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Description
Omics Integrator 2 unexpected failed when I was running tests locally. It was because it requires an internet connection. We would have to modify the source code to change this behavior. For now, this issue serves to document the behavior, and I don't intend to change it.
The error was:
E docker.errors.ContainerError: Command '['OmicsIntegrator', '-e', 'test/OmicsIntegrator2/input/oi2-edges.txt', '-p', 'test/OmicsIntegrator2/input/oi2-prizes.txt', '-o', 'test/OmicsIntegrator2/output', '--filename', 'oi2', '-w', '5', '-b', '1', '-g', '3', '-noise', '0.1', '--noisy_edges', '0', '--random_terminals', '0', '--dummyMode', 'terminals', '--seed', '2']' in image 'reedcompbio/omics-integrator-2' returned non-zero exit status 1: b'04:07:36 - OI2: INFO - Duplicated gene symbols in the prize file (we\'ll keep the max prize):\n04:07:36 - OI2: INFO - []\n04:07:36 - OI2: INFO - Members of the prize file not present in the interactome:\n04:07:36 - OI2: INFO - []\nTraceback (most recent call last):\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/connection.py", line 170, in _new_conn\n (self._dns_host, self.port), self.timeout, **extra_kw\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection\n for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):\n File "/opt/conda/envs/oi2/lib/python3.6/socket.py", line 745, in getaddrinfo\n for res in _socket.getaddrinfo(host, port, family, type, proto, flags):\nsocket.gaierror: [Errno -2] Name or service not known\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen\n chunked=chunked,\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/connectionpool.py", line 382, in _make_request\n self._validate_conn(conn)\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/connectionpool.py", line 1010, in _validate_conn\n conn.connect()\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/connection.py", line 353, in connect\n conn = self._new_conn()\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/connection.py", line 182, in _new_conn\n self, "Failed to establish a new connection: %s" % e\nurllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7ffb6fbc3ba8>: Failed to establish a new connection: [Errno -2] Name or service not known\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/requests/adapters.py", line 449, in send\n timeout=timeout\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen\n method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/urllib3/util/retry.py", line 574, in increment\n raise MaxRetryError(_pool, url, error or ResponseError(cause))\nurllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host=\'code.jquery.com\', port=443): Max retries exceeded with url: /jquery-3.2.1.slim.min.js (Caused by NewConnectionError(\'<urllib3.connection.HTTPSConnection object at 0x7ffb6fbc3ba8>: Failed to establish a new connection: [Errno -2] Name or service not known\',))\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/opt/conda/envs/oi2/bin/OmicsIntegrator", line 8, in <module>\n sys.exit(main())\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/OmicsIntegrator/__main__.py", line 83, in main\n oi.output_networkx_graph_as_interactive_html(augmented_forest, args.output_dir, args.filename+\'.html\')\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/OmicsIntegrator/graph.py", line 889, in output_networkx_graph_as_interactive_html\n filename=filename)\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/axial/axial.py", line 450, in graph\n scripts_block = _scripts_block(scripts, scripts_mode, output_dir)\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/axial/axial.py", line 81, in _scripts_block\n script_block = \'\\n\'.join([f"<script>{requests.get(script).text}</script>" for script in scripts])\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/axial/axial.py", line 81, in <listcomp>\n script_block = \'\\n\'.join([f"<script>{requests.get(script).text}</script>" for script in scripts])\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/requests/api.py", line 76, in get\n return request(\'get\', url, params=params, **kwargs)\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/requests/api.py", line 61, in request\n return session.request(method=method, url=url, **kwargs)\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/requests/sessions.py", line 542, in request\n resp = self.send(prep, **send_kwargs)\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/requests/sessions.py", line 655, in send\n r = adapter.send(request, **kwargs)\n File "/opt/conda/envs/oi2/lib/python3.6/site-packages/requests/adapters.py", line 516, in send\n raise ConnectionError(e, request=request)\nrequests.exceptions.ConnectionError: HTTPSConnectionPool(host=\'code.jquery.com\', port=443): Max retries exceeded with url: /jquery-3.2.1.slim.min.js (Caused by NewConnectionError(\'<urllib3.connection.HTTPSConnection object at 0x7ffb6fbc3ba8>: Failed to establish a new connection: [Errno -2] Name or service not known\',))\nERROR conda.cli.main_run:execute(33): Subprocess for \'conda run [\'OmicsIntegrator\', \'-e\', \'test/OmicsIntegrator2/input/oi2-edges.txt\', \'-p\', \'test/OmicsIntegrator2/input/oi2-prizes.txt\', \'-o\', \'test/OmicsIntegrator2/output\', \'--filename\', \'oi2\', \'-w\', \'5\', \'-b\', \'1\', \'-g\', \'3\', \'-noise\', \'0.1\', \'--noisy_edges\', \'0\', \'--random_terminals\', \'0\', \'--dummyMode\', \'terminals\', \'--seed\', \'2\']\' command failed. (See above for error)\n'