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2024-01-30Error reporting: Pass external error forward to GN2's error handlingFrederick Muriuki Muriithi
2024-01-30Create framework for error handling and handle connection errorsFrederick Muriuki Muriithi
2024-01-25fix on UI wordingAlexander_Kabui
2024-01-25fix issue loading gnqa prev queries on base fileAlexander_Kabui
2024-01-25add view point for gnqa search historyAlexander_Kabui
2024-01-25Add modal for search historyAlexander_Kabui
2024-01-19Add list panel implementationAlexander_Kabui
2024-01-18fix for qnqa ui letter spacingAlexander_Kabui
2024-01-16fix typo errorAlexander_Kabui
2024-01-16add UI for reference rating gn-llm documentsAlexander_Kabui
2024-01-12Correctly patch the db connection when fetching accession_id.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Co-authored-by: Alexander Kabui <alexanderkabua@gmail.com>
2024-01-12Switch NCBI link from http to https in failing test and RDF query.Munyoki Kilyungi
* gn2/tests/wqflask/show_trait/test_show_trait.py (test_get_ncbi_summary_request): Replace "http://eutils.ncbi.nlm.nih.gov" with "https://eutils.ncbi.nlm.nih.gov" * gn2/wqflask/views.py (get_probeset): Ditto. Co-authored-by: Alexander Kabui <Alexanderkabua@gmail.com> Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-10Check whether the metadata.dataset group first exists.Munyoki Kilyungi
* gn2/wqflask/templates/genotype.html: Add metadata.dataset check in and clause. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-10Add a compare button that shows the current genotype page.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-10Add dataset metadata to genotype page when a dataset is specified.Munyoki Kilyungi
* gn2/wqflask/templates/genotype.html: Add extra dataset metadata. * gn2/wqflask/views.py (get_genotype): Extend genotype URL to enable specifying the dataset name. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-09Fix the way accession_id is set + update info link on correlation pagezsloan
2024-01-09Update script's module path.Frederick Muriuki Muriithi
2024-01-09Update module pathsFrederick Muriuki Muriithi
With the reorganisation, a number of module paths changed, and need to be updated. This commit fixes a few obvious ones.
2024-01-08Update default permutations for R/qtl to 0zsloan
2024-01-08Update ncbi summary link to https, since before it was spending extra time ↵zsloan
trying (and failing) to query the http link before trying https
2024-01-08Update DB info link on search result page and trait pagezsloan
2024-01-08Fix issue where mapmodel_rqtl and mapmethod_rqtl were still named ↵zsloan
mapmodel_rqtl_geno and mapmethod_rqtl_geno respectively
2024-01-08Add a compare button that shows the current probeset page.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08Include Entrez summary for a geneID on the ProbeSet page.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08Add dataset metadata to probeset page when a dataset is specified.Munyoki Kilyungi
* gn2/wqflask/templates/probeset.html: Add extra dataset metadata elements for groups, species, tissue name and dataset link. * gn2/wqflask/views.py (get_probeset): Extend probeset URL to enable specifying the dataset name. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08add GNQA descriptionAlexander_Kabui
2024-01-08code refactoring for gn llm uiAlexander_Kabui
2024-01-08add css file for gn-llm-uiAlexander_Kabui
2024-01-08revert to use GN3_LOCAL_URL for gn3 api endpointAlexander_Kabui
2024-01-08fix url errorAlexander_Kabui
2024-01-08fix url errorAlexander_Kabui
2024-01-08merge testingAlexander_Kabui
2024-01-08revert commit gn server urlAlexander_Kabui
2024-01-06Add probeset RDF page.Munyoki Kilyungi
* gn2/wqflask/templates/probeset.html: New probeset HTML file. * gn2/wqflask/views.py (get_probeset): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-05fix errorAlexander_Kabui
2024-01-05fetch gn_server_url from current configAlexander_Kabui
2024-01-02Fix path to error GIFs.Arun Isaac
genenetwork2 is now run from the top-level directory of the repo. So, we prepend gn2 to the error GIF path. * gn2/wqflask/views.py (handle_generic_exceptions): Prepend gn2 to error GIF path.
2024-01-02Make Group Info button point to info.genenetwork.orgzsloan
2024-01-02Change the way the info button works so that it just submits a form instead ↵zsloan
of opening a window with JS
2024-01-02Move default settings into gn2 module.Arun Isaac
2024-01-02Consistently use GN_VERSION from app config.Arun Isaac
GN_VERSION is set in the configuration file and read into the app config dictionary. Use that instead of re-reading from the etc/VERSION file. * gn2/utility/tools.py (gn_version): Delete function. (GN_VERSION): Delete variable. * gn2/wqflask/metadata_edits.py (display_phenotype_metadata, display_probeset_metadata, show_history): Use GN_VERSION in app config. * gn2/wqflask/views.py: Do not import GN_VERSION from gn2.utility.tools. (handle_generic_exceptions, index_page.__render__, submit_trait_form): Use GN_VERSION in app config.
2024-01-02merge changesAlexander_Kabui
2023-12-30Namespace mock paths under gn2.Arun Isaac
2023-12-29Namespace all modules under gn2.Arun Isaac
We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service.
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 11:38:35 +0000