Merge branch 'biocore:master' into vocab_samples_issues

ci/conda_requirements.txt

@@ -1,6 +1,7 @@
 flake8
 psycopg2
-flask
+flask < 3.0.0
 natsort
 pycryptodome
 pandas < 2.0.0
+werkzeug < 3.0.0

microsetta_private_api/db/patches/0139.sql

@@ -0,0 +1,92 @@
+-- This database patch copies two samples into new barcodes to reflect
+-- adjustments that were necessary in the wet lab. We don't believe this
+-- will be an ongoing need, but if it proves to be, check for new
+-- barcode-related tables before using this as a template.
+
+-- Begin copying X00236845 to 0364352596
+INSERT INTO barcodes.barcode (barcode, assigned_on, status, sample_postmark_date, biomass_remaining, sequencing_status, obsolete, create_date_time, kit_id)
+    SELECT '0364352596', assigned_on, status, sample_postmark_date, biomass_remaining, sequencing_status, obsolete, create_date_time, kit_id
+    FROM barcodes.barcode
+    WHERE barcode = 'X00236845';
+
+INSERT INTO barcodes.project_barcode (project_id, barcode)
+    SELECT project_id, '0364352596'
+    FROM barcodes.project_barcode
+    WHERE barcode = 'X00236845';
+
+-- I'm omitting the sample_barcode_file and sample_barcode_file_md5 as they're
+-- no longer used and it would be inappropriate to directly clone a different
+-- barcode's associated file.
+INSERT INTO ag.ag_kit_barcodes (ag_kit_id, barcode, site_sampled, sample_date, sample_time, notes, moldy, overloaded, other, other_text, date_of_last_email, results_ready, withdrawn, refunded, deposited, source_id, latest_sample_information_update)
+    SELECT ag_kit_id, '0364352596', site_sampled, sample_date, sample_time, notes, moldy, overloaded, other, other_text, date_of_last_email, results_ready, withdrawn, refunded, deposited, source_id, latest_sample_information_update
+    FROM ag.ag_kit_barcodes
+    WHERE barcode = 'X00236845';
+
+INSERT INTO ag.source_barcodes_surveys (barcode, survey_id)
+    SELECT '0364352596', survey_id
+    FROM ag.source_barcodes_surveys
+    WHERE barcode = 'X00236845';
+
+INSERT INTO barcodes.barcode_scans (barcode, scan_timestamp, sample_status, technician_notes)
+    SELECT '0364352596', scan_timestamp, sample_status, technician_notes
+    FROM barcodes.barcode_scans
+    WHERE barcode = 'X00236845';
+
+INSERT INTO ag.vioscreen_registry (account_id, source_id, sample_id, vio_id, deleted, registration_code)
+    WITH temp_1 AS (
+        SELECT vr.account_id, vr.source_id, vr.vio_id, vr.deleted, vr.registration_code
+        FROM ag.vioscreen_registry vr
+        INNER JOIN ag.ag_kit_barcodes akb ON vr.sample_id = akb.ag_kit_barcode_id
+        WHERE akb.barcode = 'X00236845'
+    ),
+    temp_2 AS (
+        SELECT ag_kit_barcode_id
+        FROM ag.ag_kit_barcodes
+        WHERE barcode = '0364352596'
+    )
+    SELECT temp_1.account_id, temp_1.source_id, temp_2.ag_kit_barcode_id, temp_1.vio_id, temp_1.deleted, temp_1.registration_code FROM temp_1, temp_2;
+-- End copying X00236845 to 0364352596
+
+-- Begin copying 000031307 to 0364406520
+INSERT INTO barcodes.barcode (barcode, assigned_on, status, sample_postmark_date, biomass_remaining, sequencing_status, obsolete, create_date_time, kit_id)
+    SELECT '0364406520', assigned_on, status, sample_postmark_date, biomass_remaining, sequencing_status, obsolete, create_date_time, kit_id
+    FROM barcodes.barcode
+    WHERE barcode = '000031307';
+
+INSERT INTO barcodes.project_barcode (project_id, barcode)
+    SELECT project_id, '0364406520'
+    FROM barcodes.project_barcode
+    WHERE barcode = '000031307';
+
+-- I'm omitting the sample_barcode_file and sample_barcode_file_md5 as they're
+-- no longer used and it would be inappropriate to directly clone a different
+-- barcode's associated file.
+INSERT INTO ag.ag_kit_barcodes (ag_kit_id, barcode, site_sampled, sample_date, sample_time, notes, moldy, overloaded, other, other_text, date_of_last_email, results_ready, withdrawn, refunded, deposited, source_id, latest_sample_information_update)
+    SELECT ag_kit_id, '0364406520', site_sampled, sample_date, sample_time, notes, moldy, overloaded, other, other_text, date_of_last_email, results_ready, withdrawn, refunded, deposited, source_id, latest_sample_information_update
+    FROM ag.ag_kit_barcodes
+    WHERE barcode = '000031307';
+
+INSERT INTO ag.source_barcodes_surveys (barcode, survey_id)
+    SELECT '0364406520', survey_id
+    FROM ag.source_barcodes_surveys
+    WHERE barcode = '000031307';
+
+INSERT INTO barcodes.barcode_scans (barcode, scan_timestamp, sample_status, technician_notes)
+    SELECT '0364406520', scan_timestamp, sample_status, technician_notes
+    FROM barcodes.barcode_scans
+    WHERE barcode = '000031307';
+
+INSERT INTO ag.vioscreen_registry (account_id, source_id, sample_id, vio_id, deleted, registration_code)
+    WITH temp_1 AS (
+        SELECT vr.account_id, vr.source_id, vr.vio_id, vr.deleted, vr.registration_code
+        FROM ag.vioscreen_registry vr
+        INNER JOIN ag.ag_kit_barcodes akb ON vr.sample_id = akb.ag_kit_barcode_id
+        WHERE akb.barcode = '000031307'
+    ),
+    temp_2 AS (
+        SELECT ag_kit_barcode_id
+        FROM ag.ag_kit_barcodes
+        WHERE barcode = '0364406520'
+    )
+    SELECT temp_1.account_id, temp_1.source_id, temp_2.ag_kit_barcode_id, temp_1.vio_id, temp_1.deleted, temp_1.registration_code FROM temp_1, temp_2;
+-- End copying 000031307 to 0364406520

microsetta_private_api/model/account.py

@@ -1,6 +1,7 @@
 from enum import Enum
 from microsetta_private_api.model.model_base import ModelBase
 from microsetta_private_api.model.address import Address
+from microsetta_private_api.localization import EN_US, JA_JP
 
 
 class AuthorizationMatch(Enum):
@@ -61,6 +62,8 @@ def __init__(self, account_id, email,
         self.creation_time = creation_time
         self.update_time = update_time
         self.language = language
+        if (self.language == JA_JP):
+            self.language = EN_US
         self.consent_privacy_terms = consent_privacy_terms
 
     def to_api(self):

microsetta_private_api/tasks.py

@@ -8,7 +8,7 @@
 from microsetta_private_api.repo.transaction import Transaction
 from microsetta_private_api.repo.admin_repo import AdminRepo
 from microsetta_private_api.repo.qiita_repo import QiitaRepo
-from microsetta_private_api.localization import EN_US
+from microsetta_private_api.localization import EN_US, JA_JP
 from microsetta_private_api.config_manager import SERVER_CONFIG
 import pandas as pd
 import tempfile
@@ -22,6 +22,8 @@
 @celery.task(ignore_result=True)
 def send_email(email, template_name, template_args, language):
     template = EmailMessage[template_name]
+    if language == JA_JP:
+        language = EN_US
 
     with flask_babel.force_locale(language):
         SendEmail.send(email, template, template_args)