jataware · satchelbaldwin · May 16, 2025 · May 27, 2025 · Jun 6, 2025 · Jun 6, 2025
diff --git a/Dockerfile b/Dockerfile
@@ -16,7 +16,9 @@ COPY --chown=1000:1000 . /jupyter
 RUN rm -f /jupyter/.beaker.conf
 RUN rm -f /jupyter/.env
 
-RUN uv pip install --system -v -e /jupyter
+RUN uv pip install --system /jupyter
+
+RUN chown jupyter:jupyter -R /usr/local/lib/python3.11/site-packages/biome/adhoc_data/
 
 RUN mkdir -m 777 /var/run/beaker
 
@@ -28,11 +30,5 @@ ENV BEAKER_SUBKERNEL_USER=user
 ENV BEAKER_RUN_PATH=/var/run/beaker
 ENV BEAKER_APP=biome.app.BiomeApp
 
-RUN ln -s /jupyter/src/biome/datasources /home/user/datasources
-# subkernel access / file pane
-RUN ln -s /jupyter/data /home/user/data
-# agent path resolution
-RUN ln -s /jupyter/data /home/jupyter/data
-
 # Service
 CMD ["python", "-m", "beaker_kernel.service.server", "--ip", "0.0.0.0"]
diff --git a/pyproject.toml b/pyproject.toml
@@ -7,7 +7,7 @@ name = "biome"
 dynamic = ["version"]
 description = ''
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 license = "MIT"
 keywords = []
 authors = [
@@ -25,9 +25,9 @@ classifiers = [
   "Programming Language :: Python :: Implementation :: PyPy",
 ]
 dependencies = [
-  "beaker-kernel~=1.11.0",
+  "beaker-kernel~=1.12.0",
   "adhoc-api~=2.4.0",
-  "archytas~=1.4.0",
+  "archytas~=1.5.0",
   "requests",
   "PyYAML",
   "idc-index",

diff --git a/rest_api/Dockerfile b/rest_api/Dockerfile
@@ -5,7 +5,6 @@ FROM python:3.11.5
 EXPOSE 8001
 
 COPY ./rest_api /rest_api
-COPY ./data /data
 WORKDIR /rest_api
 
 RUN pip install --upgrade --no-cache-dir pip

diff --git a/data/census-acs/2023-1yr-api-changes.csv → .../data/census-acs/2023-1yr-api-changes.csv b/data/census-acs/2023-1yr-api-changes.csv → .../data/census-acs/2023-1yr-api-changes.csv
diff --git a/data/census-ahs/census_ahs_codebook.csv → ...a/data/census-ahs/census_ahs_codebook.csv b/data/census-ahs/census_ahs_codebook.csv → ...a/data/census-ahs/census_ahs_codebook.csv
diff --git a/data/census-ahs/survey_1999.csv → ...dhoc_data/data/census-ahs/survey_1999.csv b/data/census-ahs/survey_1999.csv → ...dhoc_data/data/census-ahs/survey_1999.csv
diff --git a/data/census-ahs/survey_2001.csv → ...dhoc_data/data/census-ahs/survey_2001.csv b/data/census-ahs/survey_2001.csv → ...dhoc_data/data/census-ahs/survey_2001.csv
diff --git a/data/census-ahs/survey_2003.csv → ...dhoc_data/data/census-ahs/survey_2003.csv b/data/census-ahs/survey_2003.csv → ...dhoc_data/data/census-ahs/survey_2003.csv
diff --git a/data/census-ahs/survey_2005.csv → ...dhoc_data/data/census-ahs/survey_2005.csv b/data/census-ahs/survey_2005.csv → ...dhoc_data/data/census-ahs/survey_2005.csv
diff --git a/data/census-ahs/survey_2007.csv → ...dhoc_data/data/census-ahs/survey_2007.csv b/data/census-ahs/survey_2007.csv → ...dhoc_data/data/census-ahs/survey_2007.csv
diff --git a/data/census-ahs/survey_2009.csv → ...dhoc_data/data/census-ahs/survey_2009.csv b/data/census-ahs/survey_2009.csv → ...dhoc_data/data/census-ahs/survey_2009.csv
diff --git a/data/census-ahs/survey_2011.csv → ...dhoc_data/data/census-ahs/survey_2011.csv b/data/census-ahs/survey_2011.csv → ...dhoc_data/data/census-ahs/survey_2011.csv
diff --git a/data/census-ahs/survey_2013.csv → ...dhoc_data/data/census-ahs/survey_2013.csv b/data/census-ahs/survey_2013.csv → ...dhoc_data/data/census-ahs/survey_2013.csv
diff --git a/data/census-ahs/survey_2015.csv → ...dhoc_data/data/census-ahs/survey_2015.csv b/data/census-ahs/survey_2015.csv → ...dhoc_data/data/census-ahs/survey_2015.csv
diff --git a/data/census-ahs/survey_2017.csv → ...dhoc_data/data/census-ahs/survey_2017.csv b/data/census-ahs/survey_2017.csv → ...dhoc_data/data/census-ahs/survey_2017.csv
diff --git a/data/census-ahs/survey_2019.csv → ...dhoc_data/data/census-ahs/survey_2019.csv b/data/census-ahs/survey_2019.csv → ...dhoc_data/data/census-ahs/survey_2019.csv
diff --git a/data/census-ahs/survey_2021.csv → ...dhoc_data/data/census-ahs/survey_2021.csv b/data/census-ahs/survey_2021.csv → ...dhoc_data/data/census-ahs/survey_2021.csv
diff --git a/data/census-ahs/survey_2023.csv → ...dhoc_data/data/census-ahs/survey_2023.csv b/data/census-ahs/survey_2023.csv → ...dhoc_data/data/census-ahs/survey_2023.csv
diff --git a/data/census-nsch/2016e_topical.sas7bdat → ...a/data/census-nsch/2016e_topical.sas7bdat b/data/census-nsch/2016e_topical.sas7bdat → ...a/data/census-nsch/2016e_topical.sas7bdat
diff --git a/data/census-nsch/2017e_topical.sas7bdat → ...a/data/census-nsch/2017e_topical.sas7bdat b/data/census-nsch/2017e_topical.sas7bdat → ...a/data/census-nsch/2017e_topical.sas7bdat
diff --git a/data/census-nsch/2018e_topical.sas7bdat → ...a/data/census-nsch/2018e_topical.sas7bdat b/data/census-nsch/2018e_topical.sas7bdat → ...a/data/census-nsch/2018e_topical.sas7bdat
diff --git a/data/census-nsch/2019e_topical.sas7bdat → ...a/data/census-nsch/2019e_topical.sas7bdat b/data/census-nsch/2019e_topical.sas7bdat → ...a/data/census-nsch/2019e_topical.sas7bdat
diff --git a/data/census-nsch/2020e_topical.sas7bdat → ...a/data/census-nsch/2020e_topical.sas7bdat b/data/census-nsch/2020e_topical.sas7bdat → ...a/data/census-nsch/2020e_topical.sas7bdat
diff --git a/data/census-nsch/2021e_topical.sas7bdat → ...a/data/census-nsch/2021e_topical.sas7bdat b/data/census-nsch/2021e_topical.sas7bdat → ...a/data/census-nsch/2021e_topical.sas7bdat
diff --git a/data/census-nsch/2022e_topical.sas7bdat → ...a/data/census-nsch/2022e_topical.sas7bdat b/data/census-nsch/2022e_topical.sas7bdat → ...a/data/census-nsch/2022e_topical.sas7bdat
diff --git a/data/census-nsch/2023e_topical.sas7bdat → ...a/data/census-nsch/2023e_topical.sas7bdat b/data/census-nsch/2023e_topical.sas7bdat → ...a/data/census-nsch/2023e_topical.sas7bdat
diff --git a/.../census-nsch/nsch_dictionary_codebook.csv → .../census-nsch/nsch_dictionary_codebook.csv b/.../census-nsch/nsch_dictionary_codebook.csv → .../census-nsch/nsch_dictionary_codebook.csv
diff --git a/...asthma-prevalence-by-county-2015_2022.csv → ...asthma-prevalence-by-county-2015_2022.csv b/...asthma-prevalence-by-county-2015_2022.csv → ...asthma-prevalence-by-county-2015_2022.csv
diff --git a/data/epa-tri/EPA_TRI_Toxics_2014_2023.csv → ...data/epa-tri/EPA_TRI_Toxics_2014_2023.csv b/data/epa-tri/EPA_TRI_Toxics_2014_2023.csv → ...data/epa-tri/EPA_TRI_Toxics_2014_2023.csv
diff --git a/data/fda-gras/GRASNotices.csv → .../adhoc_data/data/fda-gras/GRASNotices.csv b/data/fda-gras/GRASNotices.csv → .../adhoc_data/data/fda-gras/GRASNotices.csv
diff --git a/...nhanes_dietary/1999_2000_DEMOGRAPHICS.xpt → ...nhanes_dietary/1999_2000_DEMOGRAPHICS.xpt b/...nhanes_dietary/1999_2000_DEMOGRAPHICS.xpt → ...nhanes_dietary/1999_2000_DEMOGRAPHICS.xpt
diff --git a/...s_dietary/1999_2000_DRXFMT_food_codes.xpt → ...s_dietary/1999_2000_DRXFMT_food_codes.xpt b/...s_dietary/1999_2000_DRXFMT_food_codes.xpt → ...s_dietary/1999_2000_DRXFMT_food_codes.xpt
diff --git a/...ary/1999_2000_DRXIFF_individual_foods.xpt → ...ary/1999_2000_DRXIFF_individual_foods.xpt b/...ary/1999_2000_DRXIFF_individual_foods.xpt → ...ary/1999_2000_DRXIFF_individual_foods.xpt
diff --git a/...nhanes_dietary/2005_2006_DEMOGRAPHICS.xpt → ...nhanes_dietary/2005_2006_DEMOGRAPHICS.xpt b/...nhanes_dietary/2005_2006_DEMOGRAPHICS.xpt → ...nhanes_dietary/2005_2006_DEMOGRAPHICS.xpt
diff --git a/...ary/2005_2006_DR1IFF_individual_foods.xpt → ...ary/2005_2006_DR1IFF_individual_foods.xpt b/...ary/2005_2006_DR1IFF_individual_foods.xpt → ...ary/2005_2006_DR1IFF_individual_foods.xpt
diff --git a/...s_dietary/2005_2006_DRXFCD_food_codes.xpt → ...s_dietary/2005_2006_DRXFCD_food_codes.xpt b/...s_dietary/2005_2006_DRXFCD_food_codes.xpt → ...s_dietary/2005_2006_DRXFCD_food_codes.xpt
diff --git a/...y/2005_2006_DRXMCD_modification_codes.xpt → ...y/2005_2006_DRXMCD_modification_codes.xpt b/...y/2005_2006_DRXMCD_modification_codes.xpt → ...y/2005_2006_DRXMCD_modification_codes.xpt
diff --git a/...nhanes_dietary/2009-2010_DEMOGRAPHICS.xpt → ...nhanes_dietary/2009-2010_DEMOGRAPHICS.xpt b/...nhanes_dietary/2009-2010_DEMOGRAPHICS.xpt → ...nhanes_dietary/2009-2010_DEMOGRAPHICS.xpt
diff --git a/...ary/2009_2010_DR1IFF_individual_foods.xpt → ...ary/2009_2010_DR1IFF_individual_foods.xpt b/...ary/2009_2010_DR1IFF_individual_foods.xpt → ...ary/2009_2010_DR1IFF_individual_foods.xpt
diff --git a/...s_dietary/2009_2010_DRXFCD_food_codes.xpt → ...s_dietary/2009_2010_DRXFCD_food_codes.xpt b/...s_dietary/2009_2010_DRXFCD_food_codes.xpt → ...s_dietary/2009_2010_DRXFCD_food_codes.xpt
diff --git a/...y/2009_2010_DRXMCD_modification_codes.xpt → ...y/2009_2010_DRXMCD_modification_codes.xpt b/...y/2009_2010_DRXMCD_modification_codes.xpt → ...y/2009_2010_DRXMCD_modification_codes.xpt
diff --git a/...nhanes_dietary/2015_2016_DEMOGRAPHICS.xpt → ...nhanes_dietary/2015_2016_DEMOGRAPHICS.xpt b/...nhanes_dietary/2015_2016_DEMOGRAPHICS.xpt → ...nhanes_dietary/2015_2016_DEMOGRAPHICS.xpt
diff --git a/...ary/2015_2016_DR1IFF_individual_foods.xpt → ...ary/2015_2016_DR1IFF_individual_foods.xpt b/...ary/2015_2016_DR1IFF_individual_foods.xpt → ...ary/2015_2016_DR1IFF_individual_foods.xpt
diff --git a/...s_dietary/2015_2016_DRXFCD_food_codes.xpt → ...s_dietary/2015_2016_DRXFCD_food_codes.xpt b/...s_dietary/2015_2016_DRXFCD_food_codes.xpt → ...s_dietary/2015_2016_DRXFCD_food_codes.xpt
diff --git a/...nhanes_dietary/2017_2020_DEMOGRAPHICS.xpt → ...nhanes_dietary/2017_2020_DEMOGRAPHICS.xpt b/...nhanes_dietary/2017_2020_DEMOGRAPHICS.xpt → ...nhanes_dietary/2017_2020_DEMOGRAPHICS.xpt
diff --git a/...ary/2017_2020_DR1IFF_individual_foods.xpt → ...ary/2017_2020_DR1IFF_individual_foods.xpt b/...ary/2017_2020_DR1IFF_individual_foods.xpt → ...ary/2017_2020_DR1IFF_individual_foods.xpt
diff --git a/...s_dietary/2017_2020_DRXFCD_food_codes.xpt → ...s_dietary/2017_2020_DRXFCD_food_codes.xpt b/...s_dietary/2017_2020_DRXFCD_food_codes.xpt → ...s_dietary/2017_2020_DRXFCD_food_codes.xpt
diff --git a/...nhanes_dietary/2021_2023_DEMOGRAPHICS.xpt → ...nhanes_dietary/2021_2023_DEMOGRAPHICS.xpt b/...nhanes_dietary/2021_2023_DEMOGRAPHICS.xpt → ...nhanes_dietary/2021_2023_DEMOGRAPHICS.xpt
diff --git a/...ary/2021_2023_DR1IFF_individual_foods.xpt → ...ary/2021_2023_DR1IFF_individual_foods.xpt b/...ary/2021_2023_DR1IFF_individual_foods.xpt → ...ary/2021_2023_DR1IFF_individual_foods.xpt
diff --git a/...s_dietary/2021_2023_DRXFCD_food_codes.xpt → ...s_dietary/2021_2023_DRXFCD_food_codes.xpt b/...s_dietary/2021_2023_DRXFCD_food_codes.xpt → ...s_dietary/2021_2023_DRXFCD_food_codes.xpt
diff --git a/...pesticide/EPest.county.estimates.2000.txt → ...pesticide/EPest.county.estimates.2000.txt b/...pesticide/EPest.county.estimates.2000.txt → ...pesticide/EPest.county.estimates.2000.txt
diff --git a/...pesticide/EPest.county.estimates.2005.txt → ...pesticide/EPest.county.estimates.2005.txt b/...pesticide/EPest.county.estimates.2005.txt → ...pesticide/EPest.county.estimates.2005.txt
diff --git a/...pesticide/EPest.county.estimates.2010.txt → ...pesticide/EPest.county.estimates.2010.txt b/...pesticide/EPest.county.estimates.2010.txt → ...pesticide/EPest.county.estimates.2010.txt
diff --git a/...e/EPest_county_estimates_2013_2017_v2.txt → ...e/EPest_county_estimates_2013_2017_v2.txt b/...e/EPest_county_estimates_2013_2017_v2.txt → ...e/EPest_county_estimates_2013_2017_v2.txt
diff --git a/...pesticide/EPest_county_estimates_2019.txt → ...pesticide/EPest_county_estimates_2019.txt b/...pesticide/EPest_county_estimates_2019.txt → ...pesticide/EPest_county_estimates_2019.txt
diff --git a/src/biome/adhoc_data/datasources/ahs/api.yaml b/src/biome/adhoc_data/datasources/ahs/api.yaml
diff --git a/...ome/datasources/ahs/documentation/docs.md → ..._data/datasources/ahs/attachments/docs.md b/...ome/datasources/ahs/documentation/docs.md → ..._data/datasources/ahs/attachments/docs.md
diff --git a/src/biome/adhoc_data/datasources/alphagenome/api.yaml b/src/biome/adhoc_data/datasources/alphagenome/api.yaml
diff --git a/...ome/documentation/alphagenome_overview.md → ...enome/attachments/alphagenome_overview.md b/...ome/documentation/alphagenome_overview.md → ...enome/attachments/alphagenome_overview.md
diff --git a/...me/documentation/alphagenome_tutorials.md → ...nome/attachments/alphagenome_tutorials.md b/...me/documentation/alphagenome_tutorials.md → ...nome/attachments/alphagenome_tutorials.md
diff --git a/src/biome/adhoc_data/datasources/aqs/api.yaml b/src/biome/adhoc_data/datasources/aqs/api.yaml
diff --git a/...me/datasources/aqs/documentation/aqs.json → ...data/datasources/aqs/attachments/aqs.json b/...me/datasources/aqs/documentation/aqs.json → ...data/datasources/aqs/attachments/aqs.json