diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 5dfea8b54..f452152d5 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 4.1.34 +current_version = 4.1.35 commit = False tag = False diff --git a/dev/docker/python/Dockerfile b/dev/docker/python/Dockerfile index 1836e4a5b..74e383d97 100644 --- a/dev/docker/python/Dockerfile +++ b/dev/docker/python/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.8-buster +FROM python:3.8-bookworm RUN apt-get update && apt-get install -y r-base && Rscript -e "install.packages(c('httr','xml2'))" diff --git a/dev/local/setup.cfg b/dev/local/setup.cfg index 588552a94..5dc9d6fa8 100644 --- a/dev/local/setup.cfg +++ b/dev/local/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = Delphi Development -version = 4.1.34 +version = 4.1.35 [options] packages = diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock index 511e8cc8d..57e785cce 100644 --- a/docs/Gemfile.lock +++ b/docs/Gemfile.lock @@ -207,14 +207,14 @@ GEM rb-fsevent (~> 0.10, >= 0.10.3) rb-inotify (~> 0.9, >= 0.9.10) mercenary (0.3.6) - mini_portile2 (2.8.8) + mini_portile2 (2.8.9) minima (2.5.1) jekyll (>= 3.5, < 5.0) jekyll-feed (~> 0.9) jekyll-seo-tag (~> 2.1) minitest (5.17.0) multipart-post (2.1.1) - nokogiri (1.18.8) + nokogiri (1.18.9) mini_portile2 (~> 2.8.2) racc (~> 1.4) octokit (4.20.0) diff --git a/integrations/server/test_covidcast_endpoints.py b/integrations/server/test_covidcast_endpoints.py index 206ed3c54..09f195f7c 100644 --- a/integrations/server/test_covidcast_endpoints.py +++ b/integrations/server/test_covidcast_endpoints.py @@ -11,6 +11,8 @@ from delphi.epidata.maintenance.covidcast_meta_cache_updater import main as update_cache from delphi.epidata.acquisition.covidcast.test_utils import CovidcastBase, CovidcastTestRow +from delphi.epidata.maintenance.coverage_crossref_updater import main as update_crossref + # use the local instance of the Epidata API BASE_URL = "http://delphi_web_epidata/epidata/covidcast" @@ -385,3 +387,19 @@ def test_coverage(self): with self.subTest("invalid geo_type"): out = self._fetch("/coverage", signal=first.signal_pair(), geo_type="doesnt_exist", format="json") self.assertEqual(len(out), 0) + + def test_geo_indicator_coverage(self): + """Request a geo_type:geo_value from the /geo_indicator_coverage endpoint.""" + + self._insert_rows([ + CovidcastTestRow.make_default_row(geo_type="state", geo_value="pa"), + CovidcastTestRow.make_default_row(geo_type="state", geo_value="ny"), + CovidcastTestRow.make_default_row(geo_type="state", geo_value="ny", signal="sig2"), + ]) + + update_crossref() + + out = self._fetch("/geo_indicator_coverage", data_source="src", signals="sig") + self.assertEqual(len(out["epidata"]), 2) + self.assertEqual(out["epidata"], ['state:ny', 'state:pa']) + diff --git a/src/client/delphi_epidata.R b/src/client/delphi_epidata.R index 56c69d722..3ab050bbe 100644 --- a/src/client/delphi_epidata.R +++ b/src/client/delphi_epidata.R @@ -15,7 +15,7 @@ Epidata <- (function() { # API base url BASE_URL <- getOption('epidata.url', default = 'https://api.delphi.cmu.edu/epidata/') - client_version <- '4.1.34' + client_version <- '4.1.35' auth <- getOption("epidata.auth", default = NA) diff --git a/src/client/delphi_epidata.js b/src/client/delphi_epidata.js index 633f40eb3..b230ff8de 100644 --- a/src/client/delphi_epidata.js +++ b/src/client/delphi_epidata.js @@ -22,7 +22,7 @@ } })(this, function (exports, fetchImpl, jQuery) { const BASE_URL = "https://api.delphi.cmu.edu/epidata/"; - const client_version = "4.1.34"; + const client_version = "4.1.35"; // Helper function to cast values and/or ranges to strings function _listitem(value) { diff --git a/src/client/packaging/npm/package-lock.json b/src/client/packaging/npm/package-lock.json index 28b4268c4..5fd7abb29 100644 --- a/src/client/packaging/npm/package-lock.json +++ b/src/client/packaging/npm/package-lock.json @@ -1,12 +1,12 @@ { "name": "delphi_epidata", - "version": "4.1.23", + "version": "4.1.34", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "delphi_epidata", - "version": "4.1.23", + "version": "4.1.34", "license": "MIT", "dependencies": { "cross-fetch": "^3.1.4" @@ -1428,6 +1428,19 @@ "integrity": "sha512-E+XQCRwSbaaiChtv6k6Dwgc+bx+Bs6vuKJHHl5kox/BaKbhiXzqQOwK4cO22yElGp2OCmjwVhT3HmxgyPGnJfQ==", "dev": true }, + "node_modules/call-bind-apply-helpers": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/call-bind-apply-helpers/-/call-bind-apply-helpers-1.0.2.tgz", + "integrity": "sha512-Sp1ablJ0ivDkSzjcaJdxEunN5/XvksFJ2sMBFfq6x0ryhQV/2b/KwFe21cMpmHtPOSij8K99/wSfoEuTObmuMQ==", + "dev": true, + "dependencies": { + "es-errors": "^1.3.0", + "function-bind": "^1.1.2" + }, + "engines": { + "node": ">= 0.4" + } + }, "node_modules/callsites": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/callsites/-/callsites-3.1.0.tgz", @@ -1717,6 +1730,20 @@ "node": ">=8" } }, + "node_modules/dunder-proto": { + "version": "1.0.1", + "resolved": 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true, "requires": { - "mime-db": "1.50.0" + "mime-db": "1.52.0" } }, "mimic-fn": { diff --git a/src/client/packaging/npm/package.json b/src/client/packaging/npm/package.json index 11752e05c..f536a0cb5 100644 --- a/src/client/packaging/npm/package.json +++ b/src/client/packaging/npm/package.json @@ -2,7 +2,7 @@ "name": "delphi_epidata", "description": "Delphi Epidata API Client", "authors": "Delphi Group", - "version": "4.1.34", + "version": "4.1.35", "license": "MIT", "homepage": "https://github.com/cmu-delphi/delphi-epidata", "bugs": { diff --git a/src/server/_config.py b/src/server/_config.py index 94ad3061a..4a0127547 100644 --- a/src/server/_config.py +++ b/src/server/_config.py @@ -7,7 +7,7 @@ load_dotenv() -VERSION = "4.1.34" +VERSION = "4.1.35" MAX_RESULTS = int(10e6) MAX_COMPATIBILITY_RESULTS = int(3650) diff --git a/src/server/endpoints/covidcast.py b/src/server/endpoints/covidcast.py index f4875fb6d..4c6b0c734 100644 --- a/src/server/endpoints/covidcast.py +++ b/src/server/endpoints/covidcast.py @@ -561,6 +561,26 @@ def handle_geo_coverage(): return execute_query(q.query, q.params, fields_string, [], []) +@bp.route("/geo_indicator_coverage", methods=("GET", "POST")) +def handle_geo_indicator_coverage(): + source_signal_sets = parse_source_signal_sets() + source_signal_sets = restrict_by_roles(source_signal_sets) + source_signal_sets, _ = create_source_signal_alias_mapper(source_signal_sets) + + q = QueryBuilder("coverage_crossref_v", "c") + fields_string = ["geo_type", "geo_value"] + + q.set_fields(fields_string) + + q.apply_source_signal_filters("source", "signal", source_signal_sets) + q.set_sort_order("geo_type", "geo_value") + q.group_by = ["c." + field for field in fields_string] # this condenses duplicate results, similar to `SELECT DISTINCT` + + def transform_row(row, proxy): + return f"{row['geo_type']}:{row['geo_value']}" + + return execute_query(q.query, q.params, fields_string, [], [], transform=transform_row) + @bp.route("/anomalies", methods=("GET", "POST")) def handle_anomalies(): """