Db migration: remove gene length #6312

inodb · 2019-06-21T21:22:06Z

This information is stored in Genome Nexus. We don't need it in
cBioPortal anymore.

Verify that it is no longer used in frontend? (it was used in Mutated Genes tab of study view)
Remove LENGTH in gene table
Remove it from API
Remove it from import code

inodb · 2019-06-21T21:23:11Z

@sheridancbio i forgot what the rules are regarding schema versioning. Where can I find that again?

inodb · 2019-06-25T20:12:09Z

core/src/main/java/org/mskcc/cbio/portal/servlet/PfamSequenceServlet.java

@@ -1,259 +0,0 @@
-/*


don't think this is used anymore either, all pfam data is in genome nexus

inodb · 2019-06-25T20:12:23Z

portal/src/main/webapp/WEB-INF/web.xml

@@ -362,15 +362,6 @@
        <url-pattern>/omaRedirect.do</url-pattern>
    </servlet-mapping>

-	<servlet>


don't think this is used anymore either, all pfam data is in genome nexus

This information is stored in Genome Nexus. We don't need it in cBioPortal anymore. Fix cBioPortal#6308

pieterlukasse

thanks @inodb . Happy to see some cleanup taking place! Looks good to me 👍

Only one small request: please also update the documentation here https://github.com/cBioPortal/cbioportal/blob/master/docs/Updating-gene-and-gene_alias-tables.md#mysql-steps (step 5).

inodb · 2019-06-26T14:54:29Z

Thanks @pieterlukasse ! Good catch! Updated

That reminds me we might have to do a mouse version of genome nexus:

genome-nexus/genome-nexus-importer#22

I don't think mouse support for cBioPortal will work currently:

#6326

pieterlukasse

thanks @inodb! Good point regarding mouse support. Thanks for logging the issue 👍

Removing gene length is a pretty substantial change

ao508

code looks good, just 2 minor requests:

remove var declarations for TEST_LENGTH* in test classes (see comments)
update usage statement in documentation

docs/Updating-gene-and-gene_alias-tables.md

web/src/test/java/org/cbioportal/web/DiscreteCopyNumberControllerTest.java

ao508 · 2019-06-26T18:47:19Z

web/src/test/java/org/cbioportal/web/GeneControllerTest.java

@@ -132,7 +130,6 @@ public void getGene() throws Exception {
        gene.setHugoGeneSymbol(HUGO_GENE_SYMBOL_1);
        gene.setType(TYPE_1);
        gene.setCytoband(CYTOBAND_1);
-        gene.setLength(LENGTH_1);


same comment here about removing the LENGTH* vars

ao508 · 2019-06-26T18:47:53Z

web/src/test/java/org/cbioportal/web/MutationControllerTest.java

@@ -283,7 +283,6 @@ public void getMutationsInMolecularProfileBySampleListIdDetailedProjection() thr
            .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.hugoGeneSymbol").value(TEST_HUGO_GENE_SYMBOL_1))
            .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.type").value(TEST_TYPE_1))
            .andExpect(MockMvcResultMatchers.jsonPath("$[0].gene.cytoband").value(TEST_CYTOBAND_1))


same comment here about removing the TEST_LENGTH* vars

inodb · 2019-06-26T19:21:01Z

@ao508 Thanks for catching those ! Updated the PR

ao508

approving changes

pvannierop · 2019-06-27T05:32:56Z

@inodb Gene length appears to be used in the lollipop plot and oncoprint components so I do not think this can be removed from GN.

  private get proteinLength(): number {
        return (this.props.store.allTranscripts.result &&
            this.props.store.activeTranscript &&
            this.props.store.transcriptsByTranscriptId[this.props.store.activeTranscript] &&
            this.props.store.transcriptsByTranscriptId[this.props.store.activeTranscript].proteinLength) ||
            Math.round(this.props.store.gene.length / 3);
    }

function formatGeneticTrackSublabel(oqlFilter: UnflattenedOQLLineFilterOutput<object>): string {
    if (isMergedTrackFilter(oqlFilter)) {
        return ""; // no oql sublabel for merged tracks - too cluttered
    } else {
        return oqlFilter.oql_line.substring(oqlFilter.gene.length).replace(";",""); // get rid of gene in beginning of OQL line, and semicolon at end
    }
}

pvannierop · 2019-06-27T07:40:05Z

I misunderstood the idea of the PR. It was remapping of gene.length from cBP-db to GN. Never mind my comment.

sheridancbio · 2019-07-17T19:23:51Z

Hi @inodb ... here were old rules we adopted for db schema version number assignment. I'm not sure what our current practice is. https://github.com/cBioPortal/cbioportal/wiki/EP-Review-Changes-to-Database-Schema

inodb requested a review from sheridancbio June 21, 2019 21:22

inodb force-pushed the remove-gene-length branch 6 times, most recently from 411c9bc to 04db2e6 Compare June 25, 2019 18:32

inodb requested review from pieterlukasse, pvannierop and ao508 and removed request for sheridancbio June 25, 2019 18:33

inodb force-pushed the remove-gene-length branch 5 times, most recently from a327ad8 to 38228fb Compare June 25, 2019 20:05

inodb commented Jun 25, 2019

View reviewed changes

Db migration: remove gene length

dd10a15

This information is stored in Genome Nexus. We don't need it in cBioPortal anymore. Fix cBioPortal#6308

inodb force-pushed the remove-gene-length branch from 38228fb to dd10a15 Compare June 25, 2019 20:22

inodb added the ready to review label Jun 25, 2019

pieterlukasse requested changes Jun 26, 2019

View reviewed changes

Remove gene length import from docs

a634658

inodb mentioned this pull request Jun 26, 2019

Support mouse annotations genome-nexus/genome-nexus-importer#22

Open

inodb requested a review from pieterlukasse June 26, 2019 14:54

pieterlukasse approved these changes Jun 26, 2019

View reviewed changes

Change db version to 2.10.0 (remove gene length)

781dede

Removing gene length is a pretty substantial change

ao508 requested changes Jun 26, 2019

View reviewed changes

Remove TEST_LENGTH vars and --gtf option

a4fcc64

inodb requested a review from ao508 June 26, 2019 19:20

ao508 approved these changes Jun 26, 2019

View reviewed changes

inodb merged commit 31eaef8 into cBioPortal:rc Jun 26, 2019

inodb mentioned this pull request Jul 3, 2019

Update rc client cBioPortal/cbioportal-frontend#2522

Merged

sheridancbio removed the ready to review label Jul 17, 2019

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Db migration: remove gene length #6312

Db migration: remove gene length #6312

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Db migration: remove gene length #6312

Db migration: remove gene length #6312

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