Internal code improvements for procedures and specimen processing

Returning phenotyping errors as warnings for baseline specimens

Added validation in case of issue of fetched information from Gentar

Added validation for protecting finalised baselines submission.

Updated logic for processing any new body weight procedure/parameter

Failing legacy and specialist pipeline submissions at validation

Error messages include GenTaR for removing confusion from warnings/errors

Centralised and simplified management of centre information across our databases

Added validation for incorrect phenotyping and production centre in xml

Reverted patch of 20/11/2020 as issues were discovered and stopping centers from submitting procedures with different Phenotyping centre and submitted XML center ID for colony

Changes to processing of late adult validation for colonies in iMITS to account for colonies not yet in Gentar

Prohibit further data submission for colony with all_data_sent flag is set to true on iMITS.

Phenotyping centre and submitted XML center ID should be same for colony

Status coded experiments should not be validated against the phenotyping repositories.

Late adult pipeline experiments will now be validated against late-adult phenotyping stages, and will fail if the stage is not present or doesn't have the correct status.

Fixing issue that would prevent the validator to query GenTaR for less than 25 colonies

Fixing potential null pointer exception when the validator is unable to retrieve any phenotyping information from the phenotyping repositories (iMits/GenTaR)

Bug fixing release for v2020.10.20: No GenTaR credentials are needed

XSD: min of 1 procedure per experiment (effectively experiments cannot be submitted without a procedure)

iMits/GenTaR production centre is validated against XSD CentreILARcode (ignoring case)

• Early Adult procedures will be validated against the EA stage of the plan of their specimen
• Late Adult procedures will be validated against the LA stage of the plan of their specimen
• Specimens and line procedures will need to have a Plan with at least one valid EA or LA stage or both
• The plan for each entity is matched using its colony, for experiments that is their specimen’s colony
• Valid stages for data submission: [“Phenotyping Registered", "Rederivation Complete", "Phenotyping Started”]

Removing validation warnings related to the project field

Adding xml logs for value out of bounds exceptions (1024 characters for simple parameters, 255 for all other values/increment values/URLs)

Fixing missing error logs for date-time validation failures

Calorimetry procedures: all Simple Parameters of type DATETIME and all Series Parameters increments of type datetime will be validated against ISO 8601 standard (accepted formats are YYYY-MM-DDThh:mm:ss+00:00 and YYYY-MM-DDThh:mm:ssZ)

Oldest valid specimen date of birth moving from DOB > 2010-01-01 to DOB > 2007-01-01

Error message "colonyID '%s' for specimen '%s' is not defined in iMits" replaced by "Did not find genotype confirmed, active colony '%s' on iMits with status other than rederivation started for specimen '%s'"

Adding new endpoint /validation/strains/list, returns all DCC acceptable strains

Currently if a centre submits an optional parameter with a blank value/empty string etc. Validation treats it as a null value. A warning is given, but it is accepted.
Going forward, if the tag exists for an optional parameter, it will be validated as any other parameter would be, so blank/empty values will be failed.
If you do not intend to submit an optional parameter, the tag must be omitted from the XML. This new validation rule will be enforced on the crawler from 27th Feb 2020. See crawler roadmap for further details.

Improving empty string detection

Fixing incorrect invalidation of production centre by switching to iMits "cohort_production_centre_name" instead of "production_centre_name"

Adding check for preventing procedures with multiply defined Series Media Parameter Values to pass validation

Fixing validation rule that would incorrectly invalidate a specimen when its strain was correct both in imits and in the xml

Updated strain validation logic

Fixing invalidation of status coded line procedures with unknown colony id. The colony will not be validated if a line procedure is status coded

Re-introduced the integer type check for numerical values, the check had been merged with the floating point numbers check in previous releases

Fixed bug that would produce an exception when a line failed to validate its colony with imits

Fixed bug that was causing multiple decelerations of the same simple parameter but with different sequence id to fail validation

Introduced stability improvements