intermine

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We are upgrading Python client to Python 3.8. We need to make some changes in this repository: - [x] Update testmine to Gradle 4.9 so that travis on Python repository...

asherpasha

Proposed core GWAS model

3

I propose the following as the core GWAS model. It is similar to the HumanMine model, but has more flexibility with phenotypes and such. In particular, I create a Phenotype...

sammyjava

@rachellyne please add more info, if you have. Not able to reproduce locally.

danielabutano

Update datasets.xml to contains all the datasets (with their descriptions)

3

FlyMine has 38/68 with empty descriptions HumanMine has 19/39 datasets with empty descriptions

danielabutano

run `./gradlew install --warning-mode all` in bio/sources and you get: The following annotation processors were detected on the compile classpath: 'org.apache.logging.log4j.core.config.plugins.processor.PluginProcessor'. Detecting annotation processors on the compile classpath is deprecated...

sammyjava

See the example here: > https://www.flymine.org/flymine/service/query/results?query=%20%3Cquery%20model%3D%22genomic%22%20view%3D%22Gene.secondaryIdentifier%0AGene.symbol%20Gene.primaryIdentifier%20Gene.organism.name%22%20%3E%3Cconstraint%0Apath%3D%22Gene%22%20op%3D%22IN%22%20value%3D%22Gene%20list%20for%20all%20organisms%2014%20Apr%202020%0A20.15%22%20code%3D%22A%22%20%2F%3E%3C%2Fquery%3E it should return 403 and not 500

danielabutano

Misleading message if property src.data.dir it's not properly configured in the project.xml file

1

If in a obo source, we configure ` ` instead of ` ` the console prints out the message > Don't know how to deal with file null thrown [here](https://github.com/intermine/intermine/blob/dev/bio/core/src/main/java/org/intermine/bio/task/OboConverterTask.java#L110)...

danielabutano

A the moment there is not XML validation to the project.xml configuration file. For example the wrong XML here: ` ` leads to the misleading message > java.lang.IllegalArgumentException: class "org.intermine.model.bio.null"...

danielabutano

In the project.xml file, for bio-source gff, if you do no set the property name="gff3.seqClsName" you have this error message > Execution failed for task ':dbmodel:retrieveSingleSource'. > java.lang.IllegalArgumentException: class "org.intermine.model.bio.null"...

danielabutano

from a support request human gene PTGR2 orthologue for D. rerio should be a LDO, not a O. source: ``` HUMAN|HGNC=20149|UniProtKB=Q8N8N7 DANRE|ZFIN=ZDB-GENE-050506-71|UniProtKB=X1WFL9 LDO Euteleostomi PTHR43205 ``` is marked as orthologue...

sergiocontrino