Activity for Mihai Glonț
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Mihai Glonț committed [r882]
nudge search engines into indexing the current website instead of this one.
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update decommissioning announcement styling and date.
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Write EOL outside while loop when inserting timestamp into downloaded files.
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Reworked HtmlEncodingFilter because HttpServletRequest is immutable.
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More XSS-related fixes.
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Make getHTMLEncodedParameter actually encode parameters.
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avoid path traversal attacks when requesting static pages.
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Avoid XSS attacks on the search page.
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fix javadoc typo
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Rephrased link to JUMMP in light of the retirement date for this website.
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Updated submission link since JUMMP has moved to wwww.
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Links to JUMMP should use https://
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Remove beta from link to JUMMP
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Fix logo src on Caltech homepage.
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More GDPR-related changes.
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Updated the cookie banner to include the GDPR privacy notice.
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Avoid XSS vulnerability when downloading models.
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Allow search requests to terminate after interruptions.
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Interrupt search threads running longer than 2 seconds.
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Close Lucene analyser even if a search throws an exception.
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Deal with empty email addresses when recording model creators.
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Avoid NPE if logical operator for advanced search is not provided.
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Fix stale groupId for registry-lib in pom.xml
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Add Maven integration.
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Ignore Maven and IntelliJ artefacts.
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fixed type casting error when converting comp submodels to biopax
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Fixed database connection leak in healthcheck servlet.
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Handle potential NPEs when dealing with PDGSMM search results.
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Improved reporting of search query execution time.
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Ensure search workers are stopped even in case of exceptions:
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Return after handling a PDGSMM file download request.
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Use try-with-resources to ensure GoDao db connections get closed.
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Use a dedicated shared lock for acquiring db connections.
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use HTTPS on main homepage.
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Use protocol-relative URIs for GO chart dependencies.
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Redirect submissions to JUMMP
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added link to BioModels Jummp
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Switched to HTTPS for Europe PMC and ChEBI endpoints
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fixed https icon for expanding PDGSMM search tips
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Use identifiers.org URI for BioModels citation.
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Updated citation used by the model notes editor.
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Usability enhancements to the browse PDGSM models page.
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minor pdgsmm search enhancements.
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added PDGSM models to global BioModels search results.
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Added missing link to PDGSMM to the front page navbar.
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Improved error handling when not possible to fetch a db connection.
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streamlined PDGSMM search as a means of refining browsing by disease.
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Added PDGSMM link to nav bar.
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Added PDGSMM-specific search.
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Updated logo for MoM RSS feed.
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display annotations for pdgsmm models.
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Minor wording improvements for PDGSMM pages
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Added PDGSMM disease archive links.
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updated database schema to include the pdgsm_models table.
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Dropped gender & age from browse PDGSMM by disease table.
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Minor improvements to browse PDGSMM page:
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Added means of browsing PDGSM models by disease type.
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Committing servlet for downloading model files.
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added license information to recently-created pdgsmm source files.
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Added publication link and missing classes for ModelMonth entry for pdgsmm.
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Return null instead of throwing an exception for null ModelMonth arguments.
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removed unnecessary semicolon.
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Refined styling for buttons on PDGSM model display page.
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Fixed download for patient-derived genome scale metabolic models.
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Added basic means of viewing a patient-derived genome scale metabolic models.
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minor javadoc fixes.
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Added SBML L2V5 to accepted formats.
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added AgedBrain acknowledgements.
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Updated JSBML.
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Fixed javadoc for SBMLUtilities.generateNoAnno argument.
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fixed Ant script for Java 8.
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increased min pagination size
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Added Plant Ontology and BioAssay Ontology to t...
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fixed typo in LibSBMLFacade error message.
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cleaned up extraneous log statements in gpcr se...
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catch potential exceptions when closing result ...
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Added back-end for displaying models relating t...
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Added links to metabolic and logical models in ...
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Simplified test for compartment types in ModelB...
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updated version of jsbml.
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don't assume the model history will always cont...
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minor improvements to error logging when batch-...
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updated message for ND map.
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Updated image caption on ND map page.
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Updated sections covering annotation/publication.
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general updates to the introduction.
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refreshed interaction with IOF and updated requ...
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JUM-96 line wrapping, README in markdown, gener...
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completed overhaul of tech overview.
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extended coverage of technical overview.
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added favicon.
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Improved defence against awkward annotations.
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remove broken mime type for jsp to allow diff'ing.
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Added the neurodegenerative disease map page.
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Cater for undefined publication volume in Europ...
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fixed css typo.
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Added info-box styling to submission guidelines...
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fixup: java cannot switch on Strings.
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semicolons...
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Allow PDF as additional file type.
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