Release Delphi Epidata 4.1.44 - #1753
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* Create rvdss_historic.py * Create rvdss_update.py * create utils.py for common functions * create constants.py and update utils * Update rvdss_historic.py * Update rvdss_update.py * fix typo and add missing abbreviation to constants * fix typo * add missing geo * Update constants.py * Revert "Update constants.py" This reverts commit 07ed998. * Revert "add missing geo" This reverts commit 08f908a. * fix geo and virus abbreviation * remove "province of" from geo_values * construct urls automatically * comment constants * note historic urls don't need to be updated * be stricter about importing local fns * move dashboard file names to constants * move run-the-whole-pipeline code into main() * add code to calculate number of positive tests back in * update abbreviate_geo to remove periods and other spelling * fix lab name missing province * comment historic script * move output file names to constants * replace boolean comparisons with pythonic "not" * actually put csv names in constants * break more helper functions and add doctsrings * add more comments * calculate update dates in a new function * combine different spellings of labs * change slash to underscore in constants and move more processing code into seperate function * rvdss interface and new fn layout so current/historical data can be easily fetched (#1551) * add basic sql tables -- needs update with real col names * rename files * add main fn with CLI; remove date range params in package frontend fn stubs * start filling out historical fn stubs * rest of new fn layout. adds CLI * dashboard results can be stored directly in list in fetch_historical_dashboard_data * Add in archived dashboards, and calculate start year from data * address todos and fix historical fetching * Change misspelled CB to BC * Update imports --------- Co-authored-by: cchuong <cchuong2000@gmail.com> * test outline * add regex as dependency * add unidecode as dependency * import relative to delphi.epidata * switch all rvdss tests from unittest to pytest; basic abbr virus tests * Update test_utils.py * Add tests and testdata * Add utils tests and move test data * Add testdata of historic reports * Add additional tests and testdata * Update sql table definitions and add extra na values to historic data script * Add extra values that should be read as NA and counts with spaces in them * update sql keys * Update pull_historic.py * Update rvdss.sql * remove unused code and table definition * add extra edge cases, and duplicate checking * remove saving to csv * remove scripts for manual testing * add extra duplication checks and check if tables exists * add logger * add basic integration tests * Combine multiple tables into one * stop scraping unused table * skeleton integration tests * Check for duplicate indexes and use merge to combine tables * test extra edge case * Clean up old comments * cleanup old code to do with unused tables * update tests for new table structure * Update unit tests and remove unused functions/tests * Update functions to combine tables * Update unit tests to check dtype and column order * historic report data is a single dict not a list * pass both years in the season instead of the startyear * Remove unused variables and move logger * Change http to https * add RVDSS endpoint and python client support * Fix 2012 being used instead of 2013 in the first two weeks of the 2013-2014 season * Update patch function to take multiple seasons * Add extra NA string and fix combining table function * review feedback. simplify and clean up rvdss server code * export rvdss endpoint * update actions/cache version * Add more edge cases, fix incorrect time_values * Convert epiweek and date types * Insert columns only if they are in the data being inserted * Fix geo_type typo * Add time_type and fix typo * Combine different lab names that refer to the same lab * Update categorization of geo_types * Update test data and tests to reflect new geo_type labelling * add integration test skeletons * move alias to variable * remove not null constraint from val columns and switch time_value and issue to int8 * typo in fake credentials * switch rvdss to filter on epiweek col instead of time_value * change tests and percent positive to floats and reorder columns * Change issue and time_value to integers instead of dates, and updated tests * change data to dict and update integration tests * fix integration test connection mock * replace nan with None to match expected output * replace nans with Nones. reset_index to get index cols into SQL * Add tests requesting lists and single values of parameters * remove unused code * Add additional tests using wildcard syntax for time_values and issue * update epiweek handling * drop index column in case one is produced when reseting the index * Check for duplicated time_values * move short constants to top of file * Change open option and logger message * pass headers directly to fetch_current_dashboard_data instead of redefining them * Use constant for update filename * Remove no longer available URLS * When number of tests is 0, percent positivity should be NULL * check date format in a try-catch * print contents * remove print statement * rewind file position before checking date --------- Co-authored-by: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Add rvdss to deployment tasks
…ator (#1750) * when there are zero total tests, overwrite zero percent positivity to be null instead * modify tests to check 0 test handling
* very rough draft of nwss docs
* A complete draft
* actually previewed, various bugs. Added pop & date info
* don't actually have biobot
* intro and license
* provider table
* normalization method table
* formatting
* todos
* adding api docs for pophive
* docs: reorder parent pages
* docs(v5): initial v5 subpage.
* docs(nwss): update nwss documentation for v5 API
* docs(nwss): add by signal description and reference to auxiliar endpoint.
* docs(nwss): create v5-signals folder for v5 indicators.
* docs(v5): add reference to v5 in main page.
* docs(v5): add reference to the sources and signals
* docs(nwss): add sample sites information
* docs(v5): add better explanation or snapshot an archive endpoints.
* docs(epic-cosmos): format epic Cosmos documentationa and add references to signal and v5 pages.
* docs: remove innecesary mention of V5 on Other Endpoints
* docs(v5): correct Sources and Signals parent name
* docs(nwss): correct link to auxiliar data
* docs(nwss): Update suffices definitions
* docs(nwss): correct post precessing definition
* Apply suggestions from David
Co-authored-by: David Weber <david.weber2@pm.me>
* Apply extra suggestions from David
Co-authored-by: Javier {∅, Rdz} <39629918+JavierMtzRdz@users.noreply.github.com>
* docs(epic-cosmos): clarify the reference date
* docs: add data ingestion start to pophive and nwss
* docs(v5): update legacy API mention
* docs(v5): adding queries construction page
* docs(epic_cosmos): add note on reporting cadence
---------
Co-authored-by: dsweber2 <david.weber2@pm.me>
Co-authored-by: Nat DeFries <42820733+nmdefries@users.noreply.github.com>
Co-authored-by: aysim319 <aysim319@users.noreply.github.com>
* When there are 0 flu tests, subtype percent positivity should be null * calculate total positive flu types from positive subtype tests * add current season to list of seasons to be patched * change infs to None * replace() single values to avoid stray NaNs remaining --------- Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>
chore: sync main->dev
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We're ignoring the SonarCloud checks (and could consider turning them off). It doesn't like one of the HTML test files for |
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Releasing Delphi Epidata 4.1.44.