10.Nov.2022

(fixed) #43 Remove 2 assertion method columns to match Nov 2022 ClinVar submission file changes.
these are the specific column changes

(remove) Assertion method (AK)
(remove) Assertion method citation (AL)

06.May.2022

(fixed) #21 Modified the output to match March 2022 ClinVar submission excel file format column changes
these are the specific column changes

• (remove) Trace or probe data (V)
• (remove) Official allele name (AA)
• (remove) Condition category (AH)
• (added) Assertion score (between Clin Sig & Date Last Eval)
• (remove) Number of chromosomes with variant (BQ)
• (remove) Citations or URLs that cannot be represented in evidence citations column (CA)

(fixed) #22 Clinvar Submitter Service is returning 400 error
Root cause: When calling the with variant that has no b38 or preferred name the clinvar-submitter service was throwing an uncaught exception Resolution: Added capability to grab the b37 hgvs and refseq accession if b38 and preferred name is not available. As well, as embedded a new ERROR code *E-203 to handle exceptional situations when neither b38, b37 or preferred names exist. The new error code will be embedded in the output that is pasted in the corresponding hgvs and refseq columns if this occurs.

(fixed) #24 Some mode of inheritance values not compatible with ClinVar format
Root cause: in the VCI there is the option to choose inheritance pattern 'adjectives' which are currently added within parantheses at the end of the inheritance term selected. When an 'adjective' suffix is selected in VCI it breaks the format expected in the ClinVar submission. Resolution: While there is not a perfect alignment between all of the VCI moi terms and clinvar's allowed terms, we can alleviate this issue by dropping the paranthesed 'adjective' selection when it exists on a MOI term other than 'Other'. When 'Other' is selecte with an moi 'adjective' we will use the 'adjective'. This will allow almost all combinations from VCI to work with ClinVar. For those that don't align there would need to be a request to change the VCI selections or ClinVar allowed terms or to define a finer mapping to be incorporated in this service's translation.

First true production deployment

Fix for mondo bungling the 'exactMatch' property

MONDO had historically included 'exactMatch' as a distinct property,
viewable in the OLS JSON. The data previously included here now shows
up as a list of strings, with keys separated by spaces, under the
property_value key. Added code to read this key and add the contained
strings back to the annotation key as it was before.

I expect this is an error in the data produced by MONDO and that they
will fix it eventually. This change should not break after MONDO gets
their act together, but it is reasonable to remove it after their data
reverts to its previous form.