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paulineribeyre merged 2 commits into from
Aug 27, 2026
+20 −12
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Gen3Submission: error check fixes #316

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05248e0
Gen3Submission: error check fixes
paulineribeyre Aug 27, 2026
baedd4d
Apply automatic documentation changes
paulineribeyre Aug 27, 2026
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16 changes: 10 additions & 6 deletions docs/_build/html/_modules/gen3/submission.html
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Original file line number Diff line number Diff line change
Expand Up @@ -314,11 +314,11 @@ <h1>Source code for gen3.submission</h1><div class="highlight"><pre>
<span class="n">uuids_to_delete</span> <span class="o">=</span> <span class="n">uuids</span><span class="p">[</span><span class="n">batch_size</span> <span class="o">*</span> <span class="n">i</span> <span class="p">:</span> <span class="n">batch_size</span> <span class="o">*</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)]</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">uuids_to_delete</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span>
<span class="s2">"</span><span class="si">{}</span><span class="s2">/</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">api_url</span><span class="p">,</span> <span class="s2">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">uuids_to_delete</span><span class="p">)),</span>
<span class="n">auth</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_auth_provider</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span>
<span class="s2">"</span><span class="si">{}</span><span class="s2">/</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">api_url</span><span class="p">,</span> <span class="s2">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">uuids_to_delete</span><span class="p">)),</span>
<span class="n">auth</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_auth_provider</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">raise_for_status_and_print_error</span><span class="p">(</span><span class="n">output</span><span class="p">)</span>
<span class="k">except</span> <span class="n">requests</span><span class="o">.</span><span class="n">exceptions</span><span class="o">.</span><span class="n">HTTPError</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span>
Expand Down Expand Up @@ -423,7 +423,9 @@ <h1>Source code for gen3.submission</h1><div class="highlight"><pre>
<span class="n">api_url</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/api/v0/submission/</span><span class="si">{}</span><span class="s2">/</span><span class="si">{}</span><span class="s2">/export?ids=</span><span class="si">{}</span><span class="s2">&amp;format=</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_endpoint</span><span class="p">,</span> <span class="n">program</span><span class="p">,</span> <span class="n">project</span><span class="p">,</span> <span class="n">uuid</span><span class="p">,</span> <span class="n">fileformat</span>
<span class="p">)</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">api_url</span><span class="p">,</span> <span class="n">auth</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_auth_provider</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
<span class="n">response</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">api_url</span><span class="p">,</span> <span class="n">auth</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_auth_provider</span><span class="p">)</span>
<span class="n">raise_for_status_and_print_error</span><span class="p">(</span><span class="n">response</span><span class="p">)</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">response</span><span class="o">.</span><span class="n">text</span>
<span class="k">if</span> <span class="n">filename</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">if</span> <span class="n">fileformat</span> <span class="o">==</span> <span class="s2">"json"</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
Expand Down Expand Up @@ -462,7 +464,9 @@ <h1>Source code for gen3.submission</h1><div class="highlight"><pre>
<span class="n">api_url</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/api/v0/submission/</span><span class="si">{}</span><span class="s2">/</span><span class="si">{}</span><span class="s2">/export/?node_label=</span><span class="si">{}</span><span class="s2">&amp;format=</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_endpoint</span><span class="p">,</span> <span class="n">program</span><span class="p">,</span> <span class="n">project</span><span class="p">,</span> <span class="n">node_type</span><span class="p">,</span> <span class="n">fileformat</span>
<span class="p">)</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">api_url</span><span class="p">,</span> <span class="n">auth</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_auth_provider</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
<span class="n">response</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">api_url</span><span class="p">,</span> <span class="n">auth</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_auth_provider</span><span class="p">)</span>
<span class="n">raise_for_status_and_print_error</span><span class="p">(</span><span class="n">response</span><span class="p">)</span>
<span class="n">output</span> <span class="o">=</span> <span class="n">response</span><span class="o">.</span><span class="n">text</span>
<span class="k">if</span> <span class="n">filename</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">if</span> <span class="n">fileformat</span> <span class="o">==</span> <span class="s2">"json"</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
Expand Down
16 changes: 10 additions & 6 deletions gen3/submission.py
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Original file line number Diff line number Diff line change
Expand Up @@ -247,11 +247,11 @@ def delete_records(self, program, project, uuids, batch_size=100):
uuids_to_delete = uuids[batch_size * i : batch_size * (i + 1)]
if len(uuids_to_delete) == 0:
break
output = requests.delete(
"{}/{}".format(api_url, ",".join(uuids_to_delete)),
auth=self._auth_provider,
)
try:
output = requests.delete(
"{}/{}".format(api_url, ",".join(uuids_to_delete)),
auth=self._auth_provider,
)
raise_for_status_and_print_error(output)
except requests.exceptions.HTTPError:
print(
Expand Down Expand Up @@ -347,7 +347,9 @@ def export_record(self, program, project, uuid, fileformat, filename=None):
api_url = "{}/api/v0/submission/{}/{}/export?ids={}&format={}".format(
self._endpoint, program, project, uuid, fileformat
)
output = requests.get(api_url, auth=self._auth_provider).text
response = requests.get(api_url, auth=self._auth_provider)
raise_for_status_and_print_error(response)
output = response.text
if filename is None:
if fileformat == "json":
try:
Expand Down Expand Up @@ -383,7 +385,9 @@ def export_node(self, program, project, node_type, fileformat, filename=None):
api_url = "{}/api/v0/submission/{}/{}/export/?node_label={}&format={}".format(
self._endpoint, program, project, node_type, fileformat
)
output = requests.get(api_url, auth=self._auth_provider).text
response = requests.get(api_url, auth=self._auth_provider)
raise_for_status_and_print_error(response)
output = response.text
if filename is None:
if fileformat == "json":
try:
Expand Down
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