Internal code improvements for procedures and specimen processing

Recalculation for BWT procedures in case of DOB changed

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

Processing of multiple colonies updated.

Added validation for incorrect phenotyping and production centre in xml

Updated genotype information handling at DCC end.

Updating the code to handle a colony when it is neither present with Gentar nor iMits

Validates embryo procedures submitted to adult specimens, or adult procedures to embryo specimens.

Removed check for summary_status_name and attempt_type when fetching plans from Gentar.

Added check for handling missing mandatory fields in Gentar.

Reverted patch of 19/11/2020 as issues were discovered and stopping centers from submitting procedures with different Phenotyping centre and submitted XML center ID for colony

When a specimen is resubmitted with a changed DOB, all BWT increments for that animal will be recalculated.

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.

Fix for scenario when colony information is not found in Gentar/iMits for line procedures.

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)

Optional parameters without a value are now considered invalid

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 unzip failed phase and status for zips

Improving empty string detection in validation

Fixing duplicate submissions causing updates instead of being discarded

Fixing specimen submissions with modified production centre did not trigger an update

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 data failing Overviews because of missing check in validation related to Series Media Paraemter Values

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.