Merge pull request #17 from smart-on-fhir/mikix/chart-review

Add chart-review as a new top-level project
smart-on-fhir · Jan 18, 2024 · 80dd25c · 80dd25c
2 parents 8658b6b + e65ae9e
commit 80dd25c
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diff --git a/.gitmodules b/.gitmodules
@@ -4,3 +4,6 @@
 [submodule "sources/cumulus-etl"]
 	path = sources/cumulus-etl
 	url = https://github.com/smart-on-fhir/cumulus-etl.git
+[submodule "sources/chart-review"]
+	path = sources/chart-review
+	url = https://github.com/smart-on-fhir/chart-review.git
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -45,6 +45,7 @@ This way, docs can update as code changes more easily.
     - https://docs.smarthealthit.org/cumulus/
     - https://docs.smarthealthit.org/cumulus/etl/
     - https://docs.smarthealthit.org/cumulus/library/
+    - https://docs.smarthealthit.org/cumulus/chart-review/
   - That rule is designed to allow each repo to move files around at will, without breaking the
     world. But don't rename files willy-nilly, since any links out there on the web or user
     bookmarks/history might break if a filename changes.

diff --git a/README.md b/README.md
@@ -33,3 +33,4 @@ When in doubt, you can post questions and suggestions here.
 But there are other useful repos that host separate pieces of Cumulus:
 - Cumulus ETL: the [cumulus-etl](https://github.com/smart-on-fhir/cumulus-etl) project
 - Cumulus Library: the [cumulus-library](https://github.com/smart-on-fhir/cumulus-library) project
+- Chart Review: the [chart-review](https://github.com/smart-on-fhir/chart-review) project
diff --git a/docs/_includes/nav_footer_custom.html b/docs/_includes/nav_footer_custom.html
@@ -1,8 +1,8 @@
 <footer class="site-footer">
   <a href="https://github.com/smart-on-fhir/cumulus">
   <picture>
-    <source srcset="assets/github-mark-white.svg" media="(prefers-color-scheme: dark)" />
-    <img style="height: 1em; width: auto" src="assets/github-mark.svg" alt="" />
+    <source srcset="/cumulus/assets/github-mark-white.svg" media="(prefers-color-scheme: dark)" />
+    <img style="height: 1em; width: auto" src="/cumulus/assets/github-mark.svg" alt="" />
   </picture>
   Source</a>.<br>
   A <a href="https://smarthealthit.org/">SMART</a> project.

diff --git a/docs/contact.md b/docs/contact.md
@@ -28,6 +28,7 @@ But if you want to search for existing reports, here are the main Cumulus subpro
 - When in doubt: the general [cumulus](https://github.com/smart-on-fhir/cumulus) project
 - Cumulus ETL: the [cumulus-etl](https://github.com/smart-on-fhir/cumulus-etl) project
 - Cumulus Library: the [cumulus-library](https://github.com/smart-on-fhir/cumulus-library) project
+- Chart Review: the [chart-review](https://github.com/smart-on-fhir/chart-review) project
 
 ## Code of Conduct
 

diff --git a/prep.sh b/prep.sh
@@ -57,4 +57,5 @@ git submodule update --init --remote
 
 # Only use nav_order 10-20 for submodules
 copy_docs cumulus-etl etl 10
-copy_docs cumulus-library library 11
+copy_docs cumulus-library library 11
+copy_docs chart-review chart-review 12
diff --git a/sources/chart-review b/sources/chart-review
diff --git a/sources/cumulus-etl b/sources/cumulus-etl
diff --git a/sources/cumulus-library b/sources/cumulus-library
+44 −3		.github/workflows/ci.yaml
+4 −4		.github/workflows/docker-hub.yaml
+11 −1		compose.yaml
+0 −3		cumulus_etl/chart_review/__init__.py
+10 −4		cumulus_etl/cli.py
+1 −1		cumulus_etl/deid/philter-config.toml
+19 −1		cumulus_etl/errors.py
+6 −1		cumulus_etl/etl/studies/covid_symptom/covid_ctakes.py
+7 −1		cumulus_etl/etl/studies/covid_symptom/covid_tasks.py
+13 −1		cumulus_etl/etl/tasks/nlp_task.py
+3 −8		cumulus_etl/fhir/fhir_auth.py
+2 −2		cumulus_etl/fhir/fhir_utils.py
+8 −5		cumulus_etl/loaders/fhir/bulk_export.py
+37 −3		cumulus_etl/nlp/watcher.py
+3 −0		cumulus_etl/upload_notes/__init__.py
+9 −9		cumulus_etl/upload_notes/cli.py
+0 −0		cumulus_etl/upload_notes/downloader.py
+0 −0		cumulus_etl/upload_notes/labelstudio.py
+0 −0		cumulus_etl/upload_notes/selector.py
+45 −45		docs/chart-review.md
+1 −1		pyproject.toml
+4 −4		tests/data/covid/output/covid_symptom__nlp_results/covid_symptom__nlp_results.000.ndjson
+2 −2		.../covid/term-exists/covid_symptom__nlp_results_term_exists/covid_symptom__nlp_results_term_exists.000.ndjson
+9 −0		tests/data/nlp-regression/expected-output/covid_symptom__nlp_results.000.meta
+16 −0		tests/data/nlp-regression/expected-output/covid_symptom__nlp_results.000.ndjson
+5 −0		tests/data/nlp-regression/input/DocumentReference.ndjson
+8 −0		tests/data/nlp-regression/input/README.md
+1 −0		tests/data/nlp-regression/phi/codebook.json
+48 −1		tests/etl/test_etl_cli.py
+5 −3		tests/fhir/test_fhir_client.py
+6 −3		tests/test_cli.py
+0 −0		tests/upload_notes/__init__.py
+24 −24		tests/upload_notes/test_upload_cli.py
+4 −4		tests/upload_notes/test_upload_labelstudio.py
+9 −0		cumulus_library/.sqlfluff
+1 −1		cumulus_library/__init__.py
+12 −5		cumulus_library/base_table_builder.py
+161 −99		cumulus_library/cli.py
+26 −1		cumulus_library/cli_parser.py
+103 −3		cumulus_library/databases.py
+17 −0		cumulus_library/enums.py
+10 −8		cumulus_library/errors.py
+12 −0		cumulus_library/helper.py
+60 −0		cumulus_library/protected_table_builder.py
+8 −2		cumulus_library/statistics/counts.py
+148 −57		cumulus_library/statistics/psm.py
+97 −0		cumulus_library/studies/core/builder_condition.py
+176 −0		cumulus_library/studies/core/builder_condition.sql
+0 −43		cumulus_library/studies/core/builder_condition_codeableconcept.py
+12 −5		cumulus_library/studies/core/builder_core_medication.py
+1 −1		cumulus_library/studies/core/builder_encounter_coding.py
+1 −1		cumulus_library/studies/core/builder_patient_extension.py
+23 −0		cumulus_library/studies/core/builder_prereq_tables.py
+0 −90		cumulus_library/studies/core/condition.sql
+51 −0		cumulus_library/studies/core/core_templates/condition.sql.jinja
+16 −0		cumulus_library/studies/core/core_templates/core_templates.py
+38 −0		cumulus_library/studies/core/core_templates/core_utils.jinja
+14 −4		cumulus_library/studies/core/count_core.py
+1 −1		cumulus_library/studies/core/fhir_lookup_tables.sql
+2 −2		cumulus_library/studies/core/fhir_mapping_tables.sql
+3 −6		cumulus_library/studies/core/manifest.toml
+19 −6		cumulus_library/studies/template/manifest.toml
+1 −1		cumulus_library/studies/vocab/vocab_icd_builder.py
+266 −82		cumulus_library/study_parser.py
+2 −0		cumulus_library/template_sql/alias_table.sql.jinja
+4 −2		cumulus_library/template_sql/column_datatype.sql.jinja
+4 −3		cumulus_library/template_sql/ctas_empty.sql.jinja
+4 −0		cumulus_library/template_sql/insert_into.sql.jinja
+1 −0		cumulus_library/template_sql/select_all.sql.jinja
+56 −17		cumulus_library/template_sql/statistics/count.sql.jinja
+24 −0		cumulus_library/template_sql/statistics/counts_templates.py
+1 −1		cumulus_library/template_sql/statistics/psm_create_covariate_table.sql.jinja
+2 −0		cumulus_library/template_sql/statistics/psm_templates.py
+47 −31		cumulus_library/template_sql/templates.py
+68 −70		cumulus_library/template_sql/utils.py
+34 −1		docs/statistics.md
+10 −10		docs/statistics/propensity-score-matching.md
+3 −1		pyproject.toml
+125 −16		tests/conftest.py
+460 −460		tests/regression/reference/core__count_condition_month.csv
+ −		tests/regression/reference/core__count_condition_month.parquet
+ −		tests/regression/reference/core__count_documentreference_month.parquet
+ −		tests/regression/reference/core__count_encounter_enc_type_month.parquet
+ −		tests/regression/reference/core__count_encounter_month.parquet
+ −		tests/regression/reference/core__count_encounter_priority_month.parquet
+ −		tests/regression/reference/core__count_encounter_service_month.parquet
+ −		tests/regression/reference/core__count_encounter_type.parquet
+ −		tests/regression/reference/core__count_encounter_type_month.parquet
+ −		tests/regression/reference/core__count_medicationrequest_month.parquet
+ −		tests/regression/reference/core__count_observation_lab_month.parquet
+270 −270		tests/regression/reference/core__count_patient.csv
+ −		tests/regression/reference/core__count_patient.parquet
+ −		tests/regression/reference/core__meta_date.parquet
+ −		tests/regression/reference/core__meta_version.parquet
+118 −16		tests/test_cli.py
+45 −0		tests/test_conftest.py
+8 −3		tests/test_core.py
+38 −16		tests/test_counts_templates.py
+6 −6		tests/test_data/core/core__count_documentreference_month.txt
+19 −19		tests/test_data/core/core__count_encounter_month.txt
+12 −0		tests/test_data/core/core__count_medicationrequest_month.txt
+7 −7		tests/test_data/core/core__count_observation_lab_month.txt
+16 −16		tests/test_data/core/core__documentreference.txt
+50 −50		tests/test_data/core/core__patient.txt
+ −		tests/test_data/duckdb_data/duck.db
+7 −0		tests/test_data/psm/manifest.toml
+3 −0		tests/test_data/psm/psm_cohort.sql
+5 −4		tests/test_data/psm/psm_config.toml
+5 −4		tests/test_data/psm/psm_config_no_optional.toml
+7 −0		tests/test_data/study_invalid_bad_query/manifest.toml
+1 −0		tests/test_data/study_invalid_bad_query/test.sql
+1 −1		tests/test_data/study_python_counts_valid/module1.py
+1 −1		tests/test_data/study_python_counts_valid/module2.py
+1 −1		tests/test_data/study_python_no_subclass/module1.py
+1 −1		tests/test_data/study_python_no_subclass/module2.py
+1 −1		tests/test_data/study_python_valid/module1.py
+1 −1		tests/test_data/study_python_valid/module2.py
+26 −1		tests/test_duckdb.py
+42 −22		tests/test_psm.py
+9 −3		tests/test_psm_templates.py
+239 −57		tests/test_study_parser.py
+51 −58		tests/test_template_utils.py
+93 −35		tests/test_templates.py