Update auto deploy to dev: add venv #99
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* Update requirements_hub.txt (#91) * Add manual deploy to dev. (#94) * Add manual deploy to dev. * Add break line * Add on push for test. * Add on push for test. * Change deploy triggered manually. * Upgrade web to biothings api 0.12.2 (#95) * Update auto deploy to dev: add venv (#99) * Auto archive genomics_api (#103)
everaldorodrigo
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* lineage-mutations first version. * lineage-mutations using ES query_string. * Split code in functions. * Change querystring params: lineages and mutations. * Parse ES query result to API response. * Parse ES query result to API response. * Improve the code. * Configure genomics ES indices. * Add new ES indices to /lineage. * Add new ES indices to /location-lookup. * Add unit test to lineage-mutations. * Refactor lineage. * Refactor lineage. * Refactor location-details. * Refactor location-details. * Refactor sequence-count. * Refactor /global-prevalence. * Added test. * Refactor /lineage-mutations. * Refactor /prevalence-by-location and /mutation-details. * Fix tests. * Refactor /mutations-by-lineage. * Fix tests. * Passing all tests. However, more tests are needed. * Add tests. * Refactor /mutation-details. * Create genomics v3. * 💅 * Fix tests according with new data release. * Clean ES queries. * Refactor /mutations-by-lineage. * Refactor handlers to v3 and create test. * Refactor ./global-prevalence on v3. * Refactor ./prevalence-by-location * Refactor ./lineage-by-country * Remove unused code. * Refactor. * Refactor ./sequence-count * Remove unused code. * Refactor ./mutations-by-lineage * Refactor ./prevalence-by-location * Add query param q to ./prevalence-by-location * Remove location_id from ./prevalence-by-location result key. * Refactor ./mutations-by-lineage * 💅 tests * Format code. * Format code. * Format code. * Format code. * Format code. * Change query delimiter to '|' in ./prevalence-by-location * Format code. * Format code. * Improve tests. * Format code. * Improve compatibability from v3 to v2. * Code refactor. * Fix ./sequence-count route result. * Refactor: add params adapter to lineage-mutations-v3. * Add 'q' param to lineage-mutations v3. * Fix tests: compare core function. * Fix performance issue in ./prevalence-by-location * Fix issue in ./prevalence-by-location using 'OR' * Add tests. * Refactor ./lineage-by-sub-admin-most-recent * Improve performance querying specific ES index. * Add headers to v3 base handler. * Add headers to v2 and v3 base handler. * Add headers to v2 and v3 base handler. * Add 'q' param to ./mutations-by-lineage v3. * Fix issue in ./lineage-by-sub-admin-most-recent. * Format code and add escape to es queries string fields. * Add v3 routes. * Add v3 routes. * Fix test. * Fix test. * fix prevalence-by-location. * Fix prevalence-by-location. * Refactor splitting in files. * Clean code. * Fix ./lineage-by-sub-admin-most-recent * Remove unused code. * Fix mutation-details. * Remove unused code. * Fix mutations according to new data structure. * Remove unused code. * Format code. * Format code. * Upgrade scipy * Remove unused code. * Change ES queries to DSL. * Fix gisaid auth warning for aiohttp.ClientSession. * Add new field pangolin_lineage_crumbs to 'q' queries. * Set API_VERSION to v3 * Update handlers-refactoring with master (#108) * Update requirements_hub.txt (#91) * Add manual deploy to dev. (#94) * Add manual deploy to dev. * Add break line * Add on push for test. * Add on push for test. * Change deploy triggered manually. * Upgrade web to biothings api 0.12.2 (#95) * Update auto deploy to dev: add venv (#99) * Auto archive genomics_api (#103) * Add default biothings endpoints. Ex: /status
everaldorodrigo
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Jan 4, 2024
* update readme for new location of index.py * init * add pointer to genomics api page * Count documents instead of mutations. Closes outbreak-info/outbreak.info#208 * Added check if key in dict * comparison script * Update issue templates * updated config for covid19 * updated config for resources * Added utility function to get total hits for ES6/7 * Added parameter for ES7 * genomics test suite * install biothings from https URL for easier web deployment * fix: doc_type no longer needed * update genomics tests * minimize requirements_web * pin markupsafe version in requirements * fix: 🔨 vuex link * tests update * added in Marco's change for genomics. * remove unused handlers.py file * Update index.html Remove fixed size causing mobile view issue * test refactor/factoring * update default operator for resources query builder to AND * Bump libs (#52) * Upgrade libs. * update resources search to filter new NDE sources * Update pipeline.py * update filtering for zenodo * Updated install commands * increase default response timeout to 10m * update metadata handler to handle no-downtime style index name * Update base.py * Update util.py * commenting print statements out of handlers * Add Zenodo badge * nginx clear cache util * Add an example for lineage and mutation query parser * test index tests * delay deletes in waves * tested cache * Add size parameter to API lookup functions * Fix input validation * update file first for idempotence. shorten delay * Add API version 2, Add gene parameter to /lineage-mutations, Refactor handler following biothings.web format * rewrite coroutine to async def * Switch to use the config file for customizing an API; Add pre-comit * Add genomics API version 2: /lineage-mutations, /lineage, /location * simplify static handler setting * Add time windows to longitudinal queries; Fix default args params * Fix missing await; Fix size=0 in query * Copy PrevalenceAllLineagesByLocationHandler from the origin version and Fix format code; Copy document from the origin version * Add time window to the prevalence-by-location-all-lineages API; Refator following biothings convention * switched v2 handlers to prod * Delete .github/ISSUE_TEMPLATE directory * Update docs.md * Document prevalence-by-position * Update docs.md * Update docs.md * adding local builder and mapper * updated hub.py for 0.11.x biothings * updated config_hub.py for 0.11.x biothings * remove compare_results.p from repo * updated requirements_hub.txt * Merge branch 'guru_dev' (#84) * Merge branch 'guru_dev' --------- Co-authored-by: remoteeng00 <remoteeng00@gmail.com> Co-authored-by: Chunlei Wu <newgene@users.noreply.github.com> Co-authored-by: remoteeng00 <67749546+remoteeng00@users.noreply.github.com> Co-authored-by: Chunlei Wu <anewgene@yahoo.com> * Update docs.md * Set pangolin_lineage to be not required (#86) * added handlers for significance endpoint * accidentally deleted requirements * reverted requirements.txt * added break line * i added a new line this time for sure * fixed significance endpoint * removed unneeded import in significance and added growth_rate handlers * changed es index to correct one * Fix ref to dev api * Removed base app list from genomics handlers and added min_date, max_date arguments to mutations-by-lineage handler * Set global daily prevalence as deprecated * Update docs.md * Finish half-written sentence * removed logging and prints used for testing * Update hub icon. (#89) * Update requirements_hub.txt (#91) * Add manual deploy to dev. (#94) * Add manual deploy to dev. * Add break line * Add on push for test. * Add on push for test. * Change deploy triggered manually. * Upgrade web to biothings api 0.12.2 (#95) * Update auto deploy to dev: add venv (#99) * Auto archive genomics_api (#103) * Handlers refactoring (#96) * lineage-mutations first version. * lineage-mutations using ES query_string. * Split code in functions. * Change querystring params: lineages and mutations. * Parse ES query result to API response. * Parse ES query result to API response. * Improve the code. * Configure genomics ES indices. * Add new ES indices to /lineage. * Add new ES indices to /location-lookup. * Add unit test to lineage-mutations. * Refactor lineage. * Refactor lineage. * Refactor location-details. * Refactor location-details. * Refactor sequence-count. * Refactor /global-prevalence. * Added test. * Refactor /lineage-mutations. * Refactor /prevalence-by-location and /mutation-details. * Fix tests. * Refactor /mutations-by-lineage. * Fix tests. * Passing all tests. However, more tests are needed. * Add tests. * Refactor /mutation-details. * Create genomics v3. * 💅 * Fix tests according with new data release. * Clean ES queries. * Refactor /mutations-by-lineage. * Refactor handlers to v3 and create test. * Refactor ./global-prevalence on v3. * Refactor ./prevalence-by-location * Refactor ./lineage-by-country * Remove unused code. * Refactor. * Refactor ./sequence-count * Remove unused code. * Refactor ./mutations-by-lineage * Refactor ./prevalence-by-location * Add query param q to ./prevalence-by-location * Remove location_id from ./prevalence-by-location result key. * Refactor ./mutations-by-lineage * 💅 tests * Format code. * Format code. * Format code. * Format code. * Format code. * Change query delimiter to '|' in ./prevalence-by-location * Format code. * Format code. * Improve tests. * Format code. * Improve compatibability from v3 to v2. * Code refactor. * Fix ./sequence-count route result. * Refactor: add params adapter to lineage-mutations-v3. * Add 'q' param to lineage-mutations v3. * Fix tests: compare core function. * Fix performance issue in ./prevalence-by-location * Fix issue in ./prevalence-by-location using 'OR' * Add tests. * Refactor ./lineage-by-sub-admin-most-recent * Improve performance querying specific ES index. * Add headers to v3 base handler. * Add headers to v2 and v3 base handler. * Add headers to v2 and v3 base handler. * Add 'q' param to ./mutations-by-lineage v3. * Fix issue in ./lineage-by-sub-admin-most-recent. * Format code and add escape to es queries string fields. * Add v3 routes. * Add v3 routes. * Fix test. * Fix test. * fix prevalence-by-location. * Fix prevalence-by-location. * Refactor splitting in files. * Clean code. * Fix ./lineage-by-sub-admin-most-recent * Remove unused code. * Fix mutation-details. * Remove unused code. * Fix mutations according to new data structure. * Remove unused code. * Format code. * Format code. * Upgrade scipy * Remove unused code. * Change ES queries to DSL. * Fix gisaid auth warning for aiohttp.ClientSession. * Add new field pangolin_lineage_crumbs to 'q' queries. * Set API_VERSION to v3 * Update handlers-refactoring with master (#108) * Update requirements_hub.txt (#91) * Add manual deploy to dev. (#94) * Add manual deploy to dev. * Add break line * Add on push for test. * Add on push for test. * Change deploy triggered manually. * Upgrade web to biothings api 0.12.2 (#95) * Update auto deploy to dev: add venv (#99) * Auto archive genomics_api (#103) * Add default biothings endpoints. Ex: /status * Improve tests and metadata. (#109) * Fix query with chars: [ and ] (#110) * Add tests to fix query with chars: [ and ] (#111) * web/handlers/genomics/gisaid_auth.py (#112) * Add auth to default endpoints (#113) * Increase timeout to ES queries. (#114) --------- Co-authored-by: Julia Mullen <julia.l.mullen@gmail.com> Co-authored-by: Marco Cano <artofmarco@gmail.com> Co-authored-by: gkarthik <xraydiffraction@gmail.com> Co-authored-by: Laura Hughes <flaneuse@users.noreply.github.com> Co-authored-by: Chunlei Wu <newgene@users.noreply.github.com> Co-authored-by: remoteeng00 <remoteeng00@gmail.com> Co-authored-by: Chunlei Wu <anewgene@yahoo.com> Co-authored-by: remoteeng00 <67749546+remoteeng00@users.noreply.github.com> Co-authored-by: jal347 <linjason.03@gmail.com> Co-authored-by: Jason Lin <35415519+jal347@users.noreply.github.com>
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