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GSoC 2018 Dara Akdag
This project was done within the Google Summer of Code 2018.
The main objective of this project was to figure out why there was a mismatch in the ontology tags displayed on the pathway pages and the information stored in the GPML file of the same pathway. This mismatch was not present in all pathways and thus some investigation work was required to figure out why the ontology tags were fetched inconsistently. The secondary objective was to create recommendation functionality, to suggest pathway specific ontology tags fetched with the BioPortal recommender API, when the pathway first is created.
The main objective has been completed. After some investigation it became clear the ontology tags where fetched from the database and not the GPML file. Rewriting the function that fetched the tags from the database to fetch the tags from the GPML solved the mismatch problem previously observed. To make the functionality available on the soon upgraded version of WikiPathways (newest version of mediawiki), a decision was made to create a sub-module which contains all functionality pertaining the ontology tags. This extension was created, which included rearranging some files and dependencies across the whole project.
Apart from the main objectives, a lot of debugging was done to figure out solve problems which had sneaked in to the codebase of the upgraded WikiPathways version. The goal of upgraded WikiPathways solution is to solve a long standing problem, which makes it difficult to update the site due to the handmade submodule design. As this version is still under construction many bugs has sneaked into the codebase. Thus when the project first started, a lot of time was spent on figuring out why the ontology tags were not displayed at all. The debugging of this problem lead to identifying missing scripts, that were not moved properly, which lead to the functionality not being compiled and executed. Especially bugs related to follow script were resolved. https://github.com/wikipathways/wikipathways-upgrade-2017/pull/29/commits/403a871552532fff6cb09cb53c49fe5afa5ff97e#diff-d2895d8a2a4e2569c39f8da395be59ceR299
Among other ad hoc bug discoveries were a deprecated use of AJAX functionality, which was replaced to follow the current MediaWiki convention. Also, a future problems with deprecated Yahoo! API functionality was identified, which ideally should be replaced in the near future.
Regarding the second part of the project, a preliminary recommender script has been developed in php, and the pertaining BioPortal queries have been identified.
The recommender script need to be finished, which includes correcting the current API call with the appropriate BioPortal API call. Then it needs to be implemented as a suggestions box on the newly created pathway page.
http://gsoc18bawiz.blogspot.com/
- OntologyTag sub-module: https://github.com/wikipathways/mediawiki-extensions-WikiPathways-OntologyTags
- Commits to clean up current upgrade codebase and include new sub-module: https://github.com/wikipathways/mediawiki-extensions-WikiPathways/pull/1/commits/c39489d4cee0f8f8f2fee0b7c89ec188d3ad0df3 https://github.com/wikipathways/wikipathways-upgrade-2017/pull/29/commits/403a871552532fff6cb09cb53c49fe5afa5ff97e
- Bug fix in current codebase: https://github.com/wikipathways/wikipathways.org/pull/79