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lengthen sample stable id field #9404

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merged 1 commit into from
Mar 24, 2022
Merged

lengthen sample stable id field #9404

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11 changes: 11 additions & 0 deletions core/src/main/scripts/importer/validateData.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,9 @@
# Global variable for the regex that checks hexadecimal colors
COLOR_REGEX = re.compile("^#[a-fA-F0-9]{6}$")

# global character limit on sample stable ids
MAX_SAMPLE_STABLE_ID_LENGTH = 63

# ----------------------------------------------------------------------------

VALIDATOR_IDS = {
Expand Down Expand Up @@ -2667,6 +2670,14 @@ def checkLine(self, data):
'column_number': col_index + 1,
'cause': value})
continue
if len(value.strip()) > MAX_SAMPLE_STABLE_ID_LENGTH:
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Thank you! We've run into this a few times.

self.logger.error(
'SAMPLE_ID too long (%s character maximum)' % (MAX_SAMPLE_STABLE_ID_LENGTH),
extra={'line_number': self.line_number,
'column_number': col_index + 1,
'cause': value})
continue

if value in self.sample_id_lines:
if value.startswith('TCGA-'):
self.logger.warning(
Expand Down
4 changes: 2 additions & 2 deletions db-scripts/src/main/resources/cgds.sql
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Expand Up @@ -173,7 +173,7 @@ CREATE TABLE `patient` (
-- --------------------------------------------------------
CREATE TABLE `sample` (
`INTERNAL_ID` int(11) NOT NULL auto_increment,
`STABLE_ID` varchar(50) NOT NULL,
`STABLE_ID` varchar(63) NOT NULL,
`SAMPLE_TYPE` varchar(255) NOT NULL,
`PATIENT_ID` int(11) NOT NULL,
PRIMARY KEY (`INTERNAL_ID`),
Expand Down Expand Up @@ -757,4 +757,4 @@ CREATE TABLE `resource_study` (
);

-- THIS MUST BE KEPT IN SYNC WITH db.version PROPERTY IN pom.xml
INSERT INTO info VALUES ('2.12.12', NULL);
INSERT INTO info VALUES ('2.12.13', NULL);
2 changes: 1 addition & 1 deletion db-scripts/src/main/resources/gen-cgds-test-schema.sh
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Expand Up @@ -15,7 +15,7 @@
# author: ochoaa
# last update: 2019/02/13

CGDS_SCHEMA_FILE=$(find . -type f -name "*cgds.sql" | grep -v target)
CGDS_SCHEMA_FILE=$(find . -type f -name "cgds.sql" | grep -v target)
DIR=$(dirname $CGDS_SCHEMA_FILE)
CGDS_TEST_SCHEMA_FILE=$DIR/cgds-test.sql
grep -v "KEY_MUTATION_EVENT_DETAILS" $CGDS_SCHEMA_FILE > $CGDS_TEST_SCHEMA_FILE
Expand Down
4 changes: 4 additions & 0 deletions db-scripts/src/main/resources/migration.sql
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Expand Up @@ -973,3 +973,7 @@ ALTER TABLE `reference_genome_gene` DROP COLUMN `EXONIC_LENGTH`;
-- changes for issue 9032
ALTER TABLE `genetic_entity` MODIFY COLUMN `STABLE_ID` VARCHAR(255) DEFAULT NULL;
UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.12";

##version: 2.12.13
ALTER TABLE `sample` MODIFY COLUMN `STABLE_ID` VARCHAR(63) NOT NULL;
UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.13";
2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -327,7 +327,7 @@
<tomcat.session.timeout>720</tomcat.session.timeout>

<!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
<db.version>2.12.12</db.version>
<db.version>2.12.13</db.version>
</properties>

<modules>
Expand Down