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Load_func module #11

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merged 3 commits into from
Dec 24, 2023
Merged

Load_func module #11

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3ffca15
bulk data infrastructure
Dec 19, 2023
e11461e
fix the past
Dec 19, 2023
8f56ab1
andle non existing functions and field_types
Dec 24, 2023
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184 changes: 109 additions & 75 deletions nbs/00_config.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,8 @@
"import json\n",
"import numpy as np\n",
"import pandas as pd\n",
"import shutil"
"import shutil\n",
"from glob import glob"
]
},
{
Expand Down Expand Up @@ -154,6 +155,39 @@
" break\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#| export\n",
"def get_dictionary_properties_file_path() -> str:\n",
" \"\"\"\n",
" Get the file path for dictionary properties - TODO: move to config file or DB.\n",
" At this point only includes field_type properties.\n",
"\n",
" Args:\n",
"\n",
" Returns:\n",
" str: the path to the file\n",
" \"\"\"\n",
" path = os.path.join(DATASETS_PATH, 'metadata', '2 - Dictionary properties - field_type.csv')\n",
" if path.startswith('s3://'):\n",
" return path\n",
" return glob(path)[0]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#| export\n",
"DICT_PROPERTY_PATH = get_dictionary_properties_file_path()"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand Down Expand Up @@ -307,43 +341,43 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>2022-06-09</td>\n",
" <td>46.053320</td>\n",
" <td>1</td>\n",
" <td>109.109591</td>\n",
" <td>38.208594</td>\n",
" <td>2023-09-23</td>\n",
" <td>71.943376</td>\n",
" <td>0</td>\n",
" <td>103.073700</td>\n",
" <td>30.827577</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>2020-03-25</td>\n",
" <td>52.837460</td>\n",
" <td>2023-10-07</td>\n",
" <td>55.110677</td>\n",
" <td>1</td>\n",
" <td>138.253504</td>\n",
" <td>46.951768</td>\n",
" <td>141.200320</td>\n",
" <td>44.265563</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2023-01-22</td>\n",
" <td>67.598596</td>\n",
" <td>2021-01-17</td>\n",
" <td>54.952484</td>\n",
" <td>0</td>\n",
" <td>76.521886</td>\n",
" <td>26.432283</td>\n",
" <td>81.943225</td>\n",
" <td>24.488435</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>2023-07-15</td>\n",
" <td>46.586319</td>\n",
" <td>2022-12-16</td>\n",
" <td>68.898440</td>\n",
" <td>0</td>\n",
" <td>85.142607</td>\n",
" <td>29.018499</td>\n",
" <td>104.493989</td>\n",
" <td>31.253664</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>2022-06-10</td>\n",
" <td>42.321703</td>\n",
" <td>1</td>\n",
" <td>78.283658</td>\n",
" <td>28.960815</td>\n",
" <td>2023-01-04</td>\n",
" <td>44.344700</td>\n",
" <td>0</td>\n",
" <td>98.777684</td>\n",
" <td>29.538773</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
Expand All @@ -352,19 +386,19 @@
"text/plain": [
" date_of_research_stage age_at_research_stage sex val1 \\\n",
"participant_id \n",
"0 2022-06-09 46.053320 1 109.109591 \n",
"1 2020-03-25 52.837460 1 138.253504 \n",
"2 2023-01-22 67.598596 0 76.521886 \n",
"3 2023-07-15 46.586319 0 85.142607 \n",
"4 2022-06-10 42.321703 1 78.283658 \n",
"0 2023-09-23 71.943376 0 103.073700 \n",
"1 2023-10-07 55.110677 1 141.200320 \n",
"2 2021-01-17 54.952484 0 81.943225 \n",
"3 2022-12-16 68.898440 0 104.493989 \n",
"4 2023-01-04 44.344700 0 98.777684 \n",
"\n",
" val2 \n",
"participant_id \n",
"0 38.208594 \n",
"1 46.951768 \n",
"2 26.432283 \n",
"3 29.018499 \n",
"4 28.960815 "
"0 30.827577 \n",
"1 44.265563 \n",
"2 24.488435 \n",
"3 31.253664 \n",
"4 29.538773 "
]
},
"execution_count": null,
Expand Down Expand Up @@ -421,43 +455,43 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>2023-01-22</td>\n",
" <td>46.586319</td>\n",
" <td>2021-01-17</td>\n",
" <td>68.898440</td>\n",
" <td>0</td>\n",
" <td>85.142607</td>\n",
" <td>38.208594</td>\n",
" <td>104.493989</td>\n",
" <td>30.827577</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>2023-07-15</td>\n",
" <td>52.837460</td>\n",
" <td>1</td>\n",
" <td>109.109591</td>\n",
" <td>28.960815</td>\n",
" <td>2022-12-16</td>\n",
" <td>55.110677</td>\n",
" <td>0</td>\n",
" <td>103.073700</td>\n",
" <td>29.538773</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2022-06-10</td>\n",
" <td>67.598596</td>\n",
" <td>1</td>\n",
" <td>78.283658</td>\n",
" <td>46.951768</td>\n",
" <td>2023-01-04</td>\n",
" <td>54.952484</td>\n",
" <td>0</td>\n",
" <td>98.777684</td>\n",
" <td>44.265563</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>2020-03-25</td>\n",
" <td>46.053320</td>\n",
" <td>2023-10-07</td>\n",
" <td>71.943376</td>\n",
" <td>1</td>\n",
" <td>76.521886</td>\n",
" <td>26.432283</td>\n",
" <td>81.943225</td>\n",
" <td>24.488435</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>2022-06-09</td>\n",
" <td>42.321703</td>\n",
" <td>2023-09-23</td>\n",
" <td>44.344700</td>\n",
" <td>0</td>\n",
" <td>138.253504</td>\n",
" <td>29.018499</td>\n",
" <td>141.200320</td>\n",
" <td>31.253664</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
Expand All @@ -466,19 +500,19 @@
"text/plain": [
" date_of_research_stage age_at_research_stage sex val1 \\\n",
"participant_id \n",
"0 2023-01-22 46.586319 0 85.142607 \n",
"1 2023-07-15 52.837460 1 109.109591 \n",
"2 2022-06-10 67.598596 1 78.283658 \n",
"3 2020-03-25 46.053320 1 76.521886 \n",
"4 2022-06-09 42.321703 0 138.253504 \n",
"0 2021-01-17 68.898440 0 104.493989 \n",
"1 2022-12-16 55.110677 0 103.073700 \n",
"2 2023-01-04 54.952484 0 98.777684 \n",
"3 2023-10-07 71.943376 1 81.943225 \n",
"4 2023-09-23 44.344700 0 141.200320 \n",
"\n",
" val2 \n",
"participant_id \n",
"0 38.208594 \n",
"1 28.960815 \n",
"2 46.951768 \n",
"3 26.432283 \n",
"4 29.018499 "
"0 30.827577 \n",
"1 29.538773 \n",
"2 44.265563 \n",
"3 24.488435 \n",
"4 31.253664 "
]
},
"execution_count": null,
Expand Down Expand Up @@ -534,39 +568,39 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>2021-08-16</td>\n",
" <td>2021-09-16</td>\n",
" <td>69.788555</td>\n",
" <td>1</td>\n",
" <td>E</td>\n",
" <td>A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>2021-02-03</td>\n",
" <td>2021-02-25</td>\n",
" <td>36.289947</td>\n",
" <td>1</td>\n",
" <td>C</td>\n",
" <td>B</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2022-04-20</td>\n",
" <td>2022-06-04</td>\n",
" <td>61.501970</td>\n",
" <td>1</td>\n",
" <td>C</td>\n",
" <td>C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>2020-07-10</td>\n",
" <td>2020-07-20</td>\n",
" <td>46.299262</td>\n",
" <td>0</td>\n",
" <td>B</td>\n",
" <td>A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>2021-02-05</td>\n",
" <td>2021-02-26</td>\n",
" <td>70.127055</td>\n",
" <td>1</td>\n",
" <td>B</td>\n",
Expand All @@ -579,11 +613,11 @@
"text/plain": [
" date_of_research_stage age_at_research_stage sex val1 val2\n",
"participant_id \n",
"0 2021-08-16 69.788555 1 E A\n",
"1 2021-02-03 36.289947 1 C B\n",
"2 2022-04-20 61.501970 1 C C\n",
"3 2020-07-10 46.299262 0 B A\n",
"4 2021-02-05 70.127055 1 B C"
"0 2021-09-16 69.788555 1 E A\n",
"1 2021-02-25 36.289947 1 C B\n",
"2 2022-06-04 61.501970 1 C C\n",
"3 2020-07-20 46.299262 0 B A\n",
"4 2021-02-26 70.127055 1 B C"
]
},
"execution_count": null,
Expand Down
40 changes: 17 additions & 23 deletions nbs/01_basic_plots.ipynb
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