"# First import the library Gargantext Notebook\n",
"from gargantext_notebook import *\n",
"\n",
"# This enables to draw graphics later\n",
"%matplotlib inline "
"# Others example"
]
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {
"collapsed": true,
"deletable": true,
"editable": true
},
"outputs": [],
"source": [
"for doc in new_docs:\n",
" new_doc = (Node( user_id = project.user_id\n",
" , parent_id = corpus.id\n",
" , typename= 'DOCUMENT'\n",
" , name=doc[\"title\"][:50]\n",
" , hyperdata=doc)\n",
" )\n",
" session.add(new_doc)\n",
"session.commit()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false,
"deletable": true,
...
...
@@ -79,9 +263,9 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 5,
"metadata": {
"collapsed": false,
"collapsed": true,
"deletable": true,
"editable": true
},
...
...
@@ -93,7 +277,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 6,
"metadata": {
"collapsed": false,
"deletable": true,
...
...
@@ -106,7 +290,7 @@
"'Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference.'"
]
},
"execution_count": 10,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
...
...
@@ -119,7 +303,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 7,
"metadata": {
"collapsed": false,
"deletable": true,
...
...
@@ -132,7 +316,7 @@
"\"The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB's goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.\""
]
},
"execution_count": 8,
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
...
...
@@ -144,7 +328,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 8,
"metadata": {
"collapsed": false,
"deletable": true,
...
...
@@ -157,7 +341,7 @@
"'Shoba Ranganathan, Christian Schönbach, Janet Kelso, Burkhard Rost, Sheila Nathan, Tin Wee Tan'"
]
},
"execution_count": 10,
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
...
...
@@ -169,7 +353,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 9,
"metadata": {
"collapsed": false,
"deletable": true,
...
...
@@ -182,7 +366,7 @@
"'BMC bioinformatics'"
]
},
"execution_count": 11,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
...
...
@@ -194,7 +378,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 10,
"metadata": {
"collapsed": true,
"deletable": true,
...
...
@@ -208,7 +392,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 11,
"metadata": {
"collapsed": false,
"deletable": true,
...
...
@@ -218,18 +402,18 @@
{
"data": {
"text/plain": [
"<matplotlib.axes._subplots.AxesSubplot at 0x7fc48a3da128>"
"<matplotlib.axes._subplots.AxesSubplot at 0x7f48069c5208>"
" (False, '\"This is an english paragraph.\\n\\nThis is an english paragraph.\\n ')]"
]
},
"execution_count": 11,
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
...
...
@@ -483,7 +624,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": null,
"metadata": {
"collapsed": true,
"deletable": true,
...
...
@@ -506,7 +647,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 16,
"metadata": {
"collapsed": false,
"deletable": true,
...
...
@@ -514,14 +655,42 @@
},
"outputs": [
{
"data": {
"text/plain": [
"154"
"ename": "ConnectionError",
"evalue": "HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))",
"\u001b[0;32m/home/alexandre/local/logiciels/python/env/3.5_20170123/lib/python3.5/site-packages/requests/packages/urllib3/connection.py\u001b[0m in \u001b[0;36m_new_conn\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 150\u001b[0m raise NewConnectionError(\n\u001b[0;32m--> 151\u001b[0;31m self, \"Failed to establish a new connection: %s\" % e)\n\u001b[0m\u001b[1;32m 152\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mNewConnectionError\u001b[0m: <requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mMaxRetryError\u001b[0m: HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;32m<ipython-input-16-b220cbbc8ecc>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mscan_hal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"machine learning AND deep\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/home/alexandre/local/logiciels/python/env/3.5_20170123/lib/python3.5/site-packages/requests/sessions.py\u001b[0m in \u001b[0;36msend\u001b[0;34m(self, request, **kwargs)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 584\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--> 585\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 586\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 587\u001b[0m \u001b[0;31m# Total elapsed time of the request (approximately)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mConnectionError\u001b[0m: HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))"
