diff --git a/.bumpversion.cfg b/.bumpversion.cfg index b2688441b..b3cdf4c17 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 4.1.6 +current_version = 4.1.7 commit = False tag = False diff --git a/.github/workflows/create-release.yml b/.github/workflows/create-release.yml index e04bf4f59..329fa76aa 100644 --- a/.github/workflows/create-release.yml +++ b/.github/workflows/create-release.yml @@ -39,7 +39,7 @@ jobs: base: main title: Release Delphi Epidata ${{ steps.version.outputs.next_tag }} labels: chore - reviewers: krivard - assignees: krivard + reviewers: melange396 + assignees: melange396 body: | Releasing Delphi Epidata ${{ steps.version.outputs.next_tag }}. diff --git a/.github/workflows/dependabot-assignments.yml b/.github/workflows/dependabot-assignments.yml index 5afa8c093..b511425f2 100644 --- a/.github/workflows/dependabot-assignments.yml +++ b/.github/workflows/dependabot-assignments.yml @@ -7,11 +7,11 @@ permissions: jobs: dependabot: runs-on: ubuntu-latest - env: - GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + env: + GH_TOKEN: ${{ secrets.CMU_DELPHI_AUTOMATION_MACHINE_DEPENDABOT_PAT }} if: ${{ github.actor == 'dependabot[bot]' }} steps: - name: Assign team to PR run: gh pr edit "$PR_URL" --add-reviewer "cmu-delphi/code-reviewers" env: - PR_URL: ${{github.event.pull_request.html_url}} \ No newline at end of file + PR_URL: ${{github.event.pull_request.html_url}} diff --git a/.github/workflows/release-helper.yml b/.github/workflows/release-helper.yml index 083070cfa..71eb94d9f 100644 --- a/.github/workflows/release-helper.yml +++ b/.github/workflows/release-helper.yml @@ -147,7 +147,7 @@ jobs: base: dev title: "chore: sync main->dev" labels: chore - reviewers: krivard - assignees: krivard + reviewers: melange396 + assignees: melange396 body: | Syncing Main->Dev. diff --git a/.github/workflows/update_gdocs_data.yml b/.github/workflows/update_gdocs_data.yml index a79fa1c77..c2d6f0c07 100644 --- a/.github/workflows/update_gdocs_data.yml +++ b/.github/workflows/update_gdocs_data.yml @@ -31,7 +31,7 @@ jobs: commit-message: 'chore: update docs' title: Update Google Docs Meta Data labels: chore - reviewers: krivard - assignees: krivard + reviewers: melange396 + assignees: melange396 body: | Updating Google Docs Meta Data diff --git a/deploy.json b/deploy.json index 8dc3e91de..c1ee1ab07 100644 --- a/deploy.json +++ b/deploy.json @@ -217,6 +217,16 @@ "add-header-comment": true }, + "// maintenance", + { + "type": "move", + "src": "src/maintenance/", + "dst": "[[package]]/maintenance/", + "match": "^.*\\.(py)$", + "recursive": true, + "add-header-comment": true + }, + "// move flask tests out of the way", { "type": "move", diff --git a/dev/local/setup.cfg b/dev/local/setup.cfg index f435a1136..c36750505 100644 --- a/dev/local/setup.cfg +++ b/dev/local/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = Delphi Development -version = 4.1.6 +version = 4.1.7 [options] packages = diff --git a/docs/symptom-survey/publications.md b/docs/symptom-survey/publications.md index 49c705351..d72277455 100644 --- a/docs/symptom-survey/publications.md +++ b/docs/symptom-survey/publications.md @@ -26,6 +26,10 @@ Pandemic"](https://www.pnas.org/topic/548) in *PNAS*: Research publications using the survey data include: +- Kobayashi H, Saenz-Escarcega R, Fulk A, Agusto FB (2023). [Understanding + mental health trends during COVID-19 pandemic in the United States using + network analysis](https://doi.org/10.1371/journal.pone.0286857). *PLoS + ONE* 18(6): e0286857. - GK Charles, SP Braunstein, JL Barker, et al (2023). [How do psychobehavioural variables shed light on heterogeneity in COVID-19 vaccine acceptance? Evidence from United States general population surveys on a probability panel and @@ -43,7 +47,7 @@ Research publications using the survey data include: - M. Rubinstein, A. Haviland, and J. Breslau (2023). [The effect of COVID-19 vaccinations on self-reported depression and anxiety during February 2021](https://doi.org/10.1080/2330443X.2023.2190008). *Statistics and Public - Policy.* + Policy* 10 (1), 2190008. - Rönn MM, Menzies NA, Salomon JA (2023). [Vaccination and voting patterns in the United States: analysis of COVID-19 and flu surveys from 2010 to 2022](https://doi.org/10.1016/j.amepre.2023.03.001). *American Journal of @@ -69,15 +73,15 @@ Research publications using the survey data include: over time: Culture, uncertainty avoidance, and vaccine side-effect concerns](https://doi.org/10.1037/pspa0000320). *Journal of Personality and Social Psychology* 124 (4), 683-706. +- C. Lupton-Smith, E. Badillo Goicoechea, M. Collins, J. Lessler, M. K. + Grabowski & E. A. Stuart (2023). [Consistency between Household and County + Measures of Onsite Schooling during the COVID-19 + Pandemic](https://doi.org/10.1080/19345747.2022.2131660). *Journal of Research + on Educational Effectiveness* 16 (3), 419-441. - Rader, B., Astley, C.M., Sewalk, K. et al (2022). [Spatial modeling of vaccine deserts as barriers to controlling SARS-CoV-2](https://doi.org/10.1038/s43856-022-00183-8). *Communications Medicine* 2, 141. -- C. Lupton-Smith, E. Badillo Goicoechea, M. Collins, J. Lessler, M. K. - Grabowski & E. A. Stuart (2022). [Consistency between Household and County - Measures of Onsite Schooling during the COVID-19 - Pandemic](https://doi.org/10.1080/19345747.2022.2131660). *Journal of Research - on Educational Effectiveness*. - Nguyen, Q.C., Yardi, I., Gutierrez, F.X.M. et al. (2022). [Leveraging 13 million responses to the U.S. COVID-19 Trends and Impact Survey to examine vaccine hesitancy, vaccination, and mask wearing, January 2021-February diff --git a/integrations/acquisition/covidcast/test_covidcast_meta_caching.py b/integrations/acquisition/covidcast/test_covidcast_meta_caching.py index e746c4ef1..6e4c6378f 100644 --- a/integrations/acquisition/covidcast/test_covidcast_meta_caching.py +++ b/integrations/acquisition/covidcast/test_covidcast_meta_caching.py @@ -13,7 +13,7 @@ from delphi.epidata.client.delphi_epidata import Epidata import delphi.operations.secrets as secrets import delphi.epidata.acquisition.covidcast.database as live -from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main +from delphi.epidata.maintenance.covidcast_meta_cache_updater import main # py3tester coverage target (equivalent to `import *`) __test_target__ = ( diff --git a/integrations/client/test_delphi_epidata.py b/integrations/client/test_delphi_epidata.py index 9698d1274..4ef1fa6a3 100644 --- a/integrations/client/test_delphi_epidata.py +++ b/integrations/client/test_delphi_epidata.py @@ -11,7 +11,7 @@ # third party import delphi.operations.secrets as secrets -from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main as update_covidcast_meta_cache +from delphi.epidata.maintenance.covidcast_meta_cache_updater import main as update_covidcast_meta_cache from delphi.epidata.acquisition.covidcast.test_utils import CovidcastBase, CovidcastTestRow, FIPS, MSA from delphi.epidata.client.delphi_epidata import Epidata from delphi_utils import Nans diff --git a/integrations/server/test_covidcast_endpoints.py b/integrations/server/test_covidcast_endpoints.py index 41b74ac03..c86bb10d6 100644 --- a/integrations/server/test_covidcast_endpoints.py +++ b/integrations/server/test_covidcast_endpoints.py @@ -9,7 +9,7 @@ import requests import pandas as pd -from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main as update_cache +from delphi.epidata.maintenance.covidcast_meta_cache_updater import main as update_cache from delphi.epidata.acquisition.covidcast.test_utils import CovidcastBase, CovidcastTestRow # use the local instance of the Epidata API diff --git a/integrations/server/test_covidcast_meta.py b/integrations/server/test_covidcast_meta.py index 95a51e354..ad297f1e8 100644 --- a/integrations/server/test_covidcast_meta.py +++ b/integrations/server/test_covidcast_meta.py @@ -9,7 +9,7 @@ #first party from delphi_utils import Nans -from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main as update_cache +from delphi.epidata.maintenance.covidcast_meta_cache_updater import main as update_cache import delphi.operations.secrets as secrets # use the local instance of the Epidata API diff --git a/requirements.dev.txt b/requirements.dev.txt index 6b7b6b5db..a92efdf8d 100644 --- a/requirements.dev.txt +++ b/requirements.dev.txt @@ -1,4 +1,4 @@ -aiohttp==3.8.3 +aiohttp==3.8.5 black>=20.8b1 bump2version==1.0.1 covidcast==0.1.5 diff --git a/src/acquisition/covidcast/database.py b/src/acquisition/covidcast/database.py index 31dd3f77e..871061b81 100644 --- a/src/acquisition/covidcast/database.py +++ b/src/acquisition/covidcast/database.py @@ -526,13 +526,7 @@ def worker(): t.join() logger.info("all threads terminated") - # sort the metadata because threaded workers dgaf - sorting_fields = "data_source signal time_type geo_type".split() - sortable_fields_fn = lambda x: [(field, x[field]) for field in sorting_fields] - prepended_sortables_fn = lambda x: sortable_fields_fn(x) + list(x.items()) - tuple_representation = list(map(prepended_sortables_fn, meta)) - tuple_representation.sort() - meta = list(map(dict, tuple_representation)) # back to dict form + meta = sorted(meta, key=lambda x: (x['data_source'], x['signal'], x['time_type'], x['geo_type'])) return meta diff --git a/src/acquisition/covidcast/generate_islatest_fix_sql.py b/src/acquisition/covidcast/generate_islatest_fix_sql.py deleted file mode 100644 index 115a7d131..000000000 --- a/src/acquisition/covidcast/generate_islatest_fix_sql.py +++ /dev/null @@ -1,63 +0,0 @@ -# what data to operate on -base_where_clause = "WHERE `source`='jhu-csse' AND `time_type`='day'" -### base_where_clause = "WHERE `source`='src2' AND `time_type`='day'" ### - - -# signal name construction -# NOTE: selecting these (unique) from the database takes 7-8 mins, so reconstructing here for efficiency -# TODO: maybe just put the damn UNIQUE query in here so you dont fat-finger it again george. -# also these hardcoded signals are unique to JHU data, or are at least not used by all sources. -signals = [] -for case in ('confirmed_', 'deaths_'): - for period in ('7dav_', ''): # NOTE: that is a V as in "7 Day AVerage", not a "Y" as in "7 DAY" - for count in ('cumulative_', 'incidence_'): - for typ in ('num', 'prop'): - signals.append(case+period+count+typ) -### signals = ['sig2'] ### -# variable to split on, 'time_value' is good because its high cardinality is suitable for chunking -PARTITION_VARIABLE = 'time_value' -PARTITION_SPLITS = [20200101 + i*100 for i in range(10)] # first day of the month for jan - oct 2020 in YYYYMMDD form -### PARTITION_SPLITS = [1,2] ### - - -print(''' --- --- run this as: --- python3 generate_islatest_fix_sql.py > islatest_fix.sql --- mysql -vvv -p epidata < islatest_fix.sql --- or: --- date ; (python3 generate_islatest_fix_sql.py | mysql -vvv -p epidata ) ; date --- -''') - -# create temp table -print("CREATE TABLE `islatest_fix` (`latest_id` INT(11) NOT NULL, PRIMARY KEY (`latest_id`)) ENGINE=InnoDB DEFAULT CHARSET=utf8;") - -# find latest issue by partition (and by signal) and save primary ids into temp table -for partition_index in range(len(PARTITION_SPLITS)+1): - ge_condition = 'TRUE' if partition_index == 0 else f'`{PARTITION_VARIABLE}` >= {PARTITION_SPLITS[partition_index - 1]}' - l_condition = 'TRUE' if partition_index == len(PARTITION_SPLITS) else f'`{PARTITION_VARIABLE}` < {PARTITION_SPLITS[partition_index]}' - partition_condition = f'({ge_condition}) AND ({l_condition})' - for sig in signals: - where_clause = base_where_clause + " AND `signal`='%s' AND %s" % (sig, partition_condition) - - print(''' -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - ''' + where_clause + ''' - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); -''') - -# clear any current (potentially erroneous) is_latest_issue flags -print("UPDATE `covidcast` SET `is_latest_issue`=0 " + base_where_clause + " AND `is_latest_issue`=1;") - -# re-set proper is_latest_issue flags -print("UPDATE (SELECT `latest_id` FROM `islatest_fix`) xxx LEFT JOIN `covidcast` ON `xxx`.`latest_id`=`covidcast`.`id` SET `covidcast`.`is_latest_issue`=1;") - -# clean up temp table -print("-- TODO: drop this table") -print("-- DROP TABLE `islatest_fix`;") \ No newline at end of file diff --git a/src/acquisition/covidcast/islatest_fix.sql b/src/acquisition/covidcast/islatest_fix.sql deleted file mode 100644 index cd5475c74..000000000 --- a/src/acquisition/covidcast/islatest_fix.sql +++ /dev/null @@ -1,1774 +0,0 @@ - --- --- run this as: --- python3 generate_islatest_fix_sql.py > islatest_fix.sql --- mysql -vvv -p epidata < islatest_fix.sql --- or: --- date ; (python3 generate_islatest_fix_sql.py | mysql -vvv -p epidata ) ; date --- - -CREATE TABLE `islatest_fix` (`latest_id` INT(11) NOT NULL, PRIMARY KEY (`latest_id`)) ENGINE=InnoDB DEFAULT CHARSET=utf8; - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_cumulative_num' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_cumulative_prop' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_incidence_num' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_incidence_prop' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_num' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_prop' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_incidence_num' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_incidence_prop' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_num' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_prop' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_num' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_prop' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_num' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_prop' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_num' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_prop' AND (TRUE) AND (`time_value` < 20200101) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_cumulative_num' AND (`time_value` >= 20200101) AND (`time_value` < 20200201) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_cumulative_prop' AND (`time_value` >= 20200101) AND (`time_value` < 20200201) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - 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WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_num' AND (`time_value` >= 20200201) AND (`time_value` < 20200301) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_prop' AND (`time_value` >= 20200201) AND (`time_value` < 20200301) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - 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WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_num' AND (`time_value` >= 20200201) AND (`time_value` < 20200301) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_prop' AND (`time_value` >= 20200201) AND (`time_value` < 20200301) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_num' AND (`time_value` >= 20200201) AND (`time_value` < 20200301) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_prop' AND (`time_value` >= 20200201) AND (`time_value` < 20200301) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - 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WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_num' AND (`time_value` >= 20200301) AND (`time_value` < 20200401) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_prop' AND (`time_value` >= 20200301) AND (`time_value` < 20200401) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - 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WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_incidence_num' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_incidence_prop' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_num' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_prop' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_incidence_num' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_incidence_prop' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_num' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_prop' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_num' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_prop' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_num' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_prop' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_num' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_prop' AND (`time_value` >= 20200401) AND (`time_value` < 20200501) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_cumulative_num' AND (`time_value` >= 20200501) AND (`time_value` < 20200601) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_cumulative_prop' AND (`time_value` >= 20200501) AND (`time_value` < 20200601) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - 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WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_num' AND (`time_value` >= 20200601) AND (`time_value` < 20200701) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_prop' AND (`time_value` >= 20200601) AND (`time_value` < 20200701) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_num' AND (`time_value` >= 20200601) AND (`time_value` < 20200701) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_prop' AND (`time_value` >= 20200601) AND (`time_value` < 20200701) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_num' AND (`time_value` >= 20200601) AND (`time_value` < 20200701) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_prop' AND (`time_value` >= 20200601) AND (`time_value` < 20200701) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_cumulative_num' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_cumulative_prop' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_incidence_num' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_incidence_prop' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_num' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_prop' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_incidence_num' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_incidence_prop' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_num' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_prop' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_num' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_prop' AND (`time_value` >= 20200701) AND (`time_value` < 20200801) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - 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WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_incidence_num' AND (`time_value` >= 20200901) AND (`time_value` < 20201001) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_7dav_incidence_prop' AND (`time_value` >= 20200901) AND (`time_value` < 20201001) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_num' AND (`time_value` >= 20200901) AND (`time_value` < 20201001) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_cumulative_prop' AND (`time_value` >= 20200901) AND (`time_value` < 20201001) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - 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WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_num' AND (`time_value` >= 20200901) AND (`time_value` < 20201001) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_prop' AND (`time_value` >= 20200901) AND (`time_value` < 20201001) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_num' AND (`time_value` >= 20200901) AND (`time_value` < 20201001) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_prop' AND (`time_value` >= 20200901) AND (`time_value` < 20201001) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - 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WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_incidence_num' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='confirmed_incidence_prop' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_num' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_cumulative_prop' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_num' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_7dav_incidence_prop' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_num' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_cumulative_prop' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_num' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - - -INSERT INTO `islatest_fix` - SELECT id FROM - ( SELECT `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, MAX(`issue`) AS `issue` FROM `covidcast` - WHERE `source`='jhu-csse' AND `time_type`='day' AND `signal`='deaths_incidence_prop' AND (`time_value` >= 20201001) AND (TRUE) - GROUP BY `source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value` - ) b - LEFT JOIN `covidcast` a - USING (`source`, `signal`, `time_type`, `geo_type`, `geo_value`, `time_value`, `issue`); - -UPDATE `covidcast` SET `is_latest_issue`=0 WHERE `source`='jhu-csse' AND `time_type`='day' AND `is_latest_issue`=1; -UPDATE (SELECT `latest_id` FROM `islatest_fix`) xxx LEFT JOIN `covidcast` ON `xxx`.`latest_id`=`covidcast`.`id` SET `covidcast`.`is_latest_issue`=1; --- TODO: drop this table --- DROP TABLE `islatest_fix`; diff --git a/src/acquisition/covidcast/migrate_epidata_to_v4.py b/src/acquisition/covidcast/migrate_epidata_to_v4.py deleted file mode 100644 index f5522337e..000000000 --- a/src/acquisition/covidcast/migrate_epidata_to_v4.py +++ /dev/null @@ -1,187 +0,0 @@ -import argparse -import sys -import time -from delphi.epidata.acquisition.covidcast.database import Database - -# run as: -# python3 -u -m delphi.epidata.acquisition.covidcast.migrate_epidata_to_v4 -# ("-u" allows unbuffered print statements so we can watch timing in closer-to-real-time) - - -#####import delphi.operations.secrets as secrets -#####secrets.db.host = '172.30.n.n' # aka 'epidata-db-qa-01' -#####secrets.db.epi = ('delphi', 'xxxxxxxx') -# ^ these are already set appropriately on qa-automation in/by the operations module ^ - - -# TODO: make cli flags for these two variables: -use_transaction_wrappers = False -use_autocommit = False - -# TODO: maybe output: was autocommit enabled? was table locking used? what isolation type was used? were indexes enabled? were uniqueness checks enabled? - -# TODO: consider dropping indexes before moving data and recreating them afterward - -''' - -mysql> select count(id) from epidata.covidcast; -+------------+ -| count(id) | -+------------+ -| 2647381579 | -+------------+ -1 row in set (13 min 49.32 sec) - -mysql> select max(id) from epidata.covidcast; -+------------+ -| max(id) | -+------------+ -| 3740757041 | -+------------+ -1 row in set (0.00 sec) - --- so ~71% coverage of actual rows per allocated ids ( 2647381579 / 3740757041 = .70771278379851347314 ) - -mysql> select time_value, issue from epidata.covidcast where id=3740757041; -+------------+----------+ -| time_value | issue | -+------------+----------+ -| 20210927 | 20210930 | -+------------+----------+ -1 row in set (0.01 sec) - -mysql> select now(); -+---------------------+ -| now() | -+---------------------+ -| 2022-05-16 16:45:34 | -+---------------------+ -1 row in set (0.00 sec) - -''' - -def start_tx(cursor): - cursor.execute('SET SESSION TRANSACTION ISOLATION LEVEL READ UNCOMMITTED;') - cursor.execute('SET autocommit=0;') # starts a transaction as suggested in https://dev.mysql.com/doc/refman/8.0/en/lock-tables.html - # NOTE: locks must be specified for any aliases of table names that are used - cursor.execute('''LOCK TABLES epidata.covidcast AS cc READ, - epimetric_load WRITE, epimetric_load AS sl WRITE, - epimetric_full WRITE, - epimetric_latest WRITE, - signal_dim WRITE, signal_dim AS sd READ, - geo_dim WRITE, geo_dim AS gd READ;''') - cursor.execute('SET unique_checks=0;') - -def finish_tx(cursor): - cursor.execute('SET unique_checks=1;') - cursor.execute('COMMIT;') - cursor.execute('UNLOCK TABLES;') - - -def do_batches(db, start, upper_lim, batch_size): - # NOTE: upper_lim is not actually selected for ; make sure it exceeds any ids you want to include - batch_lower = start - - while batch_lower < upper_lim: - batch_upper = min(batch_lower + batch_size, upper_lim) - - # NOTE: first rows of column names are identical, second rows are for specifying a rename and a literal - batch_sql = f""" - INSERT INTO epimetric_load ( - `issue`, `source`, `signal`, geo_type, geo_value, time_type, time_value, `value`, stderr, sample_size, `lag`, value_updated_timestamp, is_latest_issue, missing_value, missing_stderr, missing_sample_size - ) SELECT - `issue`, `source`, `signal`, geo_type, geo_value, time_type, time_value, `value`, stderr, sample_size, `lag`, value_updated_timestamp, is_latest_issue, missing_value, missing_stderr, missing_sample_size - FROM epidata.covidcast AS cc - USE INDEX(`PRIMARY`) - WHERE {batch_lower} <= cc.id AND cc.id < {batch_upper}; """ - # TODO: use LIMIT instead of id range?? - # TODO: might it be worth adding "ORDER BY id ASC" ? - - if use_transaction_wrappers: - start_tx(db._cursor) - - print(f"-=-=-=-=-=-=-=- RUNNING BATCH STARTING AT {batch_lower} -=-=-=-=-=-=-=-") - print(f"-=-=-=-=-=-=-=- RUNNING ''INSERT INTO SELECT FROM''... ", end="") - t = time.time() - db._cursor.execute(batch_sql) - print(f"elapsed: {time.time()-t} sec, rows: {db._cursor.rowcount} -=-=-=-=-=-=-=-") - - t = time.time() - db.run_dbjobs() - print(f"-=-=-=-=-=-=-=- RAN db_jobs()... elapsed: {time.time()-t} sec -=-=-=-=-=-=-=-") - - print("-=-=-=-=-=-=-=- RUNNING commit()... ", end="") - t = time.time() - db.commit() - if use_transaction_wrappers: - finish_tx(db._cursor) - print(f"elapsed: {time.time()-t} sec -=-=-=-=-=-=-=-") - - print("\n\n") - # move pointer for next batch - batch_lower = batch_upper - - -def main(destination_schema, batch_size, start_id, upper_lim_override): - Database.DATABASE_NAME = destination_schema - db = Database() - db.connect() - if use_autocommit: - db._connection.autocommit = True - - if upper_lim_override: - upper_lim = upper_lim_override - else: - # find upper limit for data to be imported - db._cursor.execute("SELECT MAX(id) FROM epidata.covidcast;") - for (max_id,) in db._cursor: - upper_lim = 1 + max_id - - print(f"migrating data to schema '{destination_schema}', with batch size {batch_size} and {start_id} <= ids < {upper_lim}") - if start_id==0: - print("this WILL truncate any existing v4 tables") - print() - if input("type 'yes' to continue: ") != 'yes': - sys.exit('operation cancelled!') - - print(f"starting run at: {time.strftime('%c')}") - - if start_id==0: - # clear tables in the v4 schema - print("truncating tables...") - for table in "epimetric_load epimetric_latest epimetric_full geo_dim signal_dim".split(): - db._cursor.execute(f"TRUNCATE TABLE {table}") - db.commit() - start_id = 1 - - # run batch loop - do_batches(db, start_id, upper_lim, batch_size) - - # get table counts [the quick and dirty way] - print("-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-") - db._cursor.execute(f"SELECT MAX(epimetric_id) FROM epimetric_full;") - for (max_id,) in db._cursor: - print(f"epimetric_full: {max_id}") - db._cursor.execute(f"SELECT MAX(epimetric_id) FROM epimetric_latest;") - for (max_id,) in db._cursor: - print(f"epimetric_latest: {max_id} (this should be <= the number above)") - db._cursor.execute(f"SELECT COUNT(signal_key_id), MAX(signal_key_id) FROM signal_dim;") - for (count_id, max_id) in db._cursor: - print(f"signal_dim: count {count_id} / max {max_id}") - db._cursor.execute(f"SELECT COUNT(geo_key_id), MAX(geo_key_id) FROM geo_dim;") - for (count_id, max_id) in db._cursor: - print(f"geo_dim: count {count_id} / max {max_id}") - - return upper_lim - - -if __name__ == '__main__': - argparser = argparse.ArgumentParser() - argparser.add_argument('--destination_schema', type=str, default='covid') - argparser.add_argument('--batch_size', type=int, default=20_000_000) - argparser.add_argument('--start_id', type=int, default=0) - argparser.add_argument('--upper_lim_override', type=int) # should default to None - args = argparser.parse_args() - - upper_lim = main(args.destination_schema, args.batch_size, args.start_id, args.upper_lim_override) - print(f"the next execution of this program should include argument: --start_id={upper_lim}") diff --git a/src/client/delphi_epidata.R b/src/client/delphi_epidata.R index ee2dcda09..cdb2da385 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 <- '4.1.6' + client_version <- '4.1.7' auth <- getOption("epidata.auth", default = NA) diff --git a/src/client/delphi_epidata.js b/src/client/delphi_epidata.js index 8e1023118..6c658f86f 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 = "4.1.6"; + const client_version = "4.1.7"; // Helper function to cast values and/or ranges to strings function _listitem(value) { diff --git a/src/client/packaging/npm/package.json b/src/client/packaging/npm/package.json index dd1d22611..f80f39750 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": "4.1.6", + "version": "4.1.7", "license": "MIT", "homepage": "https://github.com/cmu-delphi/delphi-epidata", "bugs": { diff --git a/src/client/packaging/pypi/delphi_epidata/__init__.py b/src/client/packaging/pypi/delphi_epidata/__init__.py index cac388bec..80a1c0af8 100644 --- a/src/client/packaging/pypi/delphi_epidata/__init__.py +++ b/src/client/packaging/pypi/delphi_epidata/__init__.py @@ -1,4 +1,4 @@ from .delphi_epidata import Epidata name = "delphi_epidata" -__version__ = "4.1.6" +__version__ = "4.1.7" diff --git a/src/client/packaging/pypi/setup.py b/src/client/packaging/pypi/setup.py index 627e14753..c29dc1537 100644 --- a/src/client/packaging/pypi/setup.py +++ b/src/client/packaging/pypi/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="delphi_epidata", - version="4.1.6", + version="4.1.7", author="David Farrow", author_email="dfarrow0@gmail.com", description="A programmatic interface to Delphi's Epidata API.", diff --git a/src/acquisition/covidcast/covidcast_meta_cache_updater.py b/src/maintenance/covidcast_meta_cache_updater.py similarity index 100% rename from src/acquisition/covidcast/covidcast_meta_cache_updater.py rename to src/maintenance/covidcast_meta_cache_updater.py diff --git a/src/acquisition/covidcast/delete_batch.py b/src/maintenance/delete_batch.py similarity index 100% rename from src/acquisition/covidcast/delete_batch.py rename to src/maintenance/delete_batch.py diff --git a/src/maintenance/remove_outdated_keys.py b/src/maintenance/remove_outdated_keys.py new file mode 100644 index 000000000..56fea0cf9 --- /dev/null +++ b/src/maintenance/remove_outdated_keys.py @@ -0,0 +1,69 @@ +from collections import namedtuple +from smtplib import SMTP + +import delphi.operations.secrets as secrets +import mysql.connector +from delphi.epidata.server._config import API_KEY_REGISTRATION_FORM_LINK_LOCAL + +ApiUserRecord = namedtuple("APIUserRecord", ("api_key", "email", "date_diff")) + +SMTP_HOST = "relay.andrew.cmu.edu" +SMTP_PORT = 25 + +EMAIL_SUBJECT = "Your API Key was deleted." +EMAIL_FROM = "noreply@andrew.cmu.edu" +ALERT_EMAIL_MESSAGE = f"""Hi! \n Your API Key is going to be removed due to inactivity. +To renew it, pelase use it within one month from now.""" +DELETED_EMAIL_MESSAGE = f"""Hi! \n Your API Key was removed due to inactivity. +To get new one, please use registration form ({API_KEY_REGISTRATION_FORM_LINK_LOCAL}) or contact us.""" + + +def get_old_keys(cur): + cur.execute( + """ + SELECT + api_key, + email, + TIMESTAMPDIFF(MONTH, last_time_used, NOW()) AS date_diff + FROM api_user + HAVING date_diff >= 5; + """ + ) + outdated_keys = cur.fetchall() + return [ApiUserRecord(*item) for item in outdated_keys] + + +def remove_outdated_key(cur, api_key): + cur.execute( + f""" + DELETE FROM api_user WHERE api_key = "{api_key}" + """ + ) + + +def send_notification(to_addr, alert=True): + message = ALERT_EMAIL_MESSAGE if alert else DELETED_EMAIL_MESSAGE + BODY = "\r\n".join((f"FROM: {EMAIL_FROM}", f"TO: {to_addr}", f"Subject: {EMAIL_SUBJECT}", "", message)) + smtp_server = SMTP(host=SMTP_HOST, port=SMTP_PORT) + smtp_server.starttls() + smtp_server.sendmail(EMAIL_FROM, to_addr, BODY) + + +def main(): + u, p = secrets.db.epi + cnx = mysql.connector.connect(database="epidata", user=u, password=p, host=secrets.db.host) + cur = cnx.cursor() + outdated_keys_list = get_old_keys(cur) + for item in outdated_keys_list: + if item.date_diff == 5: + send_notification(item.email) + else: + remove_outdated_key(cur, item.api_key) + send_notification(item.email, alert=False) + cur.close() + cnx.commit() + cnx.close() + + +if __name__ == "__main__": + main() diff --git a/src/acquisition/covidcast/signal_dash_data_generator.py b/src/maintenance/signal_dash_data_generator.py similarity index 100% rename from src/acquisition/covidcast/signal_dash_data_generator.py rename to src/maintenance/signal_dash_data_generator.py diff --git a/src/maintenance/update_last_usage.py b/src/maintenance/update_last_usage.py new file mode 100644 index 000000000..85596778a --- /dev/null +++ b/src/maintenance/update_last_usage.py @@ -0,0 +1,38 @@ +import os +from datetime import datetime as dtime + +import delphi.operations.secrets as secrets +import mysql.connector +import redis + +REDIS_HOST = os.environ.get("REDIS_HOST", "delphi_redis") +REDIS_PASSWORD = os.environ.get("REDIS_PASSWORD", "1234") +LAST_USED_KEY_PATTERN = "*LAST_USED*" + + +def main(): + redis_cli = redis.Redis(host=REDIS_HOST, password=REDIS_PASSWORD, decode_responses=True) + u, p = secrets.db.epi + cnx = mysql.connector.connect(database="epidata", user=u, password=p, host=secrets.db.host) + cur = cnx.cursor() + + redis_keys = redis_cli.keys(pattern=LAST_USED_KEY_PATTERN) + today_date = dtime.today().date() + for key in redis_keys: + api_key, last_time_used = str(key).split("/")[1], dtime.strptime(str(redis_cli.get(key)), "%Y-%m-%d").date() + cur.execute( + f""" + UPDATE + api_user + SET last_time_used = "{last_time_used}" + WHERE api_key = "{api_key}" AND (last_time_used < "{last_time_used}" OR last_time_used IS NULL) + """ + ) + redis_cli.delete(key) + cur.close() + cnx.commit() + cnx.close() + + +if __name__ == "__main__": + main() diff --git a/src/server/_config.py b/src/server/_config.py index 5d905c968..841e93b9e 100644 --- a/src/server/_config.py +++ b/src/server/_config.py @@ -7,7 +7,7 @@ load_dotenv() -VERSION = "4.1.6" +VERSION = "4.1.7" MAX_RESULTS = int(10e6) MAX_COMPATIBILITY_RESULTS = int(3650) diff --git a/tests/maintenance/__init__.py b/tests/maintenance/__init__.py new file mode 100644 index 000000000..e197f3ec4 --- /dev/null +++ b/tests/maintenance/__init__.py @@ -0,0 +1,4 @@ +import sys +import os + +sys.path.append(os.getcwd()) diff --git a/tests/acquisition/covidcast/test_covidcast_meta_cache_updater.py b/tests/maintenance/test_covidcast_meta_cache_updater.py similarity index 91% rename from tests/acquisition/covidcast/test_covidcast_meta_cache_updater.py rename to tests/maintenance/test_covidcast_meta_cache_updater.py index 40a242e22..318206ea4 100644 --- a/tests/acquisition/covidcast/test_covidcast_meta_cache_updater.py +++ b/tests/maintenance/test_covidcast_meta_cache_updater.py @@ -5,14 +5,11 @@ import unittest from unittest.mock import MagicMock -# third party -import pandas - -from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import get_argument_parser, \ +from delphi.epidata.maintenance.covidcast_meta_cache_updater import get_argument_parser, \ main # py3tester coverage target __test_target__ = ( - 'delphi.epidata.acquisition.covidcast.' + 'delphi.epidata.maintenance.' 'covidcast_meta_cache_updater' ) diff --git a/tests/acquisition/covidcast/test_signal_dash_data_generator.py b/tests/maintenance/test_signal_dash_data_generator.py similarity index 98% rename from tests/acquisition/covidcast/test_signal_dash_data_generator.py rename to tests/maintenance/test_signal_dash_data_generator.py index 5d0c81326..09bca3227 100644 --- a/tests/acquisition/covidcast/test_signal_dash_data_generator.py +++ b/tests/maintenance/test_signal_dash_data_generator.py @@ -12,8 +12,7 @@ import pandas as pd # first party -from delphi.epidata.acquisition.covidcast import signal_dash_data_generator -from delphi.epidata.acquisition.covidcast.signal_dash_data_generator import ( +from delphi.epidata.maintenance.signal_dash_data_generator import ( get_argument_parser, Database, DashboardSignalStatus,