Activity for BioModels Database
-
Mihai Glonț committed [r882]
nudge search engines into indexing the current website instead of this one.
-
update decommissioning announcement styling and date.
-
Write EOL outside while loop when inserting timestamp into downloaded files.
-
Reworked HtmlEncodingFilter because HttpServletRequest is immutable.
-
More XSS-related fixes.
-
Make getHTMLEncodedParameter actually encode parameters.
-
avoid path traversal attacks when requesting static pages.
-
Avoid XSS attacks on the search page.
-
fix javadoc typo
-
Rephrased link to JUMMP in light of the retirement date for this website.
-
Updated submission link since JUMMP has moved to wwww.
-
Links to JUMMP should use https://
-
Remove beta from link to JUMMP
-
Fix logo src on Caltech homepage.
-
More GDPR-related changes.
-
Updated the cookie banner to include the GDPR privacy notice.
-
Avoid XSS vulnerability when downloading models.
-
Allow search requests to terminate after interruptions.
-
Interrupt search threads running longer than 2 seconds.
-
Close Lucene analyser even if a search throws an exception.
-
Deal with empty email addresses when recording model creators.
-
Avoid NPE if logical operator for advanced search is not provided.
-
Fixed database connection leak in healthcheck servlet.
-
Handle potential NPEs when dealing with PDGSMM search results.
-
Improved reporting of search query execution time.
-
Ensure search workers are stopped even in case of exceptions:
-
Return after handling a PDGSMM file download request.
-
Use try-with-resources to ensure GoDao db connections get closed.
-
Use a dedicated shared lock for acquiring db connections.
-
use HTTPS on main homepage.
-
Use protocol-relative URIs for GO chart dependencies.
-
Redirect submissions to JUMMP
-
added link to BioModels Jummp
-
Switched to HTTPS for Europe PMC and ChEBI endpoints
-
fixed https icon for expanding PDGSMM search tips
-
Use identifiers.org URI for BioModels citation.
-
Updated citation used by the model notes editor.
-
Usability enhancements to the browse PDGSM models page.
-
minor pdgsmm search enhancements.
-
added PDGSM models to global BioModels search results.
-
Nicolas Rodriguez committed [r842]
updated the jsbml jar file
-
Added missing link to PDGSMM to the front page navbar.
-
Improved error handling when not possible to fetch a db connection.
-
streamlined PDGSMM search as a means of refining browsing by disease.
-
Added PDGSMM link to nav bar.
-
Added PDGSMM-specific search.
-
Updated logo for MoM RSS feed.
-
display annotations for pdgsmm models.
-
Minor wording improvements for PDGSMM pages
-
Added PDGSMM disease archive links.
-
updated database schema to include the pdgsm_models table.
-
Dropped gender & age from browse PDGSMM by disease table.
-
Minor improvements to browse PDGSMM page:
-
Added means of browsing PDGSM models by disease type.
-
Committing servlet for downloading model files.
-
added license information to recently-created pdgsmm source files.
-
Added publication link and missing classes for ModelMonth entry for pdgsmm.
-
Return null instead of throwing an exception for null ModelMonth arguments.
-
removed unnecessary semicolon.
-
Refined styling for buttons on PDGSM model display page.
-
Fixed download for patient-derived genome scale metabolic models.
-
Added basic means of viewing a patient-derived genome scale metabolic models.
-
minor javadoc fixes.
-
Added SBML L2V5 to accepted formats.
-
added AgedBrain acknowledgements.
-
Updated JSBML.
-
Fixed javadoc for SBMLUtilities.generateNoAnno argument.
-
fixed Ant script for Java 8.
-
increased min pagination size
-
Added Plant Ontology and BioAssay Ontology to t...
-
fixed typo in LibSBMLFacade error message.
-
cleaned up extraneous log statements in gpcr se...
-
catch potential exceptions when closing result ...
-
Added back-end for displaying models relating t...
-
Added links to metabolic and logical models in ...
-
Simplified test for compartment types in ModelB...
-
updated version of jsbml.
-
don't assume the model history will always cont...
-
minor improvements to error logging when batch-...
-
updated message for ND map.
-
Updated image caption on ND map page.
-
added favicon.
-
Improved defence against awkward annotations.
-
remove broken mime type for jsp to allow diff'ing.
-
Added the neurodegenerative disease map page.
-
hopefully corrected properly the LibSBMLFacade....
-
Cater for undefined publication volume in Europ...
-
fixed css typo.
-
Added info-box styling to submission guidelines...
-
fixup: java cannot switch on Strings.
-
semicolons...
-
Allow PDF as additional file type.
-
replaced complex if-else with switch.
-
semicolons, semicolons...
-
Escape non-ASCII characters in the model notes.
-
Updated Oracle db driver.
-
changed default publicationDate hoping to avoid...
-
added back a test in SubmitModelBean to avoid r...
-
the if statement was corrected on LibSBMLFacade...
-
removed unused import.
1 >
