Problem with backslash in gene search

[fbastian]

In GitLab by @fbastian on Oct 11, 2018, 17:02

In the logs I came to the following error:

ERROR org.bgee.controller.FrontController 293 doRequest - catching java.lang.IllegalStateException: The term should match either the gene id/name or one of its synonyms. Term: upk\3a GeneTO;GeneTO [geneId=ENSG00000100373, speciesId=9606, geneBioTypeId=6, OMAParentNodeId=185046, ensemblGene=true, geneMappedToGeneIdCount=1]
    at org.bgee.model.gene.GeneService.geneMatch(GeneService.java:265)
    at org.bgee.model.gene.GeneService.lambda$searchByTerm$4(GeneService.java:245)
    at org.bgee.model.gene.GeneService.searchByTerm(GeneService.java:246)
    at org.bgee.controller.CommandSearch.processRequest(CommandSearch.java:65)
    at org.bgee.controller.FrontController.doRequest(FrontController.java:265)
    at org.bgee.controller.FrontController.doGet(FrontController.java:344)

There were several problems:

• first, the term entered by the user was not URL encoded to perform the request to the server. Depending on the Tomcat version, that might or might not generate an error of illegal character.
• Second, MySQL seems to simply discard backslash in queries, so that it could still find a match in the database for the term "upk\3a"
• Then, because of the backslash, the application was not finding out what was the matching part between the gene name, ID, and synonyms, thus generating an Exception

[fbastian]

In GitLab by @fbastian on Oct 11, 2018, 17:06

mentioned in commit af87a0a23df649cdf52270e0286ca236aabb97aa

[fbastian]

In GitLab by @fbastian on Oct 11, 2018, 17:06

closed