fix(doi): correct metadata return to use original phsids, improve doc…

docs/_build/html/_modules/gen3/auth.html

@@ -175,6 +175,10 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 <span class="sd">                that has the &#39;client_credentials&#39; grant, allowing it to obtain access tokens.</span>
 <span class="sd">        client_scopes (str, opt): Space-separated list of scopes requested for access tokens obtained from client</span>
 <span class="sd">                credentials. Default: &quot;user data openid&quot;</span>
+<span class="sd">        access_token (str, opt): provide an access token to override the use of any</span>
+<span class="sd">                API key/refresh token. This is intended for cases where you may want to</span>
+<span class="sd">                pass a token that was issued to a particular OIDC client (rather than acting on</span>
+<span class="sd">                your own direct behalf, you can provide a key that was client-issued to your user)</span>
 
 <span class="sd">    Examples:</span>
 <span class="sd">        This generates the Gen3Auth class pointed at the sandbox commons while</span>
@@ -218,13 +222,14 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
         <span class="n">idp</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
         <span class="n">client_credentials</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
         <span class="n">client_scopes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+        <span class="n">access_token</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
     <span class="p">):</span>
         <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Initializing auth..&quot;</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">endpoint</span> <span class="o">=</span> <span class="n">remove_trailing_whitespace_and_slashes_in_url</span><span class="p">(</span><span class="n">endpoint</span><span class="p">)</span>
         <span class="c1"># note - `_refresh_token` is not actually a JWT refresh token - it&#39;s a</span>
         <span class="c1">#  gen3 api key with a token as the &quot;api_key&quot; property</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_refresh_token</span> <span class="o">=</span> <span class="n">refresh_token</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_access_token</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_access_token</span> <span class="o">=</span> <span class="n">access_token</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_access_token_info</span> <span class="o">=</span> <span class="kc">None</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_wts_idp</span> <span class="o">=</span> <span class="n">idp</span> <span class="ow">or</span> <span class="s2">&quot;local&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_wts_namespace</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;NAMESPACE&quot;</span><span class="p">,</span> <span class="s2">&quot;default&quot;</span><span class="p">)</span>

docs/_build/html/auth.html

@@ -36,7 +36,7 @@
 <h1>Gen3 Auth Helper<a class="headerlink" href="#gen3-auth-helper" title="Link to this heading">¶</a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="gen3.auth.Gen3Auth">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.auth.</span></span><span class="sig-name descname"><span class="pre">Gen3Auth</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">endpoint</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refresh_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refresh_token</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">idp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">client_credentials</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">client_scopes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gen3/auth.html#Gen3Auth"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.auth.Gen3Auth" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.auth.</span></span><span class="sig-name descname"><span class="pre">Gen3Auth</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">endpoint</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refresh_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refresh_token</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">idp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">client_credentials</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">client_scopes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">access_token</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gen3/auth.html#Gen3Auth"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.auth.Gen3Auth" title="Link to this definition">¶</a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">AuthBase</span></code></p>
 <p>Gen3 auth helper class for use with requests auth.</p>
 <p>Implements requests.auth.AuthBase in order to support JWT authentication.
@@ -57,6 +57,10 @@ <h1>Gen3 Auth Helper<a class="headerlink" href="#gen3-auth-helper" title="Link t
 that has the ‘client_credentials’ grant, allowing it to obtain access tokens.</p></li>
 <li><p><strong>client_scopes</strong> (<em>str</em><em>, </em><em>opt</em>) – Space-separated list of scopes requested for access tokens obtained from client
 credentials. Default: “user data openid”</p></li>
+<li><p><strong>access_token</strong> (<em>str</em><em>, </em><em>opt</em>) – provide an access token to override the use of any
+API key/refresh token. This is intended for cases where you may want to
+pass a token that was issued to a particular OIDC client (rather than acting on
+your own direct behalf, you can provide a key that was client-issued to your user)</p></li>
 </ul>
 </dd>
 </dl>

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-1709222307.153123.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-1711461363.0524344.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-1709222307.5054574.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-1711461363.3879402.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>

docs/howto/discoveryMetadataTools.md

@@ -167,7 +167,7 @@ def test_manual_single_doi(publish_dois=False):
   # If your Discovery metadata records don't use the DOI as the GUID,
   # you may need to supply the URL yourself like below
   url = COMMONS_DISCOVERY_PAGE.rstrip("/") + f"/{gen3_metadata_guid}"
-  doi = DigitalObjectIdentifier(url=url, **doi_metadata)
+  doi = DigitalObjectIdentifier(url=url, use_prod=False, **doi_metadata)
 
   if publish_dois:
     logging.info(f"Publishing DOI `{identifier}`...")
@@ -176,7 +176,7 @@ def test_manual_single_doi(publish_dois=False):
   # works for only new DOIs
   # You can use this for updates: `datacite.update_doi(doi)`
   response = datacite.create_doi(doi)
-  doi = DigitalObjectIdentifier.from_datacite_create_doi_response(response)
+  doi = DigitalObjectIdentifier.from_datacite_create_doi_response(response, use_prod=False)
 
   # Persist necessary DOI Metadata in Gen3 Discovery to support the landing page
   metadata = datacite.persist_doi_metadata_in_gen3(
@@ -504,7 +504,7 @@ def main():
         "phs000179.v6",
     ]
     dbgapfhir = dbgapFHIR()
-    simplified_data = dbgapfhir.get_metadata_for_ids(phsids=studies)
+    simplified_data = dbgapfhir.get_metadata_for_ids(ids=studies)
     dbgapFHIR.write_data_to_file(simplified_data, "fhir_metadata_file.tsv")
 
     # Combine new FHIR Metadata with existing Discovery Metadata