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2024-01-16fix typo errorAlexander_Kabui
2024-01-16Merge pull request #828 from genenetwork/feature/reference-rating-uiAlexander Kabui
add UI for reference rating gn-llm documents
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>
2024-01-12doc/testing.org: Fix minor typo.Munyoki Kilyungi
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
2024-01-02Install static directory recursively.Arun Isaac
2024-01-02Fix base directory name in manifest.Arun Isaac
Earlier, we renamed the base directory from wqflask to gn2. Do likewise in the manifest.
2024-01-02Move default settings into gn2 module.Arun Isaac
2024-01-02Do not read version from separate file.Arun Isaac
There is not much use having a separate version file. Besides, not having a separate file saves us all the trouble of dealing with the path to that file.
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
2024-01-02add loading spinner for form submissionAlexander_Kabui
2024-01-02fix issue for chromium browsers:form submitting twiceAlexander_Kabui
2023-12-30setup.py: Use find_packages.Arun Isaac
2023-12-30Namespace mock paths under gn2.Arun Isaac
2023-12-29Correct path to etc/VERSION.Arun Isaac
2023-12-29Remove only up to -c in bin/genenetwork2.Arun Isaac
For example, in bin/genenetwork2 etc/default_settings.py -c -m pytest, remove only up to -c.
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.
2023-12-29use gn-serverl-url for gn3 apiAlexander_Kabui
2023-12-23use gn3 local urlAlexander_Kabui
2023-12-22Merge pull request #823 from genenetwork/feature/gn-llm-uiAlexander Kabui
Feature/gn llm UI
2023-12-22guix: Do not fix version of package.Arun Isaac