Create alias for Patient, Case, Specimen and Blood items for external use

[Nicklas Nordborg]

The SCAN-B ID that is used to keep track of all items is sensitive information that we should avoid to use externally. We should add a new unique identifier to Patient, Case, Specimen, NoSpecimen and Blood (including fullow-up blood) items. A simple running number that is zero-padded to 6 digits should be ok (same as we currently do for naming Patient items). Use 'Q' as prefix for Patients, 'C' as prefix for Case items, and 'S' as prefix for specimen/nospecimen and 'B' for blood. If a case is arriving with multiple tubes, each tube should have it's own unique identifier.

The new identifier should be saved in the "External ID" field.

Other tools can then use the external identifiers instead of the SCAN-B ids. For example:

1234567.1.l.r.lib --> Q000001.C000001.S000001.l.r.lib

Other notes:

• Since we are already using a similar scheme for the 'name' of Patients, the we should create random gaps in the external id sequence. For example by randomly incrementing with 2 instead of 1.
• Cases that are created as placeholder for retracted items should not have en external id.

[Nicklas Nordborg]

(In [4069]) References #906: Create alias for PAtient, Case, Specimen and Blood items for external use

Implemented for Case items.

[Nicklas Nordborg]

(In [4070]) References #906: Create alias for PAtient, Case, Specimen and Blood items for external use

Implemented for Blood items.

[Nicklas Nordborg]

(In [4071]) References #906: Create alias for PAtient, Case, Specimen and Blood items for external use

Implemented for Specimen/NoSpecimen items.

[Nicklas Nordborg]

(In [4073]) References #906: Create alias for PAtient, Case, Specimen and Blood items for external use

Implemented for Patient items.

[Nicklas Nordborg]

(In [4075]) References #906: Create alias for Patient, Case, Specimen and Blood items for external use

Added support for searching by external id in the case summary.

[Nicklas Nordborg]

Use 'Q' instead of 'P' as prefix for patients.

[Nicklas Nordborg]

(In [4076]) References #906: Create alias for Patient, Case, Specimen and Blood items for external use

Use 'Q' instead of 'P' for patients.

[Nicklas Nordborg]

(In [4077]) References #906: Create alias for Patient, Case, Specimen and Blood items for external use

Added 'External.ID' column to the following cohort data files:

• cohortSample.txt
• cohortCase.txt
• cohortPatient.txt
• cohortSummaryTable.txt

[Nicklas Nordborg]

(In [4078]) References #906: Create alias for Patient, Case, Specimen and Blood items for external use

Prepared the release exporter plug-in for exporting only the external id, by adding a new option (off by default).

[Nicklas Nordborg]

(In [4079]) References #906: Create alias for Patient, Case, Specimen and Blood items for external use

Added the ReleaseWriterOptions class for collecting current (and future) options. Re-factored rest of the code to use this class instead of multiple parameters when calling methods.

[Nicklas Nordborg]

(In [4084]) References #906: Create alias for Patient, Case, Specimen and Blood items for external use

The cohort tables are now generated with the external id instead of SCAN-B ID when the option to use external id is selected.

[Nicklas Nordborg]

(In [4085]) References #906: Create alias for Patient, Case, Specimen and Blood items for external use

The gene and transcript data tables now also uses the external id if that option is enabled. The file generation order had to be changed so that the cohort data tables are generated first while we generate a mapping from raw bioassay name to external id that is then used when generating the data files.