├── .babelrc ├── .coveragerc ├── .coveralls.yml ├── .dockerignore ├── .eslintrc.yml ├── .github └── workflows │ ├── github-publish-celery-flaskomics.yml │ ├── github-publish-flaskomics.yml │ └── lint_test.yml ├── .gitignore ├── .readthedocs.yml ├── CHANGELOG.md ├── LICENSE ├── Makefile ├── Pipfile ├── Pipfile.lock ├── README.md ├── app.py ├── askomics.png ├── askomics ├── __init__.py ├── api │ ├── __init__.py │ ├── admin.py │ ├── auth.py │ ├── catch_url.py │ ├── data.py │ ├── datasets.py │ ├── file.py │ ├── galaxy.py │ ├── ontology.py │ ├── query.py │ ├── results.py │ ├── sparql.py │ ├── start.py │ └── view.py ├── app.py ├── libaskomics │ ├── BedFile.py │ ├── CsvFile.py │ ├── Database.py │ ├── Dataset.py │ ├── DatasetsHandler.py │ ├── File.py │ ├── FilesHandler.py │ ├── FilesUtils.py │ ├── Galaxy.py │ ├── GffFile.py │ ├── LdapAuth.py │ ├── LocalAuth.py │ ├── Mailer.py │ ├── OntologyManager.py │ ├── Params.py │ ├── PrefixManager.py │ ├── RdfFile.py │ ├── RdfGraph.py │ ├── Result.py │ ├── ResultsHandler.py │ ├── SparqlQuery.py │ ├── SparqlQueryLauncher.py │ ├── Start.py │ ├── TriplestoreExplorer.py │ ├── Utils.py │ ├── __init__.py │ └── prefix.cc.json ├── middleware.py ├── react │ └── src │ │ ├── classes │ │ └── utils.jsx │ │ ├── components │ │ ├── autocomplete.jsx │ │ ├── template.jsx │ │ └── waiting.jsx │ │ ├── contact.jsx │ │ ├── footer.jsx │ │ ├── index.jsx │ │ ├── navbar.jsx │ │ ├── routes.jsx │ │ └── routes │ │ ├── about │ │ └── about.jsx │ │ ├── account │ │ ├── account.jsx │ │ ├── delete_account.jsx │ │ ├── update_apikey.jsx │ │ ├── update_galaxy.jsx │ │ ├── update_password.jsx │ │ └── update_profile.jsx │ │ ├── admin │ │ ├── admin.jsx │ │ ├── datasetstable.jsx │ │ ├── filestable.jsx │ │ ├── ontologies.jsx │ │ ├── prefixes.jsx │ │ ├── queriestable.jsx │ │ └── userstable.jsx │ │ ├── ask │ │ └── ask.jsx │ │ ├── data │ │ └── data.jsx │ │ ├── datasets │ │ ├── datasets.jsx │ │ └── datasetstable.jsx │ │ ├── error │ │ └── error.jsx │ │ ├── form │ │ ├── attribute.jsx │ │ ├── entity.jsx │ │ └── query.jsx │ │ ├── form_edit │ │ ├── attribute.jsx │ │ ├── entity.jsx │ │ └── query.jsx │ │ ├── integration │ │ ├── advancedoptions.jsx │ │ ├── bedpreview.jsx │ │ ├── csvtable.jsx │ │ ├── gffpreview.jsx │ │ ├── integration.jsx │ │ └── rdfpreview.jsx │ │ ├── login │ │ ├── login.jsx │ │ ├── logout.jsx │ │ ├── passwordreset.jsx │ │ └── signup.jsx │ │ ├── overview │ │ └── overview.jsx │ │ ├── query │ │ ├── attribute.jsx │ │ ├── graphfilters.js │ │ ├── linkview.jsx │ │ ├── ontolinkview.jsx │ │ ├── overviewModal.jsx │ │ ├── query.jsx │ │ └── visualization.jsx │ │ ├── results │ │ ├── results.jsx │ │ └── resultsfilestable.jsx │ │ ├── sparql │ │ ├── advancedsparql.jsx │ │ ├── resultstable.jsx │ │ └── sparql.jsx │ │ └── upload │ │ ├── filestable.jsx │ │ ├── upload.jsx │ │ ├── uploadform.jsx │ │ ├── uploadgalaxyform.jsx │ │ ├── uploadmodal.jsx │ │ └── uploadurlform.jsx ├── static │ ├── about.html │ ├── css │ │ └── askomics.css │ ├── favicon.png │ └── welcome.html ├── tasks.py └── templates │ └── index.html ├── cli ├── add_user.py ├── clear_cache.py ├── clear_cache.sh ├── config_updater.py ├── set_config.sh ├── set_user.sh ├── update_base_url.py ├── update_base_url.sh └── upload_files.py ├── config ├── askomics.ini.template └── askomics.test.ini ├── docker ├── Dockerfile ├── DockerfileAll ├── DockerfileCelery └── start_all.sh ├── docs ├── abstraction-overview.md ├── abstraction.md ├── ci.md ├── cli.md ├── configure.md ├── console.md ├── contribute.md ├── data.md ├── dev-deployment.md ├── docs.md ├── federation.md ├── galaxy.md ├── img │ ├── abstraction_2d.png │ ├── abstraction_3d.png │ ├── account_button.png │ ├── askogalaxy.png │ ├── askograph.png │ ├── attribute_box.png │ ├── attributes.png │ ├── complex_query.png │ ├── csv_convert.png │ ├── custom_nodes.png │ ├── datasets.png │ ├── de_results_preview.png │ ├── external_startpoint.png │ ├── faldo.png │ ├── files_table.png │ ├── filters.png │ ├── form.png │ ├── form_edit.png │ ├── form_example.png │ ├── galaxy_askomics_files.png │ ├── galaxy_execute_it.png │ ├── galaxy_history_result.png │ ├── galaxy_import_from_galaxy.png │ ├── galaxy_input_data.png │ ├── galaxy_search_tool.png │ ├── gff.png │ ├── gff_preview.png │ ├── integrate_external.png │ ├── linked_query.png │ ├── login_button.png │ ├── minus.png │ ├── name_attr.png │ ├── navbar.png │ ├── navbar_files.png │ ├── num_attr.png │ ├── ontology_autocomplete.png │ ├── ontology_graph.png │ ├── ontology_integration.png │ ├── ontology_link.png │ ├── preview.png │ ├── preview_results.png │ ├── qtl_preview.png │ ├── query.png │ ├── query_builder.png │ ├── results_table.png │ ├── sparql.png │ ├── startpoint.png │ ├── symbol_to_ensembl_preview.png │ ├── template.png │ ├── tsv.png │ ├── union.png │ ├── union_duplicated.png │ └── uri_label_attr.png ├── index.md ├── manage.md ├── ontologies.md ├── prefixes.md ├── production-deployment.md ├── query.md ├── requirements.txt ├── results.md ├── style.css ├── template.md └── tutorial.md ├── mkdocs.yml ├── package.json ├── requirements.txt ├── setup.py ├── test-data ├── abstraction.nt ├── abstraction.ttl ├── abstraction.xml ├── agro_min.ttl ├── de.tsv ├── gene.bed ├── gene.gff3 ├── gene.tsv ├── linked_uris.csv ├── malformed.tsv ├── qtl.tsv ├── transcripts.tsv ├── transcripts_chunk1.tsv ├── transcripts_chunk2.tsv ├── transcripts_chunk3.tsv └── uris.csv ├── tests ├── __init__.py ├── conftest.py ├── data │ ├── graphState_filtered_query.json │ ├── graphState_simple_query.json │ ├── graphState_simple_query_form.json │ ├── graphState_simple_query_form_modified.json │ ├── graphstate.json │ ├── linked_uri_query.json │ ├── query.json │ ├── startpoints.json │ └── uri_query.json ├── results │ ├── abstraction.json │ ├── data_full.json │ ├── data_public.json │ ├── graphstate.json │ ├── init.json │ ├── preview.json │ ├── preview_files.json │ ├── preview_malformed_files.json │ ├── query.sparql │ ├── result.csv │ ├── results.json │ ├── results_admin.json │ ├── results_form.json │ ├── 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