{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from ontobio.ontol_factory import OntologyFactory\n",
"\n",
"# Create ontology object, for GO\n",
"# Transparently uses remote SPARQL service.\n",
"# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do\n",
"# not re-execute cell)\n",
"ofactory = OntologyFactory()\n",
"ont = ofactory.create('go')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from ontobio.assoc_factory import AssociationSetFactory\n",
"\n",
"MOUSE = 'NCBITaxon:10090'\n",
"\n",
"# Create association set\n",
"# Transparently uses remote Monarch service.\n",
"# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do\n",
"# not re-execute cell)\n",
"afactory = AssociationSetFactory()\n",
"aset = afactory.create(ontology=ont,\n",
" subject_category='gene',\n",
" object_category='function',\n",
" taxon=MOUSE)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"aset.subjects[0:5]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"aset.jaccard_similarity('MGI:1929214', 'MGI:1917826')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"HUMAN = 'NCBITaxon:9606'\n",
"\n",
"# Create association set\n",
"# Transparently uses remote Monarch service.\n",
"# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do\n",
"# not re-execute cell)\n",
"afactory = AssociationSetFactory()\n",
"aset_human = afactory.create(ontology=ont,\n",
" subject_category='gene',\n",
" object_category='function',\n",
" taxon=HUMAN)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"ERROR:pysolr:Connection to server 'http://golr.berkeleybop.org/select/?q=%2A%3A%2A&fq=document_category%3A%22annotation%22&fq=taxon_closure%3A%22NCBITaxon%3A7955%22&facet=off&facet.limit=0&facet.mincount=1&fl=bioentity%2Cbioentity_label%2Cqualifier%2Cannotation_class&rows=100000&wt=json' timed out: HTTPConnectionPool(host='golr.berkeleybop.org', port=80): Read timed out. (read timeout=4)\n",
"Traceback (most recent call last):\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\", line 387, in _make_request\n",
" six.raise_from(e, None)\n",
" File \"<string>\", line 2, in raise_from\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\", line 383, in _make_request\n",
" httplib_response = conn.getresponse()\n",
" File \"/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py\", line 1331, in getresponse\n",
" response.begin()\n",
" File \"/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py\", line 297, in begin\n",
" version, status, reason = self._read_status()\n",
" File \"/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py\", line 258, in _read_status\n",
" line = str(self.fp.readline(_MAXLINE + 1), \"iso-8859-1\")\n",
" File \"/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/socket.py\", line 586, in readinto\n",
" return self._sock.recv_into(b)\n",
"socket.timeout: timed out\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/requests/adapters.py\", line 440, in send\n",
" timeout=timeout\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\", line 639, in urlopen\n",
" _stacktrace=sys.exc_info()[2])\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/util/retry.py\", line 357, in increment\n",
" raise six.reraise(type(error), error, _stacktrace)\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/packages/six.py\", line 686, in reraise\n",
" raise value\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\", line 601, in urlopen\n",
" chunked=chunked)\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\", line 389, in _make_request\n",
" self._raise_timeout(err=e, url=url, timeout_value=read_timeout)\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\", line 309, in _raise_timeout\n",
" raise ReadTimeoutError(self, url, \"Read timed out. (read timeout=%s)\" % timeout_value)\n",
"urllib3.exceptions.ReadTimeoutError: HTTPConnectionPool(host='golr.berkeleybop.org', port=80): Read timed out. (read timeout=4)\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/pysolr.py\", line 366, in _send_request\n",
" timeout=self.timeout)\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/requests/sessions.py\", line 515, in get\n",
" return self.request('GET', url, **kwargs)\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/requests/sessions.py\", line 502, in request\n",
" resp = self.send(prep, **send_kwargs)\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/requests/sessions.py\", line 612, in send\n",
" r = adapter.send(request, **kwargs)\n",
" File \"/Users/cjm/repos/ontobio/venv/lib/python3.6/site-packages/requests/adapters.py\", line 516, in send\n",
" raise ReadTimeout(e, request=request)\n",
"requests.exceptions.ReadTimeout: HTTPConnectionPool(host='golr.berkeleybop.org', port=80): Read timed out. (read timeout=4)\n"
]
},
{
"ename": "SolrError",
"evalue": "Connection to server 'http://golr.berkeleybop.org/select/?q=%2A%3A%2A&fq=document_category%3A%22annotation%22&fq=taxon_closure%3A%22NCBITaxon%3A7955%22&facet=off&facet.limit=0&facet.mincount=1&fl=bioentity%2Cbioentity_label%2Cqualifier%2Cannotation_class&rows=100000&wt=json' timed out: HTTPConnectionPool(host='golr.berkeleybop.org', port=80): Read timed out. (read timeout=4)",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mtimeout\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\u001b[0m in \u001b[0;36m_make_request\u001b[0;34m(self, conn, method, url, timeout, chunked, **httplib_request_kw)\u001b[0m\n\u001b[1;32m 386\u001b[0m \u001b[0;31m# otherwise it looks like a programming error was the cause.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 387\u001b[0;31m \u001b[0msix\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraise_from\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0me\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 388\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mSocketTimeout\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mBaseSSLError\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mSocketError\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/packages/six.py\u001b[0m in \u001b[0;36mraise_from\u001b[0;34m(value, from_value)\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\u001b[0m in \u001b[0;36m_make_request\u001b[0;34m(self, conn, method, url, timeout, chunked, **httplib_request_kw)\u001b[0m\n\u001b[1;32m 382\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 383\u001b[0;31m \u001b[0mhttplib_response\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgetresponse\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 384\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py\u001b[0m in \u001b[0;36mgetresponse\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1330\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1331\u001b[0;31m \u001b[0mresponse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbegin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1332\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mConnectionError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py\u001b[0m in \u001b[0;36mbegin\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 296\u001b[0m \u001b[0;32mwhile\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 297\u001b[0;31m \u001b[0mversion\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstatus\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreason\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_read_status\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 298\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mstatus\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0mCONTINUE\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py\u001b[0m in \u001b[0;36m_read_status\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 257\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_read_status\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 258\u001b[0;31m \u001b[0mline\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreadline\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_MAXLINE\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"iso-8859-1\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 259\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0m_MAXLINE\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/socket.py\u001b[0m in \u001b[0;36mreadinto\u001b[0;34m(self, b)\u001b[0m\n\u001b[1;32m 585\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 586\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_sock\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv_into\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 587\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mtimeout\u001b[0m: timed out",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mReadTimeoutError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/requests/adapters.py\u001b[0m in \u001b[0;36msend\u001b[0;34m(self, request, stream, timeout, verify, cert, proxies)\u001b[0m\n\u001b[1;32m 439\u001b[0m \u001b[0mretries\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmax_retries\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 440\u001b[0;31m \u001b[0mtimeout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 441\u001b[0m )\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\u001b[0m in \u001b[0;36murlopen\u001b[0;34m(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)\u001b[0m\n\u001b[1;32m 638\u001b[0m retries = retries.increment(method, url, error=e, _pool=self,\n\u001b[0;32m--> 639\u001b[0;31m _stacktrace=sys.exc_info()[2])\n\u001b[0m\u001b[1;32m 640\u001b[0m \u001b[0mretries\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msleep\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/util/retry.py\u001b[0m in \u001b[0;36mincrement\u001b[0;34m(self, method, url, response, error, _pool, _stacktrace)\u001b[0m\n\u001b[1;32m 356\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mread\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mFalse\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_is_method_retryable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmethod\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 357\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0msix\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreraise\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merror\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0merror\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_stacktrace\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 358\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0mread\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/packages/six.py\u001b[0m in \u001b[0;36mreraise\u001b[0;34m(tp, value, tb)\u001b[0m\n\u001b[1;32m 685\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwith_traceback\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 686\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 687\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\u001b[0m in \u001b[0;36murlopen\u001b[0;34m(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)\u001b[0m\n\u001b[1;32m 600\u001b[0m \u001b[0mbody\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mbody\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mheaders\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mheaders\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 601\u001b[0;31m chunked=chunked)\n\u001b[0m\u001b[1;32m 602\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\u001b[0m in \u001b[0;36m_make_request\u001b[0;34m(self, conn, method, url, timeout, chunked, **httplib_request_kw)\u001b[0m\n\u001b[1;32m 388\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mSocketTimeout\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mBaseSSLError\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mSocketError\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 389\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_raise_timeout\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merr\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0me\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout_value\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mread_timeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 390\u001b[0m \u001b[0;32mraise\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/urllib3/connectionpool.py\u001b[0m in \u001b[0;36m_raise_timeout\u001b[0;34m(self, err, url, timeout_value)\u001b[0m\n\u001b[1;32m 308\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mSocketTimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 309\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mReadTimeoutError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Read timed out. (read timeout=%s)\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mtimeout_value\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 310\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mReadTimeoutError\u001b[0m: HTTPConnectionPool(host='golr.berkeleybop.org', port=80): Read timed out. (read timeout=4)",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mReadTimeout\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/pysolr.py\u001b[0m in \u001b[0;36m_send_request\u001b[0;34m(self, method, path, body, headers, files)\u001b[0m\n\u001b[1;32m 365\u001b[0m resp = requests_method(url, data=bytes_body, headers=headers, files=files,\n\u001b[0;32m--> 366\u001b[0;31m timeout=self.timeout)\n\u001b[0m\u001b[1;32m 367\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mrequests\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexceptions\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mTimeout\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/requests/sessions.py\u001b[0m in \u001b[0;36mget\u001b[0;34m(self, url, **kwargs)\u001b[0m\n\u001b[1;32m 514\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetdefault\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'allow_redirects'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 515\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrequest\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'GET'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 516\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/requests/sessions.py\u001b[0m in \u001b[0;36mrequest\u001b[0;34m(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)\u001b[0m\n\u001b[1;32m 501\u001b[0m \u001b[0msend_kwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msettings\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 502\u001b[0;31m \u001b[0mresp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprep\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0msend_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 503\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/requests/sessions.py\u001b[0m in \u001b[0;36msend\u001b[0;34m(self, request, **kwargs)\u001b[0m\n\u001b[1;32m 611\u001b[0m \u001b[0;31m# Send the request\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 612\u001b[0;31m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0madapter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrequest\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 613\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/requests/adapters.py\u001b[0m in \u001b[0;36msend\u001b[0;34m(self, request, stream, timeout, verify, cert, proxies)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0me\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mReadTimeoutError\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 516\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mReadTimeout\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0me\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrequest\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mrequest\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 517\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mReadTimeout\u001b[0m: HTTPConnectionPool(host='golr.berkeleybop.org', port=80): Read timed out. (read timeout=4)",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mSolrError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-10-79ea128c10b8>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0msubject_category\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'gene'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0mobject_category\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'function'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m taxon=ZFISH)\n\u001b[0m",
"\u001b[0;32m~/repos/ontobio/ontobio/assoc_factory.py\u001b[0m in \u001b[0;36mcreate\u001b[0;34m(self, ontology, subject_category, object_category, evidence, taxon, relation, file, fmt)\u001b[0m\n\u001b[1;32m 62\u001b[0m \u001b[0mobject_category\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mobject_category\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 63\u001b[0m \u001b[0mevidence\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mevidence\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 64\u001b[0;31m taxon=taxon)\n\u001b[0m\u001b[1;32m 65\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 66\u001b[0m \u001b[0mlogging\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Creating map for {} subjects\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0massocs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/cachier/core.py\u001b[0m in \u001b[0;36mfunc_wrapper\u001b[0;34m(*args, **kwds)\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mcore\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait_on_entry_calc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 175\u001b[0m \u001b[0m_print\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'No entry found. No current calc. Calling like a boss.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 176\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0m_calc_entry\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcore\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 177\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 178\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mclear_cache\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/cachier/core.py\u001b[0m in \u001b[0;36m_calc_entry\u001b[0;34m(core, key, func, args, kwds)\u001b[0m\n\u001b[1;32m 74\u001b[0m \u001b[0mcore\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmark_entry_being_calculated\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 75\u001b[0m \u001b[0;31m# _get_executor().submit(core.mark_entry_being_calculated, key)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 76\u001b[0;31m \u001b[0mfunc_res\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 77\u001b[0m \u001b[0mcore\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_entry\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfunc_res\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 78\u001b[0m \u001b[0;31m# _get_executor().submit(core.set_entry, key, func_res)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/ontobio/assoc_factory.py\u001b[0m in \u001b[0;36mbulk_fetch_cached\u001b[0;34m(**args)\u001b[0m\n\u001b[1;32m 189\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mbulk_fetch_cached\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 190\u001b[0m \u001b[0mlogging\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Fetching assocs from store (will be cached)\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 191\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mbulk_fetch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/repos/ontobio/ontobio/golr/golr_associations.py\u001b[0m in \u001b[0;36mbulk_fetch\u001b[0;34m(subject_category, object_category, taxon, rows, **kwargs)\u001b[0m\n\u001b[1;32m 144\u001b[0m \u001b[0mrows\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mrows\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 145\u001b[0m \u001b[0miterate\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 146\u001b[0;31m **kwargs)\n\u001b[0m\u001b[1;32m 147\u001b[0m \u001b[0mlogging\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Rows retrieved: {}\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0massocs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 148\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0massocs\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/ontobio/golr/golr_associations.py\u001b[0m in \u001b[0;36msearch_associations_compact\u001b[0;34m(**kwargs)\u001b[0m\n\u001b[1;32m 75\u001b[0m searchresult = search_associations(use_compact_associations=True,\n\u001b[1;32m 76\u001b[0m \u001b[0mfacet_fields\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 77\u001b[0;31m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 78\u001b[0m )\n\u001b[1;32m 79\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0msearchresult\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'compact_associations'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/ontobio/golr/golr_associations.py\u001b[0m in \u001b[0;36msearch_associations\u001b[0;34m(**kwargs)\u001b[0m\n\u001b[1;32m 31\u001b[0m \u001b[0mlogging\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"CREATING_GOLR_QUERY {}\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 32\u001b[0m \u001b[0mq\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mGolrAssociationQuery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 33\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexec\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 34\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 35\u001b[0m def get_objects_for_subject(subject=None,\n",
"\u001b[0;32m~/repos/ontobio/ontobio/golr/golr_query.py\u001b[0m in \u001b[0;36mexec\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m 886\u001b[0m \u001b[0mparams\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolr_params\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 887\u001b[0m \u001b[0mlogging\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"PARAMS=\"\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mparams\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 888\u001b[0;31m \u001b[0mresults\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msearch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mparams\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 889\u001b[0m \u001b[0mn_docs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresults\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdocs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 890\u001b[0m \u001b[0mlogging\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Docs found: {}\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresults\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhits\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/pysolr.py\u001b[0m in \u001b[0;36msearch\u001b[0;34m(self, q, search_handler, **kwargs)\u001b[0m\n\u001b[1;32m 718\u001b[0m \u001b[0mparams\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m'q'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mq\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 719\u001b[0m \u001b[0mparams\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 720\u001b[0;31m \u001b[0mresponse\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_select\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mparams\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhandler\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0msearch_handler\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 721\u001b[0m \u001b[0mdecoded\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecoder\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresponse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 722\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/pysolr.py\u001b[0m in \u001b[0;36m_select\u001b[0;34m(self, params, handler)\u001b[0m\n\u001b[1;32m 416\u001b[0m \u001b[0;31m# Typical case.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 417\u001b[0m \u001b[0mpath\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'%s/?%s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mhandler\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparams_encoded\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 418\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_send_request\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'get'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 419\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 420\u001b[0m \u001b[0;31m# Handles very long queries by submitting as a POST.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/repos/ontobio/venv/lib/python3.6/site-packages/pysolr.py\u001b[0m in \u001b[0;36m_send_request\u001b[0;34m(self, method, path, body, headers, files)\u001b[0m\n\u001b[1;32m 368\u001b[0m \u001b[0merror_message\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"Connection to server '%s' timed out: %s\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 369\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlog\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0merror\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merror_message\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mexc_info\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 370\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mSolrError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merror_message\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 371\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mrequests\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexceptions\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mConnectionError\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 372\u001b[0m \u001b[0merror_message\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"Failed to connect to server at '%s', are you sure that URL is correct? Checking it in a browser might help: %s\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mSolrError\u001b[0m: Connection to server 'http://golr.berkeleybop.org/select/?q=%2A%3A%2A&fq=document_category%3A%22annotation%22&fq=taxon_closure%3A%22NCBITaxon%3A7955%22&facet=off&facet.limit=0&facet.mincount=1&fl=bioentity%2Cbioentity_label%2Cqualifier%2Cannotation_class&rows=100000&wt=json' timed out: HTTPConnectionPool(host='golr.berkeleybop.org', port=80): Read timed out. (read timeout=4)"
]
}
],
"source": [
"ZFISH = 'NCBITaxon:7955'\n",
"\n",
"# Create association set\n",
"# Transparently uses remote Monarch service.\n",
"# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do\n",
"# not re-execute cell)\n",
"afactory = AssociationSetFactory()\n",
"aset_zfish = afactory.create(ontology=ont,\n",
" subject_category='gene',\n",
" object_category='function',\n",
" taxon=ZFISH)"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"# TODO - do not re-read\n",
"aset = afa.create_from_gaf(url, ontology=ont)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"334682"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from collections import defaultdict\n",
"rmap = defaultdict(set)\n",
"for a in assocs:\n",
" ev = a['evidence']['type']\n",
" gene = a['subject']['id']\n",
" p = a['object']['id']\n",
" up = process_regulates(p)\n",
" for rp in up:\n",
" rmap[(gene,rp)].add('R')\n",
" rmap[(gene,p)].add('I')\n",
" \n",
"\n",
"len(rmap)"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"4921"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mixed = [(k,v) for (k,v) in rmap.items() if len(v)>1]\n",
"len(mixed)"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[(('MGI:MGI:102890', 'GO:0007049'), {'I', 'R'}),\n",
" (('MGI:MGI:1915332', 'GO:0007254'), {'I', 'R'}),\n",
" (('MGI:MGI:1338799', 'GO:0006351'), {'I', 'R'}),\n",
" (('MGI:MGI:2135607', 'GO:0006476'), {'I', 'R'}),\n",
" (('MGI:MGI:96960', 'GO:0006914'), {'I', 'R'}),\n",
" (('MGI:MGI:2183426', 'GO:0060070'), {'I', 'R'}),\n",
" (('MGI:MGI:1860488', 'GO:0007596'), {'I', 'R'}),\n",
" (('MGI:MGI:1346348', 'GO:0006366'), {'I', 'R'}),\n",
" (('MGI:MGI:107179', 'GO:0003700'), {'I', 'R'}),\n",
" (('MGI:MGI:1927468', 'GO:0045087'), {'I', 'R'}),\n",
" (('MGI:MGI:2443584', 'GO:0006351'), {'I', 'R'}),\n",
" (('MGI:MGI:109452', 'GO:0051216'), {'I', 'R'}),\n",
" (('MGI:MGI:1913464', 'GO:0007049'), {'I', 'R'}),\n",
" (('MGI:MGI:1913744', 'GO:0006915'), {'I', 'R'}),\n",
" (('MGI:MGI:2684845', 'GO:0007623'), {'I', 'R'}),\n",
" (('MGI:MGI:1202890', 'GO:0001525'), {'I', 'R'}),\n",
" (('MGI:MGI:97844', 'GO:0006887'), {'I', 'R'}),\n",
" (('MGI:MGI:1891227', 'GO:0003677'), {'I', 'R'}),\n",
" (('MGI:MGI:99474', 'GO:0016567'), {'I', 'R'}),\n",
" (('MGI:MGI:108409', 'GO:0007186'), {'I', 'R'})]"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mixed[0:20]"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'cell cycle'"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ont.label('GO:0007049')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}