in module one.tests.util)": [[44, "one.tests.util.set_up_env", false]], "setup() (downloadclient static method)": [[22, "one.remote.base.DownloadClient.setup", false]], "setup() (globus static method)": [[24, "one.remote.globus.Globus.setup", false]], "setup() (in module one.params)": [[17, "one.params.setup", false]], "setup() (one static method)": [[14, "one.api.One.setup", false]], "setup() (onealyx static method)": [[14, "one.api.OneAlyx.setup", false]], "setup() (testauthentication method)": [[38, "one.tests.test_alyxclient.TestAuthentication.setUp", false]], "setup() (testbase method)": [[36, "one.tests.remote.test_base.TestBase.setUp", false]], "setup() (testdownloadhttp method)": [[38, "one.tests.test_alyxclient.TestDownloadHTTP.setUp", false]], "setup() (testfindvariants method)": [[31, "one.tests.alf.test_alf_io.TestFindVariants.setUp", false]], "setup() (testglobus method)": [[37, "one.tests.remote.test_globus.TestGlobus.setUp", false]], "setup() (testjsonfieldmethods method)": [[38, "one.tests.test_alyxclient.TestJsonFieldMethods.setUp", false]], "setup() (testonecache method)": [[41, "one.tests.test_one.TestONECache.setUp", false]], "setup() (testonedownload method)": [[41, "one.tests.test_one.TestOneDownload.setUp", false]], "setup() (testoneparamutil method)": [[42, "one.tests.test_params.TestONEParamUtil.setUp", false]], "setup() (testoneremote method)": [[41, "one.tests.test_one.TestOneRemote.setUp", false]], "setup() (testonesetup method)": [[41, "one.tests.test_one.TestOneSetup.setUp", false]], "setup() (testparamsetup method)": [[42, "one.tests.test_params.TestParamSetup.setUp", false]], "setup() (testregistrationclient method)": [[43, "one.tests.test_registration.TestRegistrationClient.setUp", false]], "setup() (testrestcache method)": [[38, "one.tests.test_alyxclient.TestRestCache.setUp", false]], "setup() (testsalf method)": [[31, "one.tests.alf.test_alf_io.TestsAlf.setUp", false]], "setup() (testsalfpartsfilters method)": [[31, "one.tests.alf.test_alf_io.TestsAlfPartsFilters.setUp", false]], "setup() (testsloadfile method)": [[31, "one.tests.alf.test_alf_io.TestsLoadFile.setUp", false]], "setup() (testsloadfilenonstandard method)": [[31, "one.tests.alf.test_alf_io.TestsLoadFileNonStandard.setUp", false]], "setup() (testsoneparquet method)": [[33, "one.tests.alf.test_cache.TestsONEParquet.setUp", false]], "setup_rest_cache() (in module one.tests.util)": [[44, "one.tests.util.setup_rest_cache", false]], "setup_test_params() (in module one.tests.util)": [[44, "one.tests.util.setup_test_params", false]], "setupclass() (testalffolders class method)": [[31, "one.tests.alf.test_alf_io.TestALFFolders.setUpClass", false]], "setupclass() (testaws class method)": [[35, "one.tests.remote.test_aws.TestAWS.setUpClass", false]], "setupclass() (testbase class method)": [[36, "one.tests.remote.test_base.TestBase.setUpClass", false]], "setupclass() (testconverters class method)": [[40, "one.tests.test_converters.TestConverters.setUpClass", false]], "setupclass() (testglobus class method)": [[37, "one.tests.remote.test_globus.TestGlobus.setUpClass", false]], "setupclass() (testonealyx class method)": [[41, "one.tests.test_one.TestOneAlyx.setUpClass", false]], "setupclass() (testonlineconverters class method)": [[40, "one.tests.test_converters.TestOnlineConverters.setUpClass", false]], "setupclass() (testregistrationclient class method)": [[43, "one.tests.test_registration.TestRegistrationClient.setUpClass", false]], "setupclass() (testrest class method)": [[39, "one.tests.test_alyxrest.TestREST.setUpClass", false]], "source (testawspublic attribute)": [[35, "one.tests.remote.test_aws.TestAWSPublic.source", false]], "spec_description (in module one.alf.spec)": [[7, "one.alf.spec.SPEC_DESCRIPTION", false], [13, "one.alf.spec.SPEC_DESCRIPTION", false]], "status_map (in module one.remote.globus)": [[27, "one.remote.globus.STATUS_MAP", false]], "subject (testregistrationclient attribute)": [[43, "one.tests.test_registration.TestRegistrationClient.subject", false]], "tag (testregistrationclient attribute)": [[43, "one.tests.test_registration.TestRegistrationClient.tag", false]], "task_wait_async() (globus method)": [[24, "one.remote.globus.Globus.task_wait_async", false]], "teardown() (testalferr method)": [[32, "one.tests.alf.test_alf_spec.TestALFErr.tearDown", false]], "teardown() (testalffolders method)": [[31, "one.tests.alf.test_alf_io.TestALFFolders.tearDown", false]], "teardown() (testbase method)": [[36, "one.tests.remote.test_base.TestBase.tearDown", false]], "teardown() (testglobus method)": [[37, "one.tests.remote.test_globus.TestGlobus.tearDown", false]], "teardown() (testjsonfieldmethods method)": [[38, "one.tests.test_alyxclient.TestJsonFieldMethods.tearDown", false]], "teardown() (testonealyx method)": [[41, "one.tests.test_one.TestOneAlyx.tearDown", false]], "teardown() (testonecache method)": [[41, "one.tests.test_one.TestONECache.tearDown", false]], "teardown() (testonedownload method)": [[41, "one.tests.test_one.TestOneDownload.tearDown", false]], "teardown() (testrestcache method)": [[38, "one.tests.test_alyxclient.TestRestCache.tearDown", false]], "teardown() (testsalf method)": [[31, "one.tests.alf.test_alf_io.TestsAlf.tearDown", false]], "teardown() 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\ No newline at end of file
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type": [[48, "dataset-type"]], "Dataset types": [[55, "Dataset-types"]], "Datasets": [[55, "Datasets"], [66, "datasets"]], "Datasets and their types": [[55, null]], "Detailed Index": [[51, null]], "Difference between remote mode search terms": [[62, "Difference-between-remote-mode-search-terms"]], "Difference between search term behaviours": [[62, "Difference-between-search-term-behaviours"]], "Download only": [[59, "Download-only"]], "Downloading example data": [[54, "Downloading-example-data"]], "Example": [[63, "Example"]], "Example queries": [[64, "Example-queries"]], "Experiment IDs": [[56, null], [66, "experiment-ids"]], "Exploring the REST endpoints": [[64, "Exploring-the-REST-endpoints"]], "Extension": [[48, "extension"]], "Extra": [[48, "extra"]], "FAQ": [[0, null]], "Field lookup reference": [[64, "Field-lookup-reference"]], "Filtering attributes": [[59, "Filtering-attributes"]], "Filtering lists": [[58, "Filtering-lists"]], "For data sharers": [[66, "for-data-sharers"]], 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"explanation (alfobjectnotfound attribute)": [[4, "one.alf.exceptions.ALFObjectNotFound.explanation", false]], "explanation (alyxsubjectnotfound attribute)": [[4, "one.alf.exceptions.AlyxSubjectNotFound.explanation", false]], "fail (qc attribute)": [[7, "one.alf.spec.QC.FAIL", false]], "fetch_endpoints_from_alyx() (globus method)": [[24, "one.remote.globus.Globus.fetch_endpoints_from_alyx", false]], "file_record_to_url() (in module one.webclient)": [[47, "one.webclient.file_record_to_url", false]], "file_spec (in module one.alf.spec)": [[7, "one.alf.spec.FILE_SPEC", false], [9, "one.alf.spec.FILE_SPEC", false]], "filename_parts() (in module one.alf.files)": [[5, "one.alf.files.filename_parts", false]], "filter_by() (in module one.alf.io)": [[6, "one.alf.io.filter_by", false]], "filter_datasets() (in module one.util)": [[45, "one.util.filter_datasets", false]], "filter_revision_last_before() (in module one.util)": [[45, "one.util.filter_revision_last_before", false]], "find_files() (registrationclient method)": [[19, "one.registration.RegistrationClient.find_files", false]], "find_variants() (in module one.alf.io)": [[6, "one.alf.io.find_variants", false]], "folder_parts() (in module one.alf.files)": [[5, "one.alf.files.folder_parts", false]], "from_df() (alfbunch static method)": [[6, "one.alf.io.AlfBunch.from_df", false]], "full_path_parts() (in module one.alf.files)": [[5, "one.alf.files.full_path_parts", false]], "full_spec (in module one.alf.spec)": [[7, "one.alf.spec.FULL_SPEC", false], [10, "one.alf.spec.FULL_SPEC", false]], "get() (alyxclient method)": [[47, "one.webclient.AlyxClient.get", false]], "get() (in module one.params)": [[17, "one.params.get", false]], "get_alf_path() (in module one.alf.files)": [[5, "one.alf.files.get_alf_path", false]], "get_aws_access_keys() (in module one.remote.aws)": [[21, "one.remote.aws.get_aws_access_keys", false]], "get_cache_dir() (in module one.params)": [[17, "one.params.get_cache_dir", false]], "get_dataset_type() (in module one.registration)": [[19, "one.registration.get_dataset_type", false]], "get_default_client() (in module one.params)": [[17, "one.params.get_default_client", false]], "get_details() (one method)": [[14, "one.api.One.get_details", false]], "get_details() (onealyx method)": [[14, "one.api.OneAlyx.get_details", false]], "get_file() (in module one.tests.util)": [[44, "one.tests.util.get_file", false]], "get_lab_from_endpoint_id() (in module one.remote.globus)": [[24, "one.remote.globus.get_lab_from_endpoint_id", false]], "get_params_dir() (in module one.params)": [[17, "one.params.get_params_dir", false]], "get_s3_allen() (in module one.remote.aws)": [[21, "one.remote.aws.get_s3_allen", false]], "get_s3_from_alyx() (in module one.remote.aws)": [[21, "one.remote.aws.get_s3_from_alyx", false]], "get_s3_public() (in module one.remote.aws)": [[21, "one.remote.aws.get_s3_public", false]], "get_s3_virtual_host() (in module one.remote.aws)": [[21, "one.remote.aws.get_s3_virtual_host", false]], "get_session_path() (in module one.alf.files)": [[5, "one.alf.files.get_session_path", false]], "globus (class in one.remote.globus)": [[24, "one.remote.globus.Globus", false]], "http_download_file() (in module one.webclient)": [[47, "one.webclient.http_download_file", false]], "http_download_file_list() (in module one.webclient)": [[47, "one.webclient.http_download_file_list", false]], "index_last_before() (in module one.util)": [[45, "one.util.index_last_before", false]], "is_exp_ref() (conversionmixin static method)": [[16, "one.converters.ConversionMixin.is_exp_ref", false]], "is_folder() (in module one.remote.aws)": [[21, "one.remote.aws.is_folder", false]], "is_logged_in (alyxclient property)": [[47, "one.webclient.AlyxClient.is_logged_in", false]], "is_logged_in (globus property)": [[24, "one.remote.globus.Globus.is_logged_in", false]], "is_session_path() (in module one.alf.spec)": [[7, "one.alf.spec.is_session_path", false]], "is_uuid() (in module one.alf.spec)": [[7, "one.alf.spec.is_uuid", false]], "is_uuid_string() (in module one.alf.spec)": [[7, "one.alf.spec.is_uuid_string", false]], "is_valid() (in module one.alf.spec)": [[7, "one.alf.spec.is_valid", false]], "iter_datasets() (in module one.alf.io)": [[6, "one.alf.io.iter_datasets", false]], "iter_sessions() (in module one.alf.io)": [[6, "one.alf.io.iter_sessions", false]], "json_field_delete() (alyxclient method)": [[47, "one.webclient.AlyxClient.json_field_delete", false]], "json_field_remove_key() (alyxclient method)": [[47, "one.webclient.AlyxClient.json_field_remove_key", false]], "json_field_update() (alyxclient method)": [[47, "one.webclient.AlyxClient.json_field_update", false]], "json_field_write() (alyxclient method)": [[47, "one.webclient.AlyxClient.json_field_write", false]], "lazyid (class in one.util)": [[45, "one.util.LazyId", false]], "list_aggregates() (onealyx method)": [[14, "one.api.OneAlyx.list_aggregates", false]], "list_collections() (one method)": [[14, "one.api.One.list_collections", false]], "list_datasets() (one method)": [[14, "one.api.One.list_datasets", false]], "list_datasets() (onealyx method)": [[14, "one.api.OneAlyx.list_datasets", false]], "list_endpoints() (alyxclient method)": [[47, "one.webclient.AlyxClient.list_endpoints", false]], "list_revisions() (one method)": [[14, "one.api.One.list_revisions", false]], "list_subjects() (one method)": [[14, "one.api.One.list_subjects", false]], "listable() (in module one.util)": [[45, "one.util.Listable", false]], "load_aggregate() (onealyx method)": [[14, "one.api.OneAlyx.load_aggregate", false]], "load_cache() (one method)": [[14, "one.api.One.load_cache", false]], "load_cache() (onealyx method)": [[14, "one.api.OneAlyx.load_cache", false]], "load_client_params() (in module one.remote.base)": [[22, "one.remote.base.load_client_params", false]], "load_collection() (one method)": [[14, "one.api.One.load_collection", false]], "load_dataset() (one method)": [[14, "one.api.One.load_dataset", false]], "load_dataset_from_id() (one method)": [[14, "one.api.One.load_dataset_from_id", false]], "load_datasets() (one method)": [[14, "one.api.One.load_datasets", false]], "load_file_content() (in module one.alf.io)": [[6, "one.alf.io.load_file_content", false]], "load_object() (in module one.alf.io)": [[6, "one.alf.io.load_object", false]], "load_object() (one method)": [[14, "one.api.One.load_object", false]], "login() (globus method)": [[24, "one.remote.globus.Globus.login", false]], "logout() (alyxclient method)": [[47, "one.webclient.AlyxClient.logout", false]], "logout() (globus method)": [[24, "one.remote.globus.Globus.logout", false]], "ls() (globus method)": [[24, "one.remote.globus.Globus.ls", false]], "make_parquet_db() (in module one.alf.cache)": [[3, "one.alf.cache.make_parquet_db", false]], "module": [[1, "module-one", false], [2, "module-one.alf", false], [3, "module-one.alf.cache", false], [4, "module-one.alf.exceptions", false], [5, "module-one.alf.files", false], [6, "module-one.alf.io", false], [7, "module-one.alf.spec", false], [14, "module-one.api", false], [16, "module-one.converters", false], [17, "module-one.params", false], [19, "module-one.registration", false], [20, "module-one.remote", false], [21, "module-one.remote.aws", false], [22, "module-one.remote.base", false], [24, "module-one.remote.globus", false], [28, "module-one.tests", false], [29, "module-one.tests.alf", false], [30, "module-one.tests.alf.test_alf_files", false], [31, "module-one.tests.alf.test_alf_io", false], [32, "module-one.tests.alf.test_alf_spec", false], [33, "module-one.tests.alf.test_cache", false], [34, "module-one.tests.remote", false], [35, "module-one.tests.remote.test_aws", false], [36, "module-one.tests.remote.test_base", false], [37, "module-one.tests.remote.test_globus", false], [38, "module-one.tests.test_alyxclient", false], [39, "module-one.tests.test_alyxrest", false], [40, "module-one.tests.test_converters", false], [41, "module-one.tests.test_one", false], [42, "module-one.tests.test_params", false], [43, "module-one.tests.test_registration", false], [44, "module-one.tests.util", false], [45, "module-one.util", false], [47, "module-one.webclient", false]], "mv() (globus method)": [[24, "one.remote.globus.Globus.mv", false]], "n_threads (in module one.api)": [[15, "one.api.N_THREADS", false]], "next_num_folder() (in module one.alf.io)": [[6, "one.alf.io.next_num_folder", false]], "no_cache() (in module one.webclient)": [[47, "one.webclient.no_cache", false]], "not_set (qc attribute)": [[7, "one.alf.spec.QC.NOT_SET", false]], "offline (one property)": [[14, "one.api.One.offline", false]], "one": [[1, "module-one", false]], "one (class in one.api)": [[14, "one.api.One", false]], "one (testonealyx attribute)": [[41, "one.tests.test_one.TestOneAlyx.one", false]], "one (testonedownload attribute)": [[41, "one.tests.test_one.TestOneDownload.one", false]], "one (testregistrationclient attribute)": [[43, "one.tests.test_registration.TestRegistrationClient.one", false]], "one() (in module one.api)": [[14, "one.api.ONE", false]], "one.alf": [[2, "module-one.alf", false]], "one.alf.cache": [[3, "module-one.alf.cache", false]], "one.alf.exceptions": [[4, "module-one.alf.exceptions", false]], "one.alf.files": [[5, "module-one.alf.files", false]], "one.alf.io": [[6, "module-one.alf.io", false]], "one.alf.spec": [[7, "module-one.alf.spec", false]], "one.api": [[14, "module-one.api", false]], "one.converters": [[16, "module-one.converters", false]], "one.params": [[17, "module-one.params", false]], "one.registration": [[19, "module-one.registration", false]], "one.remote": [[20, "module-one.remote", false]], "one.remote.aws": [[21, "module-one.remote.aws", false]], "one.remote.base": [[22, "module-one.remote.base", false]], "one.remote.globus": [[24, "module-one.remote.globus", false]], "one.tests": [[28, "module-one.tests", false]], "one.tests.alf": [[29, "module-one.tests.alf", false]], "one.tests.alf.test_alf_files": [[30, "module-one.tests.alf.test_alf_files", false]], "one.tests.alf.test_alf_io": [[31, "module-one.tests.alf.test_alf_io", false]], "one.tests.alf.test_alf_spec": [[32, "module-one.tests.alf.test_alf_spec", false]], "one.tests.alf.test_cache": [[33, "module-one.tests.alf.test_cache", false]], "one.tests.remote": [[34, "module-one.tests.remote", false]], "one.tests.remote.test_aws": [[35, "module-one.tests.remote.test_aws", false]], "one.tests.remote.test_base": [[36, "module-one.tests.remote.test_base", false]], "one.tests.remote.test_globus": [[37, "module-one.tests.remote.test_globus", false]], "one.tests.test_alyxclient": [[38, "module-one.tests.test_alyxclient", false]], "one.tests.test_alyxrest": [[39, "module-one.tests.test_alyxrest", false]], "one.tests.test_converters": [[40, "module-one.tests.test_converters", false]], "one.tests.test_one": [[41, "module-one.tests.test_one", false]], "one.tests.test_params": [[42, "module-one.tests.test_params", false]], "one.tests.test_registration": [[43, "module-one.tests.test_registration", false]], "one.tests.util": [[44, "module-one.tests.util", false]], "one.util": [[45, "module-one.util", false]], "one.webclient": [[47, "module-one.webclient", false]], "one_path_from_dataset() (in module one.converters)": [[16, "one.converters.one_path_from_dataset", false]], "onealyx (class in one.api)": [[14, "one.api.OneAlyx", false]], "padded_sequence() (in module one.alf.files)": [[5, "one.alf.files.padded_sequence", false]], "parse_id() (in module one.util)": [[45, "one.util.parse_id", false]], "parse_values() (in module one.converters)": [[16, "one.converters.parse_values", false]], "pass (qc attribute)": [[7, "one.alf.spec.QC.PASS", false]], "patch() (alyxclient method)": [[47, "one.webclient.AlyxClient.patch", false]], "patch_cache() (in module one.util)": [[45, "one.util.patch_cache", false]], "path2eid() (conversionmixin method)": [[16, "one.converters.ConversionMixin.path2eid", false]], "path2eid() (onealyx method)": [[14, "one.api.OneAlyx.path2eid", false]], "path2record() (conversionmixin method)": [[16, "one.converters.ConversionMixin.path2record", false]], "path2ref() (conversionmixin static method)": [[16, "one.converters.ConversionMixin.path2ref", false]], "path2url() (conversionmixin method)": [[16, "one.converters.ConversionMixin.path2url", false]], "path2url() (onealyx method)": [[14, "one.api.OneAlyx.path2url", false]], "path_from_dataset() (in module one.converters)": [[16, "one.converters.path_from_dataset", false]], "path_from_filerecord() (in module one.converters)": [[16, "one.converters.path_from_filerecord", false]], "path_mock (testbase attribute)": [[36, "one.tests.remote.test_base.TestBase.path_mock", false]], "path_mock (testglobus attribute)": [[37, "one.tests.remote.test_globus.TestGlobus.path_mock", false]], "path_pattern() (in module one.alf.spec)": [[7, "one.alf.spec.path_pattern", false]], "pid2eid() (onealyx method)": [[14, "one.api.OneAlyx.pid2eid", false]], "post() (alyxclient method)": [[47, "one.webclient.AlyxClient.post", false]], "prepare_files() (registrationclient method)": [[19, "one.registration.RegistrationClient.prepare_files", false]], "print_endpoint_info() (alyxclient method)": [[47, "one.webclient.AlyxClient.print_endpoint_info", false]], "put() (alyxclient method)": [[47, "one.webclient.AlyxClient.put", false]], "qc (class in one.alf.spec)": [[7, "one.alf.spec.QC", false]], "qc_type (in module one.util)": [[45, "one.util.QC_TYPE", false], [46, "one.util.QC_TYPE", false]], "read_ts() (in module one.alf.io)": [[6, "one.alf.io.read_ts", false]], "readablealf() (in module one.alf.spec)": [[7, "one.alf.spec.readableALF", false]], "record2path() (conversionmixin method)": [[16, "one.converters.ConversionMixin.record2path", false]], "record2url() (conversionmixin method)": [[16, "one.converters.ConversionMixin.record2url", false]], "recurse() (in module one.converters)": [[16, "one.converters.recurse", false]], "ref2dict() (conversionmixin static method)": [[16, "one.converters.ConversionMixin.ref2dict", false]], "ref2eid() (conversionmixin method)": [[16, "one.converters.ConversionMixin.ref2eid", false]], "ref2path() (conversionmixin method)": [[16, "one.converters.ConversionMixin.ref2path", false]], "refresh() (in module one.util)": [[45, "one.util.refresh", false]], "refresh_cache() (one method)": [[14, "one.api.One.refresh_cache", false]], "regex() (in module one.alf.spec)": [[7, "one.alf.spec.regex", false]], "register_files() (registrationclient method)": [[19, "one.registration.RegistrationClient.register_files", false]], "register_session() (registrationclient method)": [[19, "one.registration.RegistrationClient.register_session", false]], "register_water_administration() (registrationclient method)": [[19, "one.registration.RegistrationClient.register_water_administration", false]], "register_weight() (registrationclient method)": [[19, "one.registration.RegistrationClient.register_weight", false]], "registrationclient (class in one.registration)": [[19, "one.registration.RegistrationClient", false]], "rel_path2url() (alyxclient method)": [[47, "one.webclient.AlyxClient.rel_path2url", false]], "rel_path_parts() (in module one.alf.files)": [[5, "one.alf.files.rel_path_parts", false]], "rel_path_spec (in module one.alf.spec)": [[7, "one.alf.spec.REL_PATH_SPEC", false], [11, "one.alf.spec.REL_PATH_SPEC", false]], "rel_ses_files (testsoneparquet attribute)": [[33, "one.tests.alf.test_cache.TestsONEParquet.rel_ses_files", false]], "rel_ses_path (testsoneparquet attribute)": [[33, "one.tests.alf.test_cache.TestsONEParquet.rel_ses_path", false]], "remove_empty_folders() (in module one.alf.io)": [[6, "one.alf.io.remove_empty_folders", false]], "remove_missing_datasets() (in module one.alf.cache)": [[3, "one.alf.cache.remove_missing_datasets", false]], "remove_uuid_file() (in module one.alf.io)": [[6, "one.alf.io.remove_uuid_file", false]], "remove_uuid_recursive() (in module one.alf.io)": [[6, "one.alf.io.remove_uuid_recursive", false]], "remove_uuid_string() (in module one.alf.files)": [[5, "one.alf.files.remove_uuid_string", false]], "repo (testaws attribute)": [[35, "one.tests.remote.test_aws.TestAWS.repo", false]], "repo_from_alyx() (downloadclient static method)": [[22, "one.remote.base.DownloadClient.repo_from_alyx", false]], "rest() (alyxclient method)": [[47, "one.webclient.AlyxClient.rest", false]], "rest_schemes (alyxclient property)": [[47, "one.webclient.AlyxClient.rest_schemes", false]], "revisions_datasets_table() (in module one.tests.util)": [[44, "one.tests.util.revisions_datasets_table", false]], "run_task() (globus method)": [[24, "one.remote.globus.Globus.run_task", false]], "s3_download_file() (in module one.remote.aws)": [[21, "one.remote.aws.s3_download_file", false]], "s3_download_folder() (in module one.remote.aws)": [[21, "one.remote.aws.s3_download_folder", false]], "save() (in module one.params)": [[17, "one.params.save", false]], "save_cache() (one method)": [[14, "one.api.One.save_cache", false]], "save_client_params() (in module one.remote.base)": [[22, "one.remote.base.save_client_params", false]], "save_loaded_ids() (one method)": [[14, "one.api.One.save_loaded_ids", false]], "save_metadata() (in module one.alf.io)": [[6, "one.alf.io.save_metadata", false]], "save_object_npy() (in module one.alf.io)": [[6, "one.alf.io.save_object_npy", false]], "search() (one method)": [[14, "one.api.One.search", false]], "search() (onealyx method)": [[14, "one.api.OneAlyx.search", false]], "search_insertions() (onealyx method)": [[14, "one.api.OneAlyx.search_insertions", false]], "search_terms() (one method)": [[14, "one.api.One.search_terms", false]], "search_terms() (onealyx method)": [[14, "one.api.OneAlyx.search_terms", false]], "ses2eid() (lazyid static method)": [[45, "one.util.LazyId.ses2eid", false]], "ses2records() (in module one.util)": [[45, "one.util.ses2records", false]], "ses_info (testsoneparquet attribute)": [[33, "one.tests.alf.test_cache.TestsONEParquet.ses_info", false]], "session_path (testalffolders attribute)": [[31, "one.tests.alf.test_alf_io.TestALFFolders.session_path", false]], "session_path_parts() (in module one.alf.files)": [[5, "one.alf.files.session_path_parts", false]], "session_record2path() (in module one.converters)": [[16, "one.converters.session_record2path", false]], "session_spec (in module one.alf.spec)": [[7, "one.alf.spec.SESSION_SPEC", false], [12, "one.alf.spec.SESSION_SPEC", false]], "set_up_env() (in module one.tests.util)": [[44, "one.tests.util.set_up_env", false]], "setup() (downloadclient static method)": [[22, "one.remote.base.DownloadClient.setup", false]], "setup() (globus static method)": [[24, "one.remote.globus.Globus.setup", false]], "setup() (in module one.params)": [[17, "one.params.setup", false]], "setup() (one static method)": [[14, "one.api.One.setup", false]], "setup() (onealyx static method)": [[14, "one.api.OneAlyx.setup", false]], "setup() (testauthentication method)": [[38, "one.tests.test_alyxclient.TestAuthentication.setUp", false]], "setup() (testbase method)": [[36, "one.tests.remote.test_base.TestBase.setUp", false]], "setup() (testdownloadhttp method)": [[38, "one.tests.test_alyxclient.TestDownloadHTTP.setUp", false]], "setup() (testfindvariants method)": [[31, "one.tests.alf.test_alf_io.TestFindVariants.setUp", false]], "setup() (testglobus method)": [[37, "one.tests.remote.test_globus.TestGlobus.setUp", false]], "setup() (testjsonfieldmethods method)": [[38, "one.tests.test_alyxclient.TestJsonFieldMethods.setUp", false]], "setup() (testonecache method)": [[41, "one.tests.test_one.TestONECache.setUp", false]], "setup() (testonedownload method)": [[41, "one.tests.test_one.TestOneDownload.setUp", false]], "setup() (testoneparamutil method)": [[42, "one.tests.test_params.TestONEParamUtil.setUp", false]], "setup() (testoneremote method)": [[41, "one.tests.test_one.TestOneRemote.setUp", false]], "setup() (testonesetup method)": [[41, "one.tests.test_one.TestOneSetup.setUp", false]], "setup() (testparamsetup method)": [[42, "one.tests.test_params.TestParamSetup.setUp", false]], "setup() (testregistrationclient method)": [[43, "one.tests.test_registration.TestRegistrationClient.setUp", false]], "setup() (testrestcache method)": [[38, "one.tests.test_alyxclient.TestRestCache.setUp", false]], "setup() (testsalf method)": [[31, "one.tests.alf.test_alf_io.TestsAlf.setUp", false]], "setup() (testsalfpartsfilters method)": [[31, "one.tests.alf.test_alf_io.TestsAlfPartsFilters.setUp", false]], "setup() (testsloadfile method)": [[31, "one.tests.alf.test_alf_io.TestsLoadFile.setUp", false]], "setup() (testsloadfilenonstandard method)": [[31, "one.tests.alf.test_alf_io.TestsLoadFileNonStandard.setUp", false]], "setup() (testsoneparquet method)": [[33, 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