Clearer error message when indexd record not found

.github/workflows/docs.yaml

@@ -20,7 +20,7 @@ jobs:
       with:
         ref: ${{github.event.pull_request.head.ref}}
         repository: ${{github.event.pull_request.head.repo.full_name}}
-        # Passing a PAT from the PlanXCybrog bot account here, since otherwise commit pushed by this action won't bale able to trigger other actions, see https://github.com/stefanzweifel/git-auto-commit-action?tab=readme-ov-file#commits-made-by-this-action-do-not-trigger-new-workflow-runs
+        # Passing a PAT from the PlanXCybrog bot account here, since otherwise commits pushed by this action won't be able to trigger other actions, see https://github.com/stefanzweifel/git-auto-commit-action?tab=readme-ov-file#commits-made-by-this-action-do-not-trigger-new-workflow-runs
         token: ${{ secrets.PLANXCYBORG_PAT }}
     - name: Set up Python 3.9
       uses: actions/setup-python@v1

docs/_build/html/_modules/gen3/index.html

@@ -82,6 +82,7 @@ <h1>Source code for gen3.index</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="ow">not</span> <span class="n">endpoint</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="n">service_location</span><span class="p">):</span>
             <span class="n">endpoint</span> <span class="o">+=</span> <span class="s2">&quot;/&quot;</span> <span class="o">+</span> <span class="n">service_location</span>
 
+        <span class="bp">self</span><span class="o">.</span><span class="n">endpoint</span> <span class="o">=</span> <span class="n">endpoint</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">client</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">IndexClient</span><span class="p">(</span><span class="n">endpoint</span><span class="p">,</span> <span class="n">auth</span><span class="o">=</span><span class="n">auth_provider</span><span class="p">)</span>
 
     <span class="c1">### Get Requests</span>
@@ -849,6 +850,10 @@ <h1>Source code for gen3.index</h1><div class="highlight"><pre>
             <span class="s2">&quot;content_updated_date&quot;</span><span class="p">:</span> <span class="n">content_updated_date</span><span class="p">,</span>
         <span class="p">}</span>
         <span class="n">rec</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">client</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">guid</span><span class="p">)</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">rec</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s2">&quot;No indexd record found for GUID &#39;</span><span class="si">{</span><span class="n">guid</span><span class="si">}</span><span class="s2">&#39; at &#39;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">endpoint</span><span class="si">}</span><span class="s2">&#39;&quot;</span>
+            <span class="p">)</span>
         <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">updatable_attrs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
             <span class="k">if</span> <span class="n">v</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
                 <span class="n">exec</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;rec.</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s2"> = v&quot;</span><span class="p">)</span>

docs/_build/html/tools/indexing.html

@@ -381,7 +381,7 @@ <h1>Indexing Tools<a class="headerlink" href="#indexing-tools" title="Link to th
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.indexing.verify_manifest.async_verify_object_manifest">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1739488230.1381567.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1745256298.5438318.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Link to this definition">¶</a></dt>
 <dd><p>Verify all file object records into a manifest csv</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/_build/html/tools/metadata.html

@@ -102,7 +102,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Link to th
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1739488230.392749.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1745256298.8196251.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Link to this definition">¶</a></dt>
 <dd><p>Ingest all metadata records into a manifest csv</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

gen3/cli/discovery.py

@@ -55,7 +55,7 @@ def discovery():
     "guid_field",
     help=(
         'The column / field name within the metadata that will be used as GUIDs, if not specified, will try to find a column \ field named "guid" from the metadata.'
-        "If that field doesn't exists in a certain metadata record, that record will be skipped from publishing."
+        "If that field doesn't exist in a certain metadata record, that record will be skipped from publishing."
     ),
     default=None,
     show_default=True,

gen3/index.py

@@ -48,6 +48,7 @@ def __init__(self, endpoint=None, auth_provider=None, service_location="index"):
         if not endpoint.endswith(service_location):
             endpoint += "/" + service_location
 
+        self.endpoint = endpoint
         self.client = client.IndexClient(endpoint, auth=auth_provider)
 
     ### Get Requests
@@ -747,6 +748,10 @@ def update_record(
             "content_updated_date": content_updated_date,
         }
         rec = self.client.get(guid)
+        if not rec:
+            raise ValueError(
+                f"No indexd record found for GUID '{guid}' at '{self.endpoint}'"
+            )
         for k, v in updatable_attrs.items():
             if v is not None:
                 exec(f"rec.{k} = v")

gen3/tools/metadata/discovery.py

@@ -403,7 +403,7 @@ async def publish_discovery_metadata(
         endpoint (str): HOSTNAME of a Gen3 environment, defaults to None
         omit_empty_values (bool): whether to exclude fields with empty values from the published discovery metadata, defaults to False
         guid_type (str): intended GUID type for publishing, defaults to discovery_metadata
-        guid_field (str): specify a field from the metadata that will be used as GUIDs, if not specified, will try to find a field named "guid" from the metadata, if that field doesn't exists in a certain metadata record, that record will be skipped from publishing, defaults to None
+        guid_field (str): specify a field from the metadata that will be used as GUIDs, if not specified, will try to find a field named "guid" from the metadata, if that field doesn't exist in a certain metadata record, that record will be skipped from publishing, defaults to None
         is_unregistered_metadata (bool): (for use by "study registration" feature only) whether to publish metadata as unregistered study metadata, defaults to False
         reset_unregistered_metadata (bool): (for use by "study registration" feature only) whether to reset existing study metadata back to unregistered study metadata if they exists in the local file, defaults to False
         update_registered_metadata (bool): (for use by "study registration" feature only) whether to update existing study metadata with new values if they exists in the local file, defaults to True