transmart / transmart-extensions

Elements that are being collected for refactoring but do not yet have a home. This project needs to be reviewed often!

transmart-extensions

Elements that are being collected for refactoring but do not yet have a home. This project needs to be reviewed often!

Sub-Directories (each is currently created as a plugin to add to core transmart)

transmart-java essentially isolating Java classes originally extracted from transmart-legacy-db. biomart-domain This isolates all of the domain classes associated with biomart schema. Originally extracted from transmart-legacy-db; updated to transmart-legacy-db reflect that. search-domain This isolates all of the domain classes associated with searchapp schema. Originally extracted from transmart-legacy-db; updated to transmart-legacy-db reflect that.

transmart-extensions's Issues

biomart_domain: bio_data_uuid may contains non-unique bio_data_id values

Hi,
I created new database from transmart-data master branch and it looks like biomart.bio_data_uuid doesn't contains records for bio_assay_platform (which used for "Add new analysis" and "Add new assay" on "Browse" tab). I tried to insert them manually using following command:

insert into biomart.bio_data_uid
(bio_data_id, unique_id, bio_data_type)
select p.bio_assay_platform_id, 'BAP:' || platform_accession, 'BIO_ASSAY_PLATFORM'
from biomart.bio_assay_platform p
left join biomart.bio_data_uid uid
on uid.bio_data_id = p.bio_assay_platform_id and uid.bio_data_type = 'BIO_ASSAY_PLATFORM'
where uid.bio_data_id is null;

but it fails with error:

ERROR: duplicate key value violates unique constraint "bio_data_uid_pk"
DETAIL: Key (bio_data_id)=(169331) already exists.

I checked this id and it is already occupied by BIO_CONCEPT_CODE:
169331;"ASSAY_TYPE_OF_BM_STUDIED:PROTEIN";"BIO_CONCEPT_CODE"

The easiest way to avoid this problem from my point of view it make unique contraint by pair (bio_data_type, bio_data_id) and looking for unique code using filter by type additional to filter by id.

BioData data = BioData.get(id);

should be replaced with something like:

BioData data = BioData.findWhere(id: id, type: "BIO_ASSAY_PLATFORM");

It can be incapsulated into BioData to just provide method like:

BioData.getUniqueId(platform)

Please, let me know what do you think about it and may be I'm doing something wrong. I can provide pull request if you like for this solution.