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Merge pull request MSUSAzureAccelerators#65 from MSUSAzureAccelerators/main
update utils.py
2 parents d8f3b29 + 7d3441b commit 0af66f6

11 files changed

+1281
-527
lines changed

‎01-Load-Data-ACogSearch.ipynb

+15-11
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@@ -548,7 +548,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 20,
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"execution_count": 15,
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"metadata": {
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"tags": []
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},
@@ -559,20 +559,24 @@
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"text": [
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"200\n",
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"Status: inProgress\n",
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"Items Processed: 3250\n",
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"Items Processed: 400\n",
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"True\n"
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]
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}
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],
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"source": [
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"# Optionally, get indexer status to confirm that it's running\n",
569-
"r = requests.get(os.environ['AZURE_SEARCH_ENDPOINT'] + \"/indexers/\" + indexer_name +\n",
570-
" \"/status\", headers=headers, params=params)\n",
571-
"# pprint(json.dumps(r.json(), indent=1))\n",
572-
"print(r.status_code)\n",
573-
"print(\"Status:\",r.json().get('lastResult').get('status'))\n",
574-
"print(\"Items Processed:\",r.json().get('lastResult').get('itemsProcessed'))\n",
575-
"print(r.ok)"
569+
"try:\n",
570+
" r = requests.get(os.environ['AZURE_SEARCH_ENDPOINT'] + \"/indexers/\" + indexer_name +\n",
571+
" \"/status\", headers=headers, params=params)\n",
572+
" # pprint(json.dumps(r.json(), indent=1))\n",
573+
" print(r.status_code)\n",
574+
" print(\"Status:\",r.json().get('lastResult').get('status'))\n",
575+
" print(\"Items Processed:\",r.json().get('lastResult').get('itemsProcessed'))\n",
576+
" print(r.ok)\n",
577+
" \n",
578+
"except Exception as e:\n",
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" print(\"Wait a few seconds until the process starts and run this cell again.\")"
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]
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},
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{
@@ -609,14 +613,14 @@
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"execution_count": 16,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"204\n",
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"201\n",
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"True\n"
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]
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}

‎02-LoadCSVOneToMany-ACogSearch.ipynb

+56-52
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@@ -148,69 +148,69 @@
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"text/html": [
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"<style type=\"text/css\">\n",
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"</style>\n",
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"<table id=\"T_6ac41\">\n",
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"<table id=\"T_87464\">\n",
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" <thead>\n",
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" <tr>\n",
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" <th class=\"blank level0\" >&nbsp;</th>\n",
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" <th id=\"T_6ac41_level0_col0\" class=\"col_heading level0 col0\" >cord_uid</th>\n",
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" <th id=\"T_6ac41_level0_col1\" class=\"col_heading level0 col1\" >source_x</th>\n",
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" <th id=\"T_6ac41_level0_col2\" class=\"col_heading level0 col2\" >title</th>\n",
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" <th id=\"T_6ac41_level0_col3\" class=\"col_heading level0 col3\" >abstract</th>\n",
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" <th id=\"T_6ac41_level0_col4\" class=\"col_heading level0 col4\" >authors</th>\n",
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" <th id=\"T_6ac41_level0_col5\" class=\"col_heading level0 col5\" >url</th>\n",
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" <th id=\"T_87464_level0_col0\" class=\"col_heading level0 col0\" >cord_uid</th>\n",
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" <th id=\"T_87464_level0_col1\" class=\"col_heading level0 col1\" >source_x</th>\n",
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" <th id=\"T_87464_level0_col2\" class=\"col_heading level0 col2\" >title</th>\n",
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" <th id=\"T_87464_level0_col3\" class=\"col_heading level0 col3\" >abstract</th>\n",
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" <th id=\"T_87464_level0_col4\" class=\"col_heading level0 col4\" >authors</th>\n",
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" <th id=\"T_87464_level0_col5\" class=\"col_heading level0 col5\" >url</th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th id=\"T_6ac41_level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
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" <td id=\"T_6ac41_row0_col0\" class=\"data row0 col0\" >ug7v899j</td>\n",
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" <td id=\"T_6ac41_row0_col1\" class=\"data row0 col1\" >PMC</td>\n",
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" <td id=\"T_6ac41_row0_col2\" class=\"data row0 col2\" >Clinical features of culture-p...</td>\n",
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" <td id=\"T_6ac41_row0_col3\" class=\"data row0 col3\" >OBJECTIVE: This retrospective ...</td>\n",
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" <td id=\"T_6ac41_row0_col4\" class=\"data row0 col4\" >Madani, Tariq A; Al-Ghamdi, Ai...</td>\n",
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" <td id=\"T_6ac41_row0_col5\" class=\"data row0 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/</a></td>\n",
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" <th id=\"T_87464_level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
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" <td id=\"T_87464_row0_col0\" class=\"data row0 col0\" >ug7v899j</td>\n",
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" <td id=\"T_87464_row0_col1\" class=\"data row0 col1\" >PMC</td>\n",
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" <td id=\"T_87464_row0_col2\" class=\"data row0 col2\" >Clinical features of culture-p...</td>\n",
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" <td id=\"T_87464_row0_col3\" class=\"data row0 col3\" >OBJECTIVE: This retrospective ...</td>\n",
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" <td id=\"T_87464_row0_col4\" class=\"data row0 col4\" >Madani, Tariq A; Al-Ghamdi, Ai...</td>\n",
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" <td id=\"T_87464_row0_col5\" class=\"data row0 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/</a></td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th id=\"T_6ac41_level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
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" <td id=\"T_6ac41_row1_col0\" class=\"data row1 col0\" >02tnwd4m</td>\n",
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" <td id=\"T_6ac41_row1_col1\" class=\"data row1 col1\" >PMC</td>\n",
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" <td id=\"T_6ac41_row1_col2\" class=\"data row1 col2\" >Nitric oxide: a pro-inflammato...</td>\n",
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" <td id=\"T_6ac41_row1_col3\" class=\"data row1 col3\" >Inflammatory diseases of the r...</td>\n",
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" <td id=\"T_6ac41_row1_col4\" class=\"data row1 col4\" >Vliet, Albert van der; Eiseric...</td>\n",
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" <td id=\"T_6ac41_row1_col5\" class=\"data row1 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59543/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59543/</a></td>\n",
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" <th id=\"T_87464_level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
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" <td id=\"T_87464_row1_col0\" class=\"data row1 col0\" >02tnwd4m</td>\n",
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" <td id=\"T_87464_row1_col1\" class=\"data row1 col1\" >PMC</td>\n",
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" <td id=\"T_87464_row1_col2\" class=\"data row1 col2\" >Nitric oxide: a pro-inflammato...</td>\n",
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" <td id=\"T_87464_row1_col3\" class=\"data row1 col3\" >Inflammatory diseases of the r...</td>\n",
179+
" <td id=\"T_87464_row1_col4\" class=\"data row1 col4\" >Vliet, Albert van der; Eiseric...</td>\n",
180+
" <td id=\"T_87464_row1_col5\" class=\"data row1 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59543/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59543/</a></td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th id=\"T_6ac41_level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
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" <td id=\"T_6ac41_row2_col0\" class=\"data row2 col0\" >ejv2xln0</td>\n",
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" <td id=\"T_6ac41_row2_col1\" class=\"data row2 col1\" >PMC</td>\n",
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" <td id=\"T_6ac41_row2_col2\" class=\"data row2 col2\" >Surfactant protein-D and pulmo...</td>\n",
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" <td id=\"T_6ac41_row2_col3\" class=\"data row2 col3\" >Surfactant protein-D (SP-D) pa...</td>\n",
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" <td id=\"T_6ac41_row2_col4\" class=\"data row2 col4\" >Crouch, Erika C...</td>\n",
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" <td id=\"T_6ac41_row2_col5\" class=\"data row2 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59549/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59549/</a></td>\n",
183+
" <th id=\"T_87464_level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
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" <td id=\"T_87464_row2_col0\" class=\"data row2 col0\" >ejv2xln0</td>\n",
185+
" <td id=\"T_87464_row2_col1\" class=\"data row2 col1\" >PMC</td>\n",
186+
" <td id=\"T_87464_row2_col2\" class=\"data row2 col2\" >Surfactant protein-D and pulmo...</td>\n",
187+
" <td id=\"T_87464_row2_col3\" class=\"data row2 col3\" >Surfactant protein-D (SP-D) pa...</td>\n",
188+
" <td id=\"T_87464_row2_col4\" class=\"data row2 col4\" >Crouch, Erika C...</td>\n",
189+
" <td id=\"T_87464_row2_col5\" class=\"data row2 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59549/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59549/</a></td>\n",
190190
" </tr>\n",
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" <tr>\n",
192-
" <th id=\"T_6ac41_level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
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" <td id=\"T_6ac41_row3_col0\" class=\"data row3 col0\" >2b73a28n</td>\n",
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" <td id=\"T_6ac41_row3_col1\" class=\"data row3 col1\" >PMC</td>\n",
195-
" <td id=\"T_6ac41_row3_col2\" class=\"data row3 col2\" >Role of endothelin-1 in lung d...</td>\n",
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" <td id=\"T_6ac41_row3_col3\" class=\"data row3 col3\" >Endothelin-1 (ET-1) is a 21 am...</td>\n",
197-
" <td id=\"T_6ac41_row3_col4\" class=\"data row3 col4\" >Fagan, Karen A; McMurtry, Ivan...</td>\n",
198-
" <td id=\"T_6ac41_row3_col5\" class=\"data row3 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59574/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59574/</a></td>\n",
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" <th id=\"T_87464_level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
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" <td id=\"T_87464_row3_col0\" class=\"data row3 col0\" >2b73a28n</td>\n",
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" <td id=\"T_87464_row3_col1\" class=\"data row3 col1\" >PMC</td>\n",
195+
" <td id=\"T_87464_row3_col2\" class=\"data row3 col2\" >Role of endothelin-1 in lung d...</td>\n",
196+
" <td id=\"T_87464_row3_col3\" class=\"data row3 col3\" >Endothelin-1 (ET-1) is a 21 am...</td>\n",
197+
" <td id=\"T_87464_row3_col4\" class=\"data row3 col4\" >Fagan, Karen A; McMurtry, Ivan...</td>\n",
198+
" <td id=\"T_87464_row3_col5\" class=\"data row3 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59574/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59574/</a></td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th id=\"T_6ac41_level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
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" <td id=\"T_6ac41_row4_col0\" class=\"data row4 col0\" >9785vg6d</td>\n",
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" <td id=\"T_6ac41_row4_col1\" class=\"data row4 col1\" >PMC</td>\n",
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" <td id=\"T_6ac41_row4_col2\" class=\"data row4 col2\" >Gene expression in epithelial ...</td>\n",
205-
" <td id=\"T_6ac41_row4_col3\" class=\"data row4 col3\" >Respiratory syncytial virus (R...</td>\n",
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" <td id=\"T_6ac41_row4_col4\" class=\"data row4 col4\" >Domachowske, Joseph B; Bonvill...</td>\n",
207-
" <td id=\"T_6ac41_row4_col5\" class=\"data row4 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/</a></td>\n",
201+
" <th id=\"T_87464_level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
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" <td id=\"T_87464_row4_col0\" class=\"data row4 col0\" >9785vg6d</td>\n",
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" <td id=\"T_87464_row4_col1\" class=\"data row4 col1\" >PMC</td>\n",
204+
" <td id=\"T_87464_row4_col2\" class=\"data row4 col2\" >Gene expression in epithelial ...</td>\n",
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" <td id=\"T_87464_row4_col3\" class=\"data row4 col3\" >Respiratory syncytial virus (R...</td>\n",
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" <td id=\"T_87464_row4_col4\" class=\"data row4 col4\" >Domachowske, Joseph B; Bonvill...</td>\n",
207+
" <td id=\"T_87464_row4_col5\" class=\"data row4 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/</a></td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n"
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],
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"text/plain": [
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"<pandas.io.formats.style.Styler at 0x7f31574398d0>"
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"<pandas.io.formats.style.Styler at 0x7f36d4016ad0>"
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]
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},
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"execution_count": 6,
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"execution_count": 10,
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"id": "6132c041-7213-410e-a206-1a8c7385128e",
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"metadata": {},
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"outputs": [
@@ -460,13 +460,17 @@
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],
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"source": [
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"# Optionally, get indexer status to confirm that it's running\n",
463-
"r = requests.get(os.environ['AZURE_SEARCH_ENDPOINT'] + \"/indexers/\" + indexer_name +\n",
464-
" \"/status\", headers=headers, params=params)\n",
465-
"# pprint(json.dumps(r.json(), indent=1))\n",
466-
"print(r.status_code)\n",
467-
"print(\"Status:\",r.json().get('lastResult').get('status'))\n",
468-
"print(\"Items Processed:\",r.json().get('lastResult').get('itemsProcessed'))\n",
469-
"print(r.ok)"
463+
"try:\n",
464+
" r = requests.get(os.environ['AZURE_SEARCH_ENDPOINT'] + \"/indexers/\" + indexer_name +\n",
465+
" \"/status\", headers=headers, params=params)\n",
466+
" # pprint(json.dumps(r.json(), indent=1))\n",
467+
" print(r.status_code)\n",
468+
" print(\"Status:\",r.json().get('lastResult').get('status'))\n",
469+
" print(\"Items Processed:\",r.json().get('lastResult').get('itemsProcessed'))\n",
470+
" print(r.ok)\n",
471+
" \n",
472+
"except Exception as e:\n",
473+
" print(\"Wait a few seconds until the process starts and run this cell again.\")"
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]
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},
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{
@@ -487,7 +491,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 18,
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"execution_count": 11,
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"id": "ec359823-3b9f-4b7f-af38-c3f2f916d5fa",
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"metadata": {},
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"outputs": [

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