Merge pull request #258 from uc-cdis/chore/allow-zero-size-downloads

Allow downloads of zero-size files

Author: george42-ctds

docs/_build/doctrees/environment.pickle

@@ -605,8 +605,7 @@ <h1>Source code for gen3.tools.download.drs_download</h1><div class="highlight">
     <span class="n">total_size_in_bytes</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">response</span><span class="o">.</span><span class="n">headers</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;content-length&quot;</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
 
     <span class="k">if</span> <span class="n">total_size_in_bytes</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-        <span class="n">logger</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;content-length is 0 and it should not be&quot;</span><span class="p">)</span>
-        <span class="k">return</span> <span class="kc">False</span>
+        <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;content-length is 0&quot;</span><span class="p">)</span>
 
     <span class="n">total_downloaded</span> <span class="o">=</span> <span class="mi">0</span>
     <span class="n">block_size</span> <span class="o">=</span> <span class="mi">8092</span>  <span class="c1"># 8K blocks might want to tune this.</span>

docs/_build/doctrees/tools/indexing.doctree

@@ -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-1747297958.7929213.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-1748891720.2872934.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/doctrees/tools/metadata.doctree

@@ -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-1747297959.0458963.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-1748891720.5462613.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/_build/html/_modules/gen3/tools/download/drs_download.html

@@ -549,8 +549,7 @@ def download_file_from_url(
     total_size_in_bytes = int(response.headers.get("content-length", 0))
 
     if total_size_in_bytes == 0:
-        logger.critical(f"content-length is 0 and it should not be")
-        return False
+        logger.warning(f"content-length is 0")
 
     total_downloaded = 0
     block_size = 8092  # 8K blocks might want to tune this.

docs/_build/html/searchindex.js

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "gen3"
 homepage = "https://gen3.org/"
-version = "4.27.0"
+version = "4.27.1"
 description = "Gen3 CLI and Python SDK"
 authors = ["Center for Translational Data Science at the University of Chicago <[email protected]>"]
 license = "Apache-2.0"

docs/_build/html/tools/indexing.html

@@ -286,6 +286,23 @@ def test_get_external_wts_oidc(wts_oidc, hostname):
             assert isinstance(exc, requests.exceptions.HTTPError) is True
 
 
+def test_download_file_from_url_zero_size(download_dir):
+    with requests_mock.Mocker() as m:
+        m.get(
+            url=f"https://test.commons1.io/ga4gh/drs/v1/objects/blah/access/s3",
+            headers={"content-length": "0"},
+            text="",
+        )
+
+        assert (
+            download_file_from_url(
+                "https://test.commons1.io/ga4gh/drs/v1/objects/blah/access/s3",
+                "empty_file",
+            )
+            is True
+        )
+
+
 def test_download_file_from_url_failures(download_dir):
     with requests_mock.Mocker() as m:
         m.get(