Merge 39e646e into d4a9661

microsetta_private_api/api/tests/test_integration.py

@@ -1071,7 +1071,7 @@ def _test_edit_sample_info(self, source_type):
                 cur.execute("INSERT INTO barcode_scans "
                             "(barcode, scan_timestamp, sample_status) "
                             "VALUES "
-                            "(%s, %s, 'valid')",
+                            "(%s, %s, 'sample-is-valid')",
                             (BARCODE, datetime.datetime.now()))
             t.commit()
 

microsetta_private_api/db/patches/0067.sql

@@ -6,11 +6,7 @@
 -- put into barcode
 --
 -- case 1: (happy path) scanned barcode belongs to AGP, is linked to an
--- account by way of a source, and has collection info.  Note that
--- collection date is used as a proxy for collection info
--- because all kinds of sources require collection_date for
--- a sample (whereas, e.g., environmental sources don't require
--- site_sampled, etc).
+-- account by way of a source, and has collection info.
 UPDATE barcodes.barcode
 SET sample_status = 'valid'
 FROM ag.ag_kit_barcodes, ag.source, ag.account

microsetta_private_api/db/patches/0068.sql

@@ -0,0 +1,28 @@
+-- Correct two problems in the population of barcode_scans in 0067.sql:
+
+-- Problem 1: valid sample status should be 'sample-is-valid' rather than 'valid'
+-- per request from wet lab to revert to original terminology.  Change ALL instances
+-- of 'valid' to 'sample-is-valid'.
+UPDATE barcodes.barcode_scans
+SET sample_status = 'sample-is-valid'
+WHERE sample_status = 'valid';
+
+-- Problem 2: filled site_sampled was used as a proxy for having collection info,
+-- but environmental sources don't have site_sampled filled in when they
+-- are collected.  Identify all scans of barcodes that are part of American Gut,
+-- are associated with a source, are for a sample of the type "environmental", and
+-- have been collected by the participant (as evidenced by the sample_date field
+-- being filled).  Additionally, look only at scans meeting the above criteria
+-- that additionally were done AFTER the participant-reported sample_date (so after
+-- the sample was collected) AND that have a sample_status of "no-collection-info".
+-- Given the foregoing conditions, this status is incorrect as the sample is valid;
+-- change sample_status in these cases to 'sample-is-valid'.
+UPDATE barcodes.barcode_scans
+SET sample_status = 'sample-is-valid'
+FROM ag.ag_kit_barcodes, ag.source
+WHERE barcode_scans.barcode = ag_kit_barcodes.barcode
+AND ag_kit_barcodes.source_id = source.id
+AND source.source_type = 'environmental'
+AND ag_kit_barcodes.sample_date IS not null
+AND barcode_scans.scan_timestamp >= ag_kit_barcodes.sample_date
+AND barcode_scans.sample_status = 'no-collection-info';