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* Adjustments to allow use with TopBraid 6.3 - updated topbraid queries for oncotree_version - update web request to TopBraid to include login parameter - workaround broken MSK crosswalk API link : load current links from resource file when crosswalk.disable_cvs_querying is set - resource file staticCrosswalkOncotreeMappings.txt added with current definitions (from production cache) - specify key and value types for Ehcache Cache references - switch away from deprecated ApiInfo constructor and CORS filter specification - add additional details to logging * drop crosswalk server interaction code and option
also parameterize oncotree topbraid namespace and graph id strings Co-authored-by: Divya Madala <71040191+divyamadala30@users.noreply.github.com> Co-authored-by: Robert Sheridan <7747489+sheridancbio@users.noreply.github.com>
Create Ontology to Ontology mapping tool - script and mapping definition file - update Mapping Tools page and provide README for script Co-authored-by: ramya <ramyamadupuri99@gmail.com>
Previously, only leaf nodes of the tree were counted in the total count of tumor types displayed on the home page. Now all nodes in the tree except for the root node (TISSUE) are counted in the total. Co-authored-by: Avery Wang <18199796+averyniceday@users.noreply.github.com> Co-authored-by: Robert Sheridan <7747489+sheridancbio@users.noreply.github.com>
* Update News.md * Update News.md typo fix and rephrase * Update README.md rephrase * Update News.md rephrase * Update OncoTree-Mapping-Tool.md make download link for mapping tool blue and have external link icon Co-authored-by: Robert Sheridan <sheridan@cbio.mskcc.org>
fix broken link to mapping tools tab
add graphical link icons to new news page item
* oncotree_to_oncotree.py should support python3 (cBioPortal#232) * Update to python3 * Set interpreter and add to docs * Update OncoTree-Mapping-Tool.md * adjust unit and integration tests for python3 execution * for backwards compatible behavior, sets of possible target oncotree codes are sorted during output Co-authored-by: thomasyu888 <thomasyu888@gmail.com> Co-authored-by: Thomas Yu <tyu@ip-10-5-30-58.ec2.internal> Co-authored-by: thomas.yu <thomas.yu@sagebase.org>
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news updates for 2021-11-02 release