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fix arm and bicep templates for backend and frontend
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@pablomarin
pablomarin committed Jan 2, 2025
1 parent 5de76d3 commit c1b4c49
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Showing 19 changed files with 862 additions and 781 deletions.
25 changes: 16 additions & 9 deletions 01-Load-Data-ACogSearch.ipynb
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"upload_directory = \"./data/temp_extract\" # Temporary directory to extract the zip file"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This process below takes about 11 mins"
]
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {
"tags": []
},
Expand All @@ -137,16 +144,16 @@
"name": "stderr",
"output_type": "stream",
"text": [
"Uploading Files: 100%|██████████████████████████████████████████| 3107/3107 [09:02<00:00, 5.72it/s]\n"
"Uploading Files: 100%|██████████████████████████████████████████| 3107/3107 [08:53<00:00, 5.83it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Temp Folder: ./data/temp_extract removed\n",
"CPU times: user 32.1 s, sys: 5.05 s, total: 37.1 s\n",
"Wall time: 11min 15s\n"
"CPU times: user 31.6 s, sys: 5.19 s, total: 36.8 s\n",
"Wall time: 11min\n"
]
}
],
Expand All @@ -173,7 +180,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 6,
"metadata": {
"tags": []
},
Expand Down Expand Up @@ -226,7 +233,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 8,
"metadata": {
"tags": []
},
Expand Down Expand Up @@ -717,7 +724,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 17,
"metadata": {
"tags": []
},
Expand Down Expand Up @@ -786,9 +793,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "GPTSearch2 (Python 3.12)",
"display_name": "GPTSearch3 (Python 3.12)",
"language": "python",
"name": "gptsearch2"
"name": "gptsearch3"
},
"language_info": {
"codemirror_mode": {
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104 changes: 52 additions & 52 deletions 02-LoadCSVOneToMany-ACogSearch.ipynb
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Expand Up @@ -98,16 +98,16 @@
"name": "stderr",
"output_type": "stream",
"text": [
"Uploading Files: 100%|████████████████████████████████████████████████| 1/1 [00:04<00:00, 4.69s/it]"
"Uploading Files: 100%|████████████████████████████████████████████████| 1/1 [00:06<00:00, 6.23s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Temp Folder: ./data/temp_extract removed\n",
"CPU times: user 731 ms, sys: 310 ms, total: 1.04 s\n",
"Wall time: 6.07 s\n"
"CPU times: user 767 ms, sys: 305 ms, total: 1.07 s\n",
"Wall time: 7.74 s\n"
]
},
{
Expand Down Expand Up @@ -220,69 +220,69 @@
"text/html": [
"<style type=\"text/css\">\n",
"</style>\n",
"<table id=\"T_4e8c5\">\n",
"<table id=\"T_e5366\">\n",
" <thead>\n",
" <tr>\n",
" <th class=\"blank level0\" >&nbsp;</th>\n",
" <th id=\"T_4e8c5_level0_col0\" class=\"col_heading level0 col0\" >cord_uid</th>\n",
" <th id=\"T_4e8c5_level0_col1\" class=\"col_heading level0 col1\" >source_x</th>\n",
" <th id=\"T_4e8c5_level0_col2\" class=\"col_heading level0 col2\" >title</th>\n",
" <th id=\"T_4e8c5_level0_col3\" class=\"col_heading level0 col3\" >abstract</th>\n",
" <th id=\"T_4e8c5_level0_col4\" class=\"col_heading level0 col4\" >authors</th>\n",
" <th id=\"T_4e8c5_level0_col5\" class=\"col_heading level0 col5\" >url</th>\n",
" <th id=\"T_e5366_level0_col0\" class=\"col_heading level0 col0\" >cord_uid</th>\n",
" <th id=\"T_e5366_level0_col1\" class=\"col_heading level0 col1\" >source_x</th>\n",
" <th id=\"T_e5366_level0_col2\" class=\"col_heading level0 col2\" >title</th>\n",
" <th id=\"T_e5366_level0_col3\" class=\"col_heading level0 col3\" >abstract</th>\n",
" <th id=\"T_e5366_level0_col4\" class=\"col_heading level0 col4\" >authors</th>\n",
" <th id=\"T_e5366_level0_col5\" class=\"col_heading level0 col5\" >url</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th id=\"T_4e8c5_level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
" <td id=\"T_4e8c5_row0_col0\" class=\"data row0 col0\" >ug7v899j</td>\n",
" <td id=\"T_4e8c5_row0_col1\" class=\"data row0 col1\" >PMC</td>\n",
" <td id=\"T_4e8c5_row0_col2\" class=\"data row0 col2\" >Clinical features of culture-p...</td>\n",
" <td id=\"T_4e8c5_row0_col3\" class=\"data row0 col3\" >OBJECTIVE: This retrospective ...</td>\n",
" <td id=\"T_4e8c5_row0_col4\" class=\"data row0 col4\" >Madani, Tariq A; Al-Ghamdi, Ai...</td>\n",
" <td id=\"T_4e8c5_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",
" <th id=\"T_e5366_level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
" <td id=\"T_e5366_row0_col0\" class=\"data row0 col0\" >ug7v899j</td>\n",
" <td id=\"T_e5366_row0_col1\" class=\"data row0 col1\" >PMC</td>\n",
" <td id=\"T_e5366_row0_col2\" class=\"data row0 col2\" >Clinical features of culture-p...</td>\n",
" <td id=\"T_e5366_row0_col3\" class=\"data row0 col3\" >OBJECTIVE: This retrospective ...</td>\n",
" <td id=\"T_e5366_row0_col4\" class=\"data row0 col4\" >Madani, Tariq A; Al-Ghamdi, Ai...</td>\n",
" <td id=\"T_e5366_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",
" </tr>\n",
" <tr>\n",
" <th id=\"T_4e8c5_level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
" <td id=\"T_4e8c5_row1_col0\" class=\"data row1 col0\" >02tnwd4m</td>\n",
" <td id=\"T_4e8c5_row1_col1\" class=\"data row1 col1\" >PMC</td>\n",
" <td id=\"T_4e8c5_row1_col2\" class=\"data row1 col2\" >Nitric oxide: a pro-inflammato...</td>\n",
" <td id=\"T_4e8c5_row1_col3\" class=\"data row1 col3\" >Inflammatory diseases of the r...</td>\n",
" <td id=\"T_4e8c5_row1_col4\" class=\"data row1 col4\" >Vliet, Albert van der; Eiseric...</td>\n",
" <td id=\"T_4e8c5_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",
" <th id=\"T_e5366_level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
" <td id=\"T_e5366_row1_col0\" class=\"data row1 col0\" >02tnwd4m</td>\n",
" <td id=\"T_e5366_row1_col1\" class=\"data row1 col1\" >PMC</td>\n",
" <td id=\"T_e5366_row1_col2\" class=\"data row1 col2\" >Nitric oxide: a pro-inflammato...</td>\n",
" <td id=\"T_e5366_row1_col3\" class=\"data row1 col3\" >Inflammatory diseases of the r...</td>\n",
" <td id=\"T_e5366_row1_col4\" class=\"data row1 col4\" >Vliet, Albert van der; Eiseric...</td>\n",
" <td id=\"T_e5366_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",
" </tr>\n",
" <tr>\n",
" <th id=\"T_4e8c5_level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
" <td id=\"T_4e8c5_row2_col0\" class=\"data row2 col0\" >ejv2xln0</td>\n",
" <td id=\"T_4e8c5_row2_col1\" class=\"data row2 col1\" >PMC</td>\n",
" <td id=\"T_4e8c5_row2_col2\" class=\"data row2 col2\" >Surfactant protein-D and pulmo...</td>\n",
" <td id=\"T_4e8c5_row2_col3\" class=\"data row2 col3\" >Surfactant protein-D (SP-D) pa...</td>\n",
" <td id=\"T_4e8c5_row2_col4\" class=\"data row2 col4\" >Crouch, Erika C...</td>\n",
" <td id=\"T_4e8c5_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",
" <th id=\"T_e5366_level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
" <td id=\"T_e5366_row2_col0\" class=\"data row2 col0\" >ejv2xln0</td>\n",
" <td id=\"T_e5366_row2_col1\" class=\"data row2 col1\" >PMC</td>\n",
" <td id=\"T_e5366_row2_col2\" class=\"data row2 col2\" >Surfactant protein-D and pulmo...</td>\n",
" <td id=\"T_e5366_row2_col3\" class=\"data row2 col3\" >Surfactant protein-D (SP-D) pa...</td>\n",
" <td id=\"T_e5366_row2_col4\" class=\"data row2 col4\" >Crouch, Erika C...</td>\n",
" <td id=\"T_e5366_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",
" </tr>\n",
" <tr>\n",
" <th id=\"T_4e8c5_level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
" <td id=\"T_4e8c5_row3_col0\" class=\"data row3 col0\" >2b73a28n</td>\n",
" <td id=\"T_4e8c5_row3_col1\" class=\"data row3 col1\" >PMC</td>\n",
" <td id=\"T_4e8c5_row3_col2\" class=\"data row3 col2\" >Role of endothelin-1 in lung d...</td>\n",
" <td id=\"T_4e8c5_row3_col3\" class=\"data row3 col3\" >Endothelin-1 (ET-1) is a 21 am...</td>\n",
" <td id=\"T_4e8c5_row3_col4\" class=\"data row3 col4\" >Fagan, Karen A; McMurtry, Ivan...</td>\n",
" <td id=\"T_4e8c5_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",
" <th id=\"T_e5366_level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
" <td id=\"T_e5366_row3_col0\" class=\"data row3 col0\" >2b73a28n</td>\n",
" <td id=\"T_e5366_row3_col1\" class=\"data row3 col1\" >PMC</td>\n",
" <td id=\"T_e5366_row3_col2\" class=\"data row3 col2\" >Role of endothelin-1 in lung d...</td>\n",
" <td id=\"T_e5366_row3_col3\" class=\"data row3 col3\" >Endothelin-1 (ET-1) is a 21 am...</td>\n",
" <td id=\"T_e5366_row3_col4\" class=\"data row3 col4\" >Fagan, Karen A; McMurtry, Ivan...</td>\n",
" <td id=\"T_e5366_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",
" </tr>\n",
" <tr>\n",
" <th id=\"T_4e8c5_level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
" <td id=\"T_4e8c5_row4_col0\" class=\"data row4 col0\" >9785vg6d</td>\n",
" <td id=\"T_4e8c5_row4_col1\" class=\"data row4 col1\" >PMC</td>\n",
" <td id=\"T_4e8c5_row4_col2\" class=\"data row4 col2\" >Gene expression in epithelial ...</td>\n",
" <td id=\"T_4e8c5_row4_col3\" class=\"data row4 col3\" >Respiratory syncytial virus (R...</td>\n",
" <td id=\"T_4e8c5_row4_col4\" class=\"data row4 col4\" >Domachowske, Joseph B; Bonvill...</td>\n",
" <td id=\"T_4e8c5_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",
" <th id=\"T_e5366_level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
" <td id=\"T_e5366_row4_col0\" class=\"data row4 col0\" >9785vg6d</td>\n",
" <td id=\"T_e5366_row4_col1\" class=\"data row4 col1\" >PMC</td>\n",
" <td id=\"T_e5366_row4_col2\" class=\"data row4 col2\" >Gene expression in epithelial ...</td>\n",
" <td id=\"T_e5366_row4_col3\" class=\"data row4 col3\" >Respiratory syncytial virus (R...</td>\n",
" <td id=\"T_e5366_row4_col4\" class=\"data row4 col4\" >Domachowske, Joseph B; Bonvill...</td>\n",
" <td id=\"T_e5366_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",
" </tr>\n",
" </tbody>\n",
"</table>\n"
],
"text/plain": [
"<pandas.io.formats.style.Styler at 0x7f85dc0c4e60>"
"<pandas.io.formats.style.Styler at 0x7f09e044b170>"
]
},
"execution_count": 6,
Expand Down Expand Up @@ -627,7 +627,7 @@
},
{
"cell_type": "code",
"execution_count": 21,
"execution_count": 12,
"id": "6132c041-7213-410e-a206-1a8c7385128e",
"metadata": {
"tags": []
Expand All @@ -638,8 +638,8 @@
"output_type": "stream",
"text": [
"200\n",
"Status: inProgress\n",
"Items Processed: 2500\n",
"Status: success\n",
"Items Processed: 0\n",
"True\n"
]
}
Expand Down Expand Up @@ -698,9 +698,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.10 - SDK v2",
"display_name": "GPTSearch3 (Python 3.12)",
"language": "python",
"name": "python310-sdkv2"
"name": "gptsearch3"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -712,7 +712,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.14"
"version": "3.12.8"
}
},
"nbformat": 4,
Expand Down
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