diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c84e8037..48705d31 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,14 @@ foursight Change Log ---------- +4.7.3 +===== + +* Change clean_up_webdev_wfrs to run manually and correct test UUIDs +* fastqc and fastq-first-line checks are no longer rate limited +* Correct key used for fruit fly reference files and parameters +`PR 575: cleanup and remove rate limit for select checks `_ + 4.7.2 ===== diff --git a/chalicelib_fourfront/check_setup.json b/chalicelib_fourfront/check_setup.json index dedd8bd9..b2bc9b5f 100644 --- a/chalicelib_fourfront/check_setup.json +++ b/chalicelib_fourfront/check_setup.json @@ -682,7 +682,7 @@ "title": "Clean up webdev workflows runs", "group": "Metadata checks", "schedule": { - "morning_checks_4": { + "manual_checks": { "webdev": { "dependencies": [], "kwargs": { diff --git a/chalicelib_fourfront/checks/helpers/wfr_utils.py b/chalicelib_fourfront/checks/helpers/wfr_utils.py index 68a22162..ea8f56da 100644 --- a/chalicelib_fourfront/checks/helpers/wfr_utils.py +++ b/chalicelib_fourfront/checks/helpers/wfr_utils.py @@ -227,13 +227,13 @@ # Reference Files bwa_index = {"human": "4DNFIZQZ39L9", "mouse": "4DNFI823LSI8", - "fruit-fly": '4DNFIO5MGY32', + "fruit fly": '4DNFIO5MGY32', "chicken": "4DNFIVGRYVQF", "zebrafish": "4DNFIUH46PG1"} chr_size = {"human": "4DNFI823LSII", "mouse": "4DNFI3UBJ3HZ", - "fruit-fly": '4DNFIBEEN92C', + "fruit fly": '4DNFIBEEN92C', "chicken": "4DNFIQFZW4DX", "zebrafish": "4DNFI5W8CN1M"} @@ -270,7 +270,7 @@ "HindIII": '/files-reference/4DNFI6V32T9J/', "Arima - A1, A2": '/files-reference/4DNFIE78H3K7/' }, - "fruit-fly": {'MboI': '/files-reference/4DNFIS1ZVUWO/' + "fruit fly": {'MboI': '/files-reference/4DNFIS1ZVUWO/' }, "chicken": {"HindIII": '/files-reference/4DNFITPCJFWJ/' }, @@ -289,7 +289,7 @@ # max_distance for species (used for pairsqc) max_size = {"human": None, "mouse": 8.2, - "fruit-fly": 7.5, + "fruit fly": 7.5, "chicken": 8.2, "zebrafish": 7.9} @@ -309,7 +309,7 @@ mapper = {'human': 'GRCh38', 'mouse': 'GRCm38', - 'fruit-fly': 'dm6', + 'fruit fly': 'dm6', 'chicken': 'galGal5', 'zebrafish': 'GRCz11'} diff --git a/chalicelib_fourfront/checks/wfr_checks.py b/chalicelib_fourfront/checks/wfr_checks.py index f3830ac5..176b6781 100644 --- a/chalicelib_fourfront/checks/wfr_checks.py +++ b/chalicelib_fourfront/checks/wfr_checks.py @@ -363,12 +363,6 @@ def fastqc_status(connection, **kwargs): check, skip = wfr_utils.check_indexing(check, connection) if skip: return check - # check number of total workflow runs in the past 6h - check, n_runs_available = wfr_utils.limit_number_of_runs(check, my_auth) - if n_runs_available == 0: - check.brief_output.append('Runs are limited due to docker pull rate limit') - check.status = 'WARN' - return check # Build the query (skip to be uploaded by workflow) query = ("/search/?type=File&file_format.file_format=fastq&quality_metric.uuid=No+value" @@ -2144,12 +2138,6 @@ def fastq_first_line_status(connection, **kwargs): check, skip = wfr_utils.check_indexing(check, connection) if skip: return check - # check number of total workflow runs in the past 6h - check, n_runs_available = wfr_utils.limit_number_of_runs(check, my_auth) - if n_runs_available == 0: - check.brief_output.append('Runs are limited due to docker pull rate limit') - check.status = 'WARN' - return check query = ('/search/?status=uploaded&status=pre-release&status=released+to+project&status=released' '&type=FileFastq&file_format.file_format=fastq&file_first_line=No value&status=restricted') diff --git a/chalicelib_fourfront/checks/wrangler_checks.py b/chalicelib_fourfront/checks/wrangler_checks.py index 4967ad4b..27089fdd 100644 --- a/chalicelib_fourfront/checks/wrangler_checks.py +++ b/chalicelib_fourfront/checks/wrangler_checks.py @@ -1005,7 +1005,7 @@ def patch_wfr_and_log(wfr, full_output): wait = round(random.uniform(0.1, random_wait), 1) time.sleep(wait) # input for test pseudo hi-c-processing-bam - response = ff_utils.get_metadata('68f38e45-8c66-41e2-99ab-b0b2fcd20d45', + response = ff_utils.get_metadata('1150b428-272b-4a0c-b3e6-4b405c148f7c', key=connection.ff_keys) wfrlist = response['workflow_run_inputs'] for entry in wfrlist: @@ -1016,7 +1016,7 @@ def patch_wfr_and_log(wfr, full_output): patch_wfr_and_log(entry, check.full_output) # input for test md5 and bwa-mem - response = ff_utils.get_metadata('f4864029-a8ad-4bb8-93e7-5108f462ccaa', + response = ff_utils.get_metadata('1fa2d6db-8a1f-4ba5-aa61-0558f80b0cf7', key=connection.ff_keys) wfrlist = response['workflow_run_inputs'] for entry in wfrlist: diff --git a/pyproject.toml b/pyproject.toml index cd790590..baa280a2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "foursight" -version = "4.7.2" +version = "4.7.3" description = "Serverless Chalice Application for Monitoring" authors = ["4DN-DCIC Team "] license = "MIT"