Merge pull request #398 from UW-GAC/feature/cdsa-records-cron

Add a cron job for generating CDSA records

primed/cdsa/management/commands/cdsa_records.py

@@ -12,8 +12,9 @@ class Command(BaseCommand):
 
     def add_arguments(self, parser):
         parser.add_argument(
-            "outdir",
+            "--outdir",
             help="""Output directory where reports should be written. This directory will be created.""",
+            required=True,
         )
 
     def _export_table(self, table, filename):

primed/cdsa/tests/test_commands.py

@@ -23,12 +23,12 @@ def tearDown(self):
 
     def test_output(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         self.assertIn("generating reports... done!", out.getvalue())
 
     def test_files_created(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         self.assertTrue(isdir(self.outdir))
         self.assertTrue(isfile(os.path.join(self.outdir, "representative_records.tsv")))
         self.assertTrue(isfile(os.path.join(self.outdir, "study_records.tsv")))
@@ -37,7 +37,7 @@ def test_files_created(self):
 
     def test_representative_records_zero(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "representative_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 1)
@@ -47,14 +47,14 @@ def test_representative_records_three(self):
         factories.DataAffiliateAgreementFactory.create()
         factories.NonDataAffiliateAgreementFactory.create()
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "representative_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 4)
 
     def test_study_records_zero(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "study_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 1)
@@ -64,14 +64,14 @@ def test_study_records_one(self):
             signed_agreement__is_primary=True
         )
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "study_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 2)
 
     def test_cdsa_workspace_records_zero(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "workspace_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 1)
@@ -80,7 +80,7 @@ def test_cdsa_workspace_records_one(self):
         agreement = factories.DataAffiliateAgreementFactory.create()
         factories.CDSAWorkspaceFactory.create(study=agreement.study)
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "workspace_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 2)
@@ -89,5 +89,7 @@ def test_directory_exists(self):
         os.mkdir(self.outdir)
         out = StringIO()
         with self.assertRaises(CommandError) as e:
-            call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+            call_command(
+                "cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out
+            )
         self.assertIn("already exists", str(e.exception))

primed_apps.cron

@@ -1,6 +1,12 @@
-# PRIMED_APPS crontab
+# PRIMED_APPS crontab - maintained in git primed_apps.cron
+# Send errors to primedweb email
+MAILTO="[email protected]"
+
 # nightly except sunday at 01:00
-0 1 * * MON-SAT . /var/www/django/primed_apps/primed-apps-activate.sh; python manage.py run_anvil_audit --email [email protected] --errors-only >> cron.log 2>&1
+0 1 * * MON-SAT . /var/www/django/primed_apps/primed-apps-activate.sh; python manage.py run_anvil_audit --email [email protected] --errors-only >> cron.log
 
 # sunday night at 01:00
-0 1 * * SUN . /var/www/django/primed_apps/primed-apps-activate.sh; python manage.py run_anvil_audit --email [email protected] >> cron.log 2>&1
+0 1 * * SUN . /var/www/django/primed_apps/primed-apps-activate.sh; python manage.py run_anvil_audit --email [email protected] >> cron.log
+
+# Weekly cdsa_records run Sundays at 03:00 - disabled until permissions issues are resolved
+0 3 * * SUN . /var/www/django/primed_apps/primed-apps-activate.sh; python manage.py cdsa_records --outdir /projects/primed/records/cdsa/$(date +'\%Y-\%m-\%d') >> cron.log

primed_apps_dev.cron

@@ -1,7 +1,8 @@
 # PRIMED_APPS_DEV crontab - disabled by default
+MAILTO="[email protected]"
 # can be enabled for testing.
 # nightly except sunday at 01:00
-# 0 1 * * MON-SAT . /var/www/django/primed_apps_dev/primed-apps-dev-activate.sh; python manage.py run_anvil_audit --email [email protected] --errors-only >> cron.log 2>&1
+# 0 1 * * MON-SAT . /var/www/django/primed_apps_dev/primed-apps-dev-activate.sh; python manage.py run_anvil_audit --email [email protected] --errors-only >> cron.log
 
 # sunday night at 01:00
-# 0 1 * * SUN . /var/www/django/primed_apps_dev/primed-apps-dev-activate.sh; python manage.py run_anvil_audit --email [email protected] >> cron.log 2>&1
+# 0 1 * * SUN . /var/www/django/primed_apps_dev/primed-apps-dev-activate.sh; python manage.py run_anvil_audit --email [email protected] >> cron.log