Robert Sheridan

g2s web server certificate about to expire

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The g2s web server https/ssl certificate will expire Tuesday, August 23, 2022 at 3:08:23 PM Eastern Daylight Time A renewal of the certificate is needed before that time. If we...

move mybatis dependency into persistence-mybatis

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mybatis not needed for any other modules Describe changes proposed in this pull request: - mybatis dependencies are taken out of the root pom.xml and that of the service module...

studies which have a genetic_profile_link to themselves cannot be deleted

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several years ago #2470 introduced the table genetic_profile_link, which includes these foreign key constraints: FOREIGN KEY (`REFERRING_GENETIC_PROFILE_ID` ) REFERENCES `genetic_profile` (`GENETIC_PROFILE_ID`) ON DELETE CASCADE, FOREIGN KEY (`REFERRED_GENETIC_PROFILE_ID` ) REFERENCES `genetic_profile`...

user wishes to map combination of ICDO Topology and ICDO Morphology codes

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When going from ICDO to oncotree code, the ontology-to-ontology mapping tool is unable to combine ICDO Topography and Morphology codes to select a more specific oncotree code. So, for example,...

Looking at the ontology code mapping file using the github browser: https://github.com/cBioPortal/oncotree/blob/master/scripts/ontology_to_ontology_mapping_tool/ontology_mappings.txt there appears to be unexpected characters for the record for oncotree code GBASC in the NCIT column. This...

Tooltip missing parenthesized portion of detailed cancer type

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Reported by @zhx828 : Oncotree code AMLRBM15MKL1 has detailed cancer type: "AML (megakaryoblastic) with t(1;22)(p13.3;q13.3);RBM15-MKL1" In the popup tooltip window the _name_ attribute is missing the substring "(megakaryoblastic)"

When expanding some subtrees (for example, expanding both MBN and MTNN (children of NHL)) the vertical extent of the viewport clips off a portion of the oncotree graph. Expanding other...

If the CVS system holding the metadata UMLS and NCI codes is unavailable at cache time, we (and the CVS maintenance team) should get warning messages. If we don't get...

curl -X POST --header "Content-Type: application/json" --header "Accept: application/json" -d "{ \"queries\": [ { \"exactMatch\": true, \"query\": \"TISSUE\", \"type\": \"code\" } ], \"version\": \"oncotree_latest_stable\" }" "http://oncotree.mskcc.org/oncotree/api/tumorTypes/search" Returns: "data": [ [...

Maven modules can be reorganized around reuse opportunities. If no components of the system can be used in other projects, consider combining into a single maven module.