Update req

cghr-toronto · Jul 12, 2023 · 2d41724 · 2d41724
1 parent 153bbe8
commit 2d41724
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diff --git a/requirements.txt b/requirements.txt
@@ -14,6 +14,9 @@ bleach==6.0.0
 certifi==2022.12.7
 cffi==1.15.1
 charset-normalizer==3.1.0
+click==8.1.4
+click-plugins==1.1.1
+cligj==0.7.2
 comm==0.1.3
 cryptography==40.0.2
 debugpy==1.6.7
@@ -22,7 +25,9 @@ defusedxml==0.7.1
 et-xmlfile==1.1.0
 executing==1.2.0
 fastjsonschema==2.16.3
+Fiona==1.9.4.post1
 fqdn==1.5.1
+geopandas==0.13.2
 greenlet==2.0.2
 idna==3.4
 ipykernel==6.22.0
@@ -72,6 +77,7 @@ ptyprocess==0.7.0
 pure-eval==0.2.2
 pycparser==2.21
 Pygments==2.15.1
+pyproj==3.6.0
 pyrsistent==0.19.3
 python-dateutil==2.8.2
 python-dotenv==1.0.0
@@ -84,6 +90,7 @@ requests==2.29.0
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
 Send2Trash==1.8.2
+shapely==2.0.1
 six==1.16.0
 sniffio==1.3.0
 soupsieve==2.4.1

diff --git a/src/data/icd_data.csv b/src/data/icd_data.csv
@@ -1,49 +1,53 @@
 dataset,columns,rows,description
 cghr10,3,36,"Centre for Global Health Research for ICD-10 (CGHR-10) codes for physician coded verbal autopsies.
 
- See [relevant paper](https://doi.org/10.1186/s12916-019-1353-2)."
-cmea10,3,143,"Central Medical Evaluation Agreement for ICD-10 (CMEA-10) blocks from the Centre for Global Health Research (CGHR).
+These codes group [ICD-10](https://openmortality.org/data/icd10_v1) codes into broader categories based on three age groups: adult (12 years or older), child (28 days to 11 years), and neonate (under 28 days).
 
-These blocks are used in the Central Medical Evaluation (CME) system to determine groups of ICD-10 codes considered to be in agreement for dual physician coding in Verbal Autopsies (VA).
+For more details, see the [relevant paper](https://doi.org/10.1186/s12916-019-1353-2)."
+cmea10,3,143,"Central Medical Evaluation Agreement for ICD-10 (CMEA-10) code blocks from the Centre for Global Health Research (CGHR).
 
-See [relevant paper](https://doi.org/10.1186/1741-7015-12-21)."
+These code blocks are used in the Central Medical Evaluation (CME) system to determine which groups of ICD-10 codes considered to be in agreement for dual physician coding in Verbal Autopsies (VA).
+
+For more details, see the [relevant paper](https://doi.org/10.1186/1741-7015-12-21)."
 icd10,5,12597,"International Classification of Diseases Revision 10 (ICD-10) data from the World Health Organization (WHO).
 
-See [ICD-10 Manual](https://github.com/cghr-toronto/icd/blob/main/docs/icd10_manual.pdf)."
-icd10_cghr10,4,6411,"Mappings to convert from ICD-10 to CGHR-10.
+Contains standardized codes for classifying diseases based on chapters, blocks, and categories.
+
+For more details, see the [ICD-10 Manual](https://github.com/cghr-toronto/icd/blob/main/docs/icd10_manual.pdf)."
+icd10_cghr10,4,6411,"Mappings to convert from [ICD-10](https://openmortality.org/data/icd10_v1) codes to [CGHR-10](https://openmortality.org/data/cghr10_v1) codes.
 
-Join the variable `icd10_code` to your data for the converted codes in variable `cghr10_title`."
-icd10_cmea10,3,1653,"Mappings to convert from ICD-10 to CMEA-10.
+Join the column `icd10_code` to your data for the converted codes in column `cghr10_title`."
+icd10_cmea10,3,1653,"Mappings to convert from [ICD-10](https://openmortality.org/data/icd10_v1) codes to [CMEA-10](https://openmortality.org/data/cmea10_v1) code blocks.
 
-Join the variable `icd10_code` to your data for the converted codes in variable `cmea10_title`."
-icd10_icd11,12,12597,"Mappings to convert from ICD-10 to ICD-11.
+Join the column `icd10_code` to your data for the converted codes in column `cmea10_title`."
+icd10_icd11,12,12597,"Mappings to convert from [ICD-10](https://openmortality.org/data/icd10_v1) codes to [ICD-11](https://openmortality.org/data/icd11_v1) codes.
 
-Join the variable `icd10_code` to your data for the converted codes in variable `icd11_code`."
-icd10_wbd10,11,6502,"Mappings to convert from ICD-10 to WBD-10.
+Join the column `icd10_code` to your data for the converted codes in column `icd11_code`."
+icd10_wbd10,11,6502,"Mappings to convert from [ICD-10](https://openmortality.org/data/icd10_v1) codes to [WBD-10](https://openmortality.org/data/wbd10_v1) codes.
 
-Join the variable `icd10_code` to your data for the converted codes in variable `wbd10_code`."
-icd10_wva2016,6,2384,"Mappings to convert from ICD-10 to WVA-2016.
+Join the column `icd10_code` and `wbd10_age` to your data for the converted codes in column `wbd10_code`."
+icd10_wva2016,6,2384,"Mappings to convert from [ICD-10](https://openmortality.org/data/icd10_v1) codes to [WVA-2016](https://openmortality.org/data/wva2016_v1) codes.
 
-Join the variable `icd10_code` to your data for the converted codes in variable `wva2016_code`."
-icd10_wva2022,4,4442,"Mappings to convert from ICD-10 to WVA-2022.
+Join the column `icd10_code` to your data for the converted codes in column `wva2016_code`."
+icd10_wva2022,4,4442,"Mappings to convert from [ICD-10](https://openmortality.org/data/icd10_v1) to [WVA-2022](https://openmortality.org/data/wva2022_v1).
 
-Join the variable `icd10_code` to your data for the converted codes in variable `wva2022_code`."
+Join the column `icd10_code` to your data for the converted codes in column `wva2022_code`."
 icd11,17,35459,"International Classification of Diseases Revision 11 (ICD-11) data from the World Health Organization (WHO).
 
-See [ICD-11 Manual](https://github.com/cghr-toronto/icd/blob/main/docs/icd11_manual.pdf)."
-icd11_icd10,7,17799,"Mappings to convert from ICD-11 to ICD-10.
+Contains standardized codes for classifying diseases based on chapters, blocks, and categories.
 
-Join the variable `icd11_code` to your data for the converted codes in variable `icd10_code`.
+For more details, see the [ICD-11 Manual](https://github.com/cghr-toronto/icd/blob/main/docs/icd11_manual.pdf)."
+icd11_icd10,7,17799,"Mappings to convert from [ICD-11](https://openmortality.org/data/icd11_v1) codes to [ICD-10](https://openmortality.org/data/icd10_v1) codes.
 
-**Note**: ICD-11 codes may map to multiple ICD-10 codes."
+Join the column `icd11_code` to your data for the converted codes in column `icd10_code`."
 wbd10,10,182,"Wilson's Burden of Disease for ICD-10 (WBD-10) data from the Centre for Global Health Research (CGHR).
 
-Groups International Classification of Diseases (ICD) Revision 10 codes from the World Health Organization (WHO) into broader WBD-10 codes for three age groups (adult, child, and neonate).
+Groups [ICD-10](https://openmortality.org/data/icd10_v1) codes into broader WBD-10 codes for three age groups: adult (12 years or older), child (28 days to 11 years), and neonate (under 28 days).
 
-See [relevant paper](https://doi.org/10.1186/1741-7015-12-21)."
-wva2016,10,85,"World Health Organization Verbal Autopsy 2016 (WVA-2016) codes that generalize ICD-10 codes for mortality.
+For more details, see the [relevant paper](https://doi.org/10.1186/1741-7015-12-21)."
+wva2016,10,85,"World Health Organization Verbal Autopsy 2016 (WVA-2016) codes that generalize ICD-10 codes into mortality relevant codes.
 
-See [WVA-2016 Manual](https://github.com/cghr-toronto/icd/blob/main/docs/wva2016_manual_v15.pdf)."
-wva2022,3,65,"World Health Organization Verbal Autopsy 2022 (WVA-2022) codes that generalize ICD-10 codes for mortality.
+For more details, see the [WVA-2016 Manual](https://github.com/cghr-toronto/icd/blob/main/docs/wva2016_manual_v15.pdf)."
+wva2022,3,65,"World Health Organization Verbal Autopsy 2022 (WVA-2022) codes that generalize ICD-10 codes into mortality relevant codes.
 
-See [WVA-2022 Manual](https://github.com/cghr-toronto/icd/blob/main/docs/wva2022_manual.pdf)."
+For more details, see the [WVA-2022 Manual](https://github.com/cghr-toronto/icd/blob/main/docs/wva2022_manual.pdf)."
diff --git a/src/update.ipynb b/src/update.ipynb
@@ -33,7 +33,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 91,
+   "execution_count": 1,
    "id": "a727e9a6-e2fe-429a-8ea1-a6625a8b827d",
    "metadata": {
     "execution": {
@@ -44,7 +44,19 @@
     },
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'geopandas'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mgeopandas\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mgpd\u001b[39;00m\n\u001b[1;32m      2\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mos\u001b[39;00m\n\u001b[1;32m      3\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mpandas\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mpd\u001b[39;00m\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'geopandas'"
+     ]
+    }
+   ],
    "source": [
     "import geopandas as gpd\n",
     "import os\n",
@@ -73,7 +85,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 92,
+   "execution_count": null,
    "id": "eca537a3-aba8-4138-81c5-0eef20859f53",
    "metadata": {
     "execution": {
@@ -120,7 +132,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 93,
+   "execution_count": null,
    "id": "9ac3f324-b682-474e-a248-1b98484ad495",
    "metadata": {
     "execution": {
@@ -163,7 +175,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 94,
+   "execution_count": null,
    "id": "7c264c0d-f17e-4b4a-9d24-7775985f14ae",
    "metadata": {
     "execution": {
@@ -206,7 +218,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 95,
+   "execution_count": null,
    "id": "9bd1898f-9b02-484a-9721-7bd664d222e1",
    "metadata": {
     "execution": {
@@ -494,7 +506,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 96,
+   "execution_count": null,
    "id": "5f0b4926-a3d0-40ab-b5ea-6603fbffbb02",
    "metadata": {
     "execution": {
@@ -561,7 +573,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 97,
+   "execution_count": null,
    "id": "acbbde31-c351-4fe7-96ee-29c3b499ae82",
    "metadata": {
     "execution": {
@@ -750,7 +762,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 98,
+   "execution_count": null,
    "id": "12a466bf-cdea-4a5a-881d-9c9b5548753e",
    "metadata": {
     "execution": {
@@ -816,7 +828,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 99,
+   "execution_count": null,
    "id": "415d7684-9186-4f3f-9620-14f754d2a1a7",
    "metadata": {
     "execution": {
@@ -889,7 +901,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 100,
+   "execution_count": null,
    "id": "d0bd54ae-c3b9-415f-98a2-9879e0f10419",
    "metadata": {
     "execution": {
@@ -923,7 +935,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 101,
+   "execution_count": null,
    "id": "f00ce391-8d14-4c98-ab32-c85bb662f3c8",
    "metadata": {
     "execution": {
@@ -966,7 +978,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 102,
+   "execution_count": null,
    "id": "dcb321e4-39c0-4f9f-9cdb-c4a417fd72be",
    "metadata": {
     "execution": {
@@ -1094,7 +1106,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 103,
+   "execution_count": null,
    "id": "4f7f7bd9-b5f7-4837-adb4-05f4de66406c",
    "metadata": {
     "execution": {
@@ -1208,7 +1220,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 104,
+   "execution_count": null,
    "id": "dab2dc98-b1fb-4d10-a794-006a4859243f",
    "metadata": {
     "execution": {
@@ -1250,7 +1262,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 105,
+   "execution_count": null,
    "id": "6d61a0bd-dbb7-4cd5-8954-bba4d57c9cb3",
    "metadata": {
     "execution": {
@@ -1284,7 +1296,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 106,
+   "execution_count": null,
    "id": "88d47cf7-8a22-4d3a-92f7-0196ae722c6d",
    "metadata": {
     "execution": {
@@ -1317,7 +1329,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 107,
+   "execution_count": null,
    "id": "1f86bed4-1d66-463b-b9bf-cdf2b4f2485c",
    "metadata": {
     "execution": {
@@ -1348,7 +1360,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 108,
+   "execution_count": null,
    "id": "b60bf6a8-f2c7-4df6-a55e-2809950122c3",
    "metadata": {
     "execution": {