[PathwayCommons/factoid] 83ee7c: Fixed the issues in id mapping feature (#1087)
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: 83ee7ce6696a8b05ba5d68c9b056ba45a018fd1b https://github.com/PathwayCommons/factoid/commit/83ee7ce6696a8b05ba5d68c9b056ba45a018fd1b Author: metincansiper Date: 2022-10-06 (Thu, 06 Oct 2022) Changed paths: M package-lock.json M package.json M src/server/routes/api/document/index.js A test/biopax/biopax.js A test/biopax/sampleTemplate.json Log Message: --- Fixed the issues in id mapping feature (#1087) * Working on fixing uniprot id mapping issue * Further fixes for id mapping issue * Included the updates in package-lock.json file -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/61cfa9-83ee7c%40github.com.
[PathwayCommons/factoid] e4f83a: Included the updates in package-lock.json file
Branch: refs/heads/complex_id_mapping_fix Home: https://github.com/PathwayCommons/factoid Commit: e4f83af0478222f0fc85619d2fce71382dab2b6b https://github.com/PathwayCommons/factoid/commit/e4f83af0478222f0fc85619d2fce71382dab2b6b Author: metincansiper Date: 2022-10-05 (Wed, 05 Oct 2022) Changed paths: M package-lock.json Log Message: --- Included the updates in package-lock.json file -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/complex_id_mapping_fix/a29df4-e4f83a%40github.com.
[PathwayCommons/factoid] a29df4: Further fixes for id mapping issue
Branch: refs/heads/complex_id_mapping_fix Home: https://github.com/PathwayCommons/factoid Commit: a29df4651e6ae347cafbb8885d44b5e56906bcf3 https://github.com/PathwayCommons/factoid/commit/a29df4651e6ae347cafbb8885d44b5e56906bcf3 Author: metincansiper Date: 2022-10-05 (Wed, 05 Oct 2022) Changed paths: M src/server/routes/api/document/index.js M test/biopax/biopax.js Log Message: --- Further fixes for id mapping issue -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/complex_id_mapping_fix/901e62-a29df4%40github.com.
[PathwayCommons/factoid] 901e62: Working on fixing uniprot id mapping issue
Branch: refs/heads/complex_id_mapping_fix Home: https://github.com/PathwayCommons/factoid Commit: 901e622fab6722725d277fa4ea1f49bbef1a48e4 https://github.com/PathwayCommons/factoid/commit/901e622fab6722725d277fa4ea1f49bbef1a48e4 Author: metincansiper Date: 2022-10-04 (Tue, 04 Oct 2022) Changed paths: M package.json M src/server/routes/api/document/index.js A test/biopax/biopax.js A test/biopax/sampleTemplate.json Log Message: --- Working on fixing uniprot id mapping issue -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/complex_id_mapping_fix/00-901e62%40github.com.
[PathwayCommons/factoid] 75f84d: Supplement db improvements (#940)
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: 75f84d474e4237d7d5af7ddbdc9d1908f6d78610 https://github.com/PathwayCommons/factoid/commit/75f84d474e4237d7d5af7ddbdc9d1908f6d78610 Author: metincansiper Date: 2021-03-23 (Tue, 23 Mar 2021) Changed paths: M package-lock.json M package.json M src/client/components/home.js M src/config.js M src/server/routes/api/document/index.js M src/server/routes/api/document/indra.js A src/server/routes/api/document/related-papers-queue.js Log Message: --- Supplement db improvements (#940) * Use only supported organisms while searching groundings of the entities coming from biopax * Removed a conditional console.log statement that was written for temporary testing * Fix too many request issue of indra queries * While loading documents from biopax file skip the elements whose xref is not available also skip the ones connected to such elements. * Handle the case where response is null for fetch retry * Add api/document/from-url end point to add new documents from a url and used it directly from client side. Also, made a little update in error handling of indra connecter. * Control admin email(which is subject to change) from config file * Handle related paper process through priority queues and made some other improvements regarding the related papers. * Removed a mistakenly added char * Skip the interaction when grounding search returns no result for any of its entities. Also, trash the doc if there is no valid interaction in it. * Call deleteTableRows function instead of trashing document when it has no valid interaction (in case of creating docs from biopax file) * Delete the secret from database while removing the documents with no valid interaction -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/4aed3e-75f84d%40github.com.
[PathwayCommons/factoid] 817a30: Delete the secret from database while removing the...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: 817a3037586a5ea1c9cea92c6283338d8dc0e167 https://github.com/PathwayCommons/factoid/commit/817a3037586a5ea1c9cea92c6283338d8dc0e167 Author: metincansiper Date: 2021-03-22 (Mon, 22 Mar 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Delete the secret from database while removing the documents with no valid interaction -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/7c41e0-817a30%40github.com.
[PathwayCommons/factoid] 7c41e0: Call deleteTableRows function instead of trashing ...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: 7c41e0613c12a6e58ab266f4efd9acccb8a4bf76 https://github.com/PathwayCommons/factoid/commit/7c41e0613c12a6e58ab266f4efd9acccb8a4bf76 Author: metincansiper Date: 2021-03-22 (Mon, 22 Mar 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Call deleteTableRows function instead of trashing document when it has no valid interaction (in case of creating docs from biopax file) -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/15a25a-7c41e0%40github.com.
[PathwayCommons/factoid] 15a25a: Skip the interaction when grounding search returns...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: 15a25ae2aace6dd74a2b7ce8736cb286984f52e3 https://github.com/PathwayCommons/factoid/commit/15a25ae2aace6dd74a2b7ce8736cb286984f52e3 Author: metincansiper Date: 2021-03-22 (Mon, 22 Mar 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Skip the interaction when grounding search returns no result for any of its entities. Also, trash the doc if there is no valid interaction in it. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/86bd13-15a25a%40github.com.
[PathwayCommons/factoid] 5c4733: Handle related paper process through priority queu...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: 5c4733e29f24fd6ea233e587613e8f1e6699e363 https://github.com/PathwayCommons/factoid/commit/5c4733e29f24fd6ea233e587613e8f1e6699e363 Author: metincansiper Date: 2021-03-08 (Mon, 08 Mar 2021) Changed paths: M package-lock.json M package.json M src/server/routes/api/document/index.js M src/server/routes/api/document/indra.js A src/server/routes/api/document/related-papers-queue.js Log Message: --- Handle related paper process through priority queues and made some other improvements regarding the related papers. Commit: 86bd13a01cae8354df3653f63ae6f08a306185d2 https://github.com/PathwayCommons/factoid/commit/86bd13a01cae8354df3653f63ae6f08a306185d2 Author: metincansiper Date: 2021-03-08 (Mon, 08 Mar 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Removed a mistakenly added char Compare: https://github.com/PathwayCommons/factoid/compare/aa0d25a203d6...86bd13a01cae -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/aa0d25-86bd13%40github.com.
[PathwayCommons/factoid] aa0d25: Control admin email(which is subject to change) fr...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: aa0d25a203d6fe7c147b7c72ba83f34990e8f018 https://github.com/PathwayCommons/factoid/commit/aa0d25a203d6fe7c147b7c72ba83f34990e8f018 Author: metincansiper Date: 2021-02-25 (Thu, 25 Feb 2021) Changed paths: M src/config.js M src/server/routes/api/document/index.js Log Message: --- Control admin email(which is subject to change) from config file -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/d5fdf3-aa0d25%40github.com.
[PathwayCommons/factoid] 935597: Single ORCID query for each paper (#941)
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: 93559736585be77557b1508944b7b80d9be2d5d8 https://github.com/PathwayCommons/factoid/commit/93559736585be77557b1508944b7b80d9be2d5d8 Author: metincansiper Date: 2021-02-25 (Thu, 25 Feb 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Single ORCID query for each paper (#941) * Query orcid uri for the whole paper and pull the uris per author from the query result. * fixed lint error -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/3d6443-935597%40github.com.
[PathwayCommons/factoid] bc7e03: Consider complex transformation for invalid intera...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: bc7e0378637628379038592ee3222e4e8c19ae74 https://github.com/PathwayCommons/factoid/commit/bc7e0378637628379038592ee3222e4e8c19ae74 Author: metincansiper Date: 2021-01-14 (Thu, 14 Jan 2021) Changed paths: M src/model/element/interaction-type/binding.js M src/model/element/interaction-type/interaction-type.js M src/model/element/interaction-type/interaction.js M src/model/element/interaction-type/modification.js M src/model/element/interaction-type/transcription-translation.js Log Message: --- Consider complex transformation for invalid interaction templates as well. (#927) Commit: 0c54a286d83d1fc85a04ca97a23520f84062 https://github.com/PathwayCommons/factoid/commit/0c54a286d83d1fc85a04ca97a23520f84062 Author: metincansiper Date: 2021-01-15 (Fri, 15 Jan 2021) Changed paths: M src/model/document/document.js Log Message: --- Added pathway id parameter to be consumed in factoid to biopax conversion (#928) Commit: 32110cfe547751fccf375505c97433647fdb6b7f https://github.com/PathwayCommons/factoid/commit/32110cfe547751fccf375505c97433647fdb6b7f Author: Jeffrey Wong Date: 2021-01-29 (Fri, 29 Jan 2021) Changed paths: M package-lock.json M package.json Log Message: --- 0.13.0 Commit: 7f35ffcd25c9166c3035c9150a6566b883173aae https://github.com/PathwayCommons/factoid/commit/7f35ffcd25c9166c3035c9150a6566b883173aae Author: Jeffrey Wong Date: 2021-01-29 (Fri, 29 Jan 2021) Changed paths: M package-lock.json M package.json Log Message: --- 0.14.0 Commit: 95e0f53fb2b6bab0565fae1d50b6ef4d114c7c9b https://github.com/PathwayCommons/factoid/commit/95e0f53fb2b6bab0565fae1d50b6ef4d114c7c9b Author: Max Franz Date: 2021-02-08 (Mon, 08 Feb 2021) Changed paths: M package-lock.json M package.json Log Message: --- Merge pull request #930 from PathwayCommons/v0.14.0 V0.14.0 Commit: 0da73e3f048c11b63297d8fd23c6b6a682d80e96 https://github.com/PathwayCommons/factoid/commit/0da73e3f048c11b63297d8fd23c6b6a682d80e96 Author: Max Franz Date: 2021-02-08 (Mon, 08 Feb 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- One-click editor link for related papers emails - Create empty doc when sending related papers email. - Send editor link in template to related papers email. - The email template needs to be updated to use the `editorUrl` variable. Commit: b4b579d6641c805281a45740d9b3f16d3797ca67 https://github.com/PathwayCommons/factoid/commit/b4b579d6641c805281a45740d9b3f16d3797ca67 Author: Jeffrey Wong Date: 2021-02-09 (Tue, 09 Feb 2021) Changed paths: M docker/.env M docker/docker-compose.yml A docker/templates/default.conf.template Log Message: --- - Support for the Nginx proxy - Add Zenodo env variables Commit: d69cae8db2f0651cc7c49f4bf35de49f59e7fa77 https://github.com/PathwayCommons/factoid/commit/d69cae8db2f0651cc7c49f4bf35de49f59e7fa77 Author: Jeffrey Date: 2021-02-09 (Tue, 09 Feb 2021) Changed paths: M docker/.env M docker/docker-compose.yml A docker/templates/default.conf.template Log Message: --- Merge pull request #934 from PathwayCommons/iss933_docker-nginx Docker: Nginx and Zenodo support Commit: eb58cd267d7cf6a38dd8f6655f7511de62d9d624 https://github.com/PathwayCommons/factoid/commit/eb58cd267d7cf6a38dd8f6655f7511de62d9d624 Author: Max Franz Date: 2021-02-11 (Thu, 11 Feb 2021) Changed paths: M package-lock.json M src/client/components/tasks.js M src/server/routes/api/document/index.js Log Message: --- Jeff and Max debugging #935 Seems to work better but more cleanup & config TODO Commit: 10aa5d70431f5e2a1105c69a9045efd5f6dc1e6c https://github.com/PathwayCommons/factoid/commit/10aa5d70431f5e2a1105c69a9045efd5f6dc1e6c Author: Jeffrey Wong Date: 2021-02-11 (Thu, 11 Feb 2021) Changed paths: M src/client/components/tasks.js M src/config.js M src/server/routes/api/document/index.js Log Message: --- - Client waits MAX_WAIT_TWEET ms for doc tweet info - Add back sanity checking for posting tweet (demo, already tweeted etc). Commit: 4a1203f9fa630e2176eda3d8efaffb85858e5e40 https://github.com/PathwayCommons/factoid/commit/4a1203f9fa630e2176eda3d8efaffb85858e5e40 Author: Jeffrey Date: 2021-02-11 (Thu, 11 Feb 2021) Changed paths: M package-lock.json M src/client/components/tasks.js M src/config.js M src/server/routes/api/document/index.js Log Message: --- Merge pull request #936 from PathwayCommons/tweet-935 Submit success waits a few seconds for document Tweet information Commit: 3d6443f8657d3a25c
[PathwayCommons/factoid] dacfac: fixed lint error
Branch: refs/heads/orcid-query-update Home: https://github.com/PathwayCommons/factoid Commit: dacfacb2eb7c156e006d950301e3f2016b97922d https://github.com/PathwayCommons/factoid/commit/dacfacb2eb7c156e006d950301e3f2016b97922d Author: metincansiper Date: 2021-02-23 (Tue, 23 Feb 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- fixed lint error -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/orcid-query-update/a911ac-dacfac%40github.com.
[PathwayCommons/factoid] a911ac: Query orcid uri for the whole paper and pull the u...
Branch: refs/heads/orcid-query-update Home: https://github.com/PathwayCommons/factoid Commit: a911acfb33a574cb331dca90301ccde01bba64f3 https://github.com/PathwayCommons/factoid/commit/a911acfb33a574cb331dca90301ccde01bba64f3 Author: metincansiper Date: 2021-02-23 (Tue, 23 Feb 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Query orcid uri for the whole paper and pull the uris per author from the query result. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/orcid-query-update/00-a911ac%40github.com.
[PathwayCommons/factoid] 7ed8b1: Add api/document/from-url end point to add new doc...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: 7ed8b17a5ad2a01efa23c45be75ad9e510317e55 https://github.com/PathwayCommons/factoid/commit/7ed8b17a5ad2a01efa23c45be75ad9e510317e55 Author: metincansiper Date: 2021-02-22 (Mon, 22 Feb 2021) Changed paths: M src/client/components/home.js M src/server/routes/api/document/index.js M src/server/routes/api/document/indra.js Log Message: --- Add api/document/from-url end point to add new documents from a url and used it directly from client side. Also, made a little update in error handling of indra connecter. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/7483e3-7ed8b1%40github.com.
[PathwayCommons/factoid] 7483e3: Handle the case where response is null for fetch r...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: 7483e32e174ebc6c6127838848bdf2e7da14f5b1 https://github.com/PathwayCommons/factoid/commit/7483e32e174ebc6c6127838848bdf2e7da14f5b1 Author: metincansiper Date: 2021-02-17 (Wed, 17 Feb 2021) Changed paths: M src/server/routes/api/document/indra.js Log Message: --- Handle the case where response is null for fetch retry -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/d0cab1-7483e3%40github.com.
[PathwayCommons/factoid] d0cab1: While loading documents from biopax file skip the ...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: d0cab11674c892a853cb75e6bbb699a63d31a720 https://github.com/PathwayCommons/factoid/commit/d0cab11674c892a853cb75e6bbb699a63d31a720 Author: metincansiper Date: 2021-02-17 (Wed, 17 Feb 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- While loading documents from biopax file skip the elements whose xref is not available also skip the ones connected to such elements. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/9f340b-d0cab1%40github.com.
[PathwayCommons/factoid] 9f340b: Fix too many request issue of indra queries
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: 9f340b235f7c4bc648e3fbcd7332fbe455cb3353 https://github.com/PathwayCommons/factoid/commit/9f340b235f7c4bc648e3fbcd7332fbe455cb3353 Author: metincansiper Date: 2021-02-16 (Tue, 16 Feb 2021) Changed paths: M src/client/components/home.js M src/server/routes/api/document/index.js Log Message: --- Fix too many request issue of indra queries -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/c4a910-9f340b%40github.com.
[PathwayCommons/factoid] c4a910: Removed a conditional console.log statement that w...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: c4a910c88c00f47f8a5105ff72ba58222d7f5c9f https://github.com/PathwayCommons/factoid/commit/c4a910c88c00f47f8a5105ff72ba58222d7f5c9f Author: metincansiper Date: 2021-01-15 (Fri, 15 Jan 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Removed a conditional console.log statement that was written for temporary testing -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/c22e74-c4a910%40github.com.
[PathwayCommons/factoid] 0c54a2: Added pathway id parameter to be consumed in facto...
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: 0c54a286d83d1fc85a04ca97a23520f84062 https://github.com/PathwayCommons/factoid/commit/0c54a286d83d1fc85a04ca97a23520f84062 Author: metincansiper Date: 2021-01-15 (Fri, 15 Jan 2021) Changed paths: M src/model/document/document.js Log Message: --- Added pathway id parameter to be consumed in factoid to biopax conversion (#928) -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/bc7e03-0c54a2%40github.com.
[PathwayCommons/factoid] e89182: Added pathway id parameter to be consumed in facto...
Branch: refs/heads/bp_template_docid Home: https://github.com/PathwayCommons/factoid Commit: e89182de2b92fd562ed6f8f659b16486734f8eab https://github.com/PathwayCommons/factoid/commit/e89182de2b92fd562ed6f8f659b16486734f8eab Author: metincansiper Date: 2021-01-14 (Thu, 14 Jan 2021) Changed paths: M src/model/document/document.js Log Message: --- Added pathway id parameter to be consumed in factoid to biopax conversion -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/bp_template_docid/00-e89182%40github.com.
[PathwayCommons/factoid] bc7e03: Consider complex transformation for invalid intera...
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: bc7e0378637628379038592ee3222e4e8c19ae74 https://github.com/PathwayCommons/factoid/commit/bc7e0378637628379038592ee3222e4e8c19ae74 Author: metincansiper Date: 2021-01-14 (Thu, 14 Jan 2021) Changed paths: M src/model/element/interaction-type/binding.js M src/model/element/interaction-type/interaction-type.js M src/model/element/interaction-type/interaction.js M src/model/element/interaction-type/modification.js M src/model/element/interaction-type/transcription-translation.js Log Message: --- Consider complex transformation for invalid interaction templates as well. (#927) -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/6dcd79-bc7e03%40github.com.
[PathwayCommons/factoid] c22e74: Use only supported organisms while searching groun...
Branch: refs/heads/supplement_db_filter Home: https://github.com/PathwayCommons/factoid Commit: c22e74aff53956b32fbda7f507eea7b97db93069 https://github.com/PathwayCommons/factoid/commit/c22e74aff53956b32fbda7f507eea7b97db93069 Author: metincansiper Date: 2021-01-13 (Wed, 13 Jan 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Use only supported organisms while searching groundings of the entities coming from biopax -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/supplement_db_filter/00-c22e74%40github.com.
[PathwayCommons/factoid] ce845b: Consider complex transformation for invalid intera...
Branch: refs/heads/invalid_complex_fix Home: https://github.com/PathwayCommons/factoid Commit: ce845bdb8e2c4bf56813d8911f9f3191a097 https://github.com/PathwayCommons/factoid/commit/ce845bdb8e2c4bf56813d8911f9f3191a097 Author: metincansiper Date: 2021-01-06 (Wed, 06 Jan 2021) Changed paths: M src/model/element/interaction-type/binding.js M src/model/element/interaction-type/interaction-type.js M src/model/element/interaction-type/interaction.js M src/model/element/interaction-type/modification.js M src/model/element/interaction-type/transcription-translation.js Log Message: --- Consider complex transformation for invalid interaction templates as well. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/invalid_complex_fix/00-ce845b%40github.com.
[PathwayCommons/factoid] 081742: AuthorProfiles: Provide error handling, fallback (...
Branch: refs/heads/author_profiles_error Home: https://github.com/PathwayCommons/factoid Commit: 081742857525371420174f70c5702bfc979ca992 https://github.com/PathwayCommons/factoid/commit/081742857525371420174f70c5702bfc979ca992 Author: metincansiper Date: 2021-01-05 (Tue, 05 Jan 2021) Changed paths: M src/server/routes/api/document/index.js Log Message: --- AuthorProfiles: Provide error handling, fallback (for orcid) #923 -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/author_profiles_error/00-081742%40github.com.
[PathwayCommons/factoid] 3fb0b5: Refactored RequestForm as a reusable component. (#...
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: 3fb0b53f2a9433a511786c2f5797789aa082eb65 https://github.com/PathwayCommons/factoid/commit/3fb0b53f2a9433a511786c2f5797789aa082eb65 Author: metincansiper Date: 2020-12-14 (Mon, 14 Dec 2020) Changed paths: M src/client/components/document-management.js M src/client/components/editor/index.js M src/client/components/editor/title.js M src/client/components/home.js A src/client/components/request-form.js M src/server/routes/api/document/index.js M src/styles/home.css M src/styles/index.css A src/styles/request-form.css M src/util/pubmed.js Log Message: --- Refactored RequestForm as a reusable component. (#913) * Working on refactoring RequestForm component. * More work on refactoring RequestForm component. * Added author name field to request form. * Add author name to the provided fields of a document. * Fix the opposite logic of the parameter determining whether to check if all the fields are completed in request form. * Set provided.name field instead of provided.authorName field. * Reused request form around the editor title. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/39424e-3fb0b5%40github.com.
[PathwayCommons/factoid] 6d4344: Reused request form around the editor title.
Branch: refs/heads/post_article_info Home: https://github.com/PathwayCommons/factoid Commit: 6d434488f756826389492a78d829b66c408258d2 https://github.com/PathwayCommons/factoid/commit/6d434488f756826389492a78d829b66c408258d2 Author: metincansiper Date: 2020-12-11 (Fri, 11 Dec 2020) Changed paths: M src/client/components/editor/index.js M src/client/components/editor/title.js M src/client/components/request-form.js M src/util/pubmed.js Log Message: --- Reused request form around the editor title. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/post_article_info/57a353-6d4344%40github.com.
[PathwayCommons/factoid] 57a353: Set provided.name field instead of provided.author...
Branch: refs/heads/post_article_info Home: https://github.com/PathwayCommons/factoid Commit: 57a3535cdc79dde3d5fd131f376a089dc81ada5d https://github.com/PathwayCommons/factoid/commit/57a3535cdc79dde3d5fd131f376a089dc81ada5d Author: metincansiper Date: 2020-12-09 (Wed, 09 Dec 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Set provided.name field instead of provided.authorName field. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/post_article_info/157b31-57a353%40github.com.
[PathwayCommons/factoid] 157b31: Fix the opposite logic of the parameter determinin...
Branch: refs/heads/post_article_info Home: https://github.com/PathwayCommons/factoid Commit: 157b3158f5c1e4807bc75b23428d2df4c7077dd8 https://github.com/PathwayCommons/factoid/commit/157b3158f5c1e4807bc75b23428d2df4c7077dd8 Author: metincansiper Date: 2020-12-08 (Tue, 08 Dec 2020) Changed paths: M src/client/components/request-form.js Log Message: --- Fix the opposite logic of the parameter determining whether to check if all the fields are completed in request form. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/post_article_info/4b2c36-157b31%40github.com.
[PathwayCommons/factoid] 4b2c36: Add author name to the provided fields of a document.
Branch: refs/heads/post_article_info Home: https://github.com/PathwayCommons/factoid Commit: 4b2c3667d738e9d0ee8a83ca0f90c230cd517ec0 https://github.com/PathwayCommons/factoid/commit/4b2c3667d738e9d0ee8a83ca0f90c230cd517ec0 Author: metincansiper Date: 2020-12-08 (Tue, 08 Dec 2020) Changed paths: M src/model/document/document.js M src/server/routes/api/document/index.js Log Message: --- Add author name to the provided fields of a document. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/post_article_info/bd3f4a-4b2c36%40github.com.
[PathwayCommons/factoid] bd3f4a: Added author name field to request form.
Branch: refs/heads/post_article_info Home: https://github.com/PathwayCommons/factoid Commit: bd3f4afb216a6c5e7671b2d4c0ed2e518ab6841e https://github.com/PathwayCommons/factoid/commit/bd3f4afb216a6c5e7671b2d4c0ed2e518ab6841e Author: metincansiper Date: 2020-12-07 (Mon, 07 Dec 2020) Changed paths: M src/client/components/request-form.js M src/model/document/document.js M src/server/routes/api/document/index.js Log Message: --- Added author name field to request form. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/post_article_info/77ebdf-bd3f4a%40github.com.
[PathwayCommons/factoid] dd0d76: Working on refactoring RequestForm component.
Branch: refs/heads/post_article_info Home: https://github.com/PathwayCommons/factoid Commit: dd0d7600b6b9a9256549ff979712339b7a90ce0b https://github.com/PathwayCommons/factoid/commit/dd0d7600b6b9a9256549ff979712339b7a90ce0b Author: metincansiper Date: 2020-12-04 (Fri, 04 Dec 2020) Changed paths: M src/client/components/home.js A src/client/components/request-form.js Log Message: --- Working on refactoring RequestForm component. Commit: 77ebdf82ec29eaedffaa0610d6022e1f5933713a https://github.com/PathwayCommons/factoid/commit/77ebdf82ec29eaedffaa0610d6022e1f5933713a Author: metincansiper Date: 2020-12-04 (Fri, 04 Dec 2020) Changed paths: M src/client/components/document-management.js M src/client/components/home.js M src/client/components/request-form.js M src/styles/home.css M src/styles/index.css A src/styles/request-form.css Log Message: --- More work on refactoring RequestForm component. Compare: https://github.com/PathwayCommons/factoid/compare/dd0d7600b6b9%5E...77ebdf82ec29 -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/post_article_info/00-77ebdf%40github.com.
[PathwayCommons/factoid] 678f7e: In summary page use the old way of showing author ...
Branch: refs/heads/author_page_link Home: https://github.com/PathwayCommons/factoid Commit: 678f7e5dedb0b1efcabb501c96b531a3474f79ea https://github.com/PathwayCommons/factoid/commit/678f7e5dedb0b1efcabb501c96b531a3474f79ea Author: metincansiper Date: 2020-12-02 (Wed, 02 Dec 2020) Changed paths: M src/client/components/editor/info-panel.js Log Message: --- In summary page use the old way of showing author names when author profiles data is missing. Also, use span for author names when the author page link is missing as it is used to be. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/author_page_link/376b92-678f7e%40github.com.
[PathwayCommons/factoid] fdf4a3: Query orcid urls of authors on server side.
Branch: refs/heads/author_page_link Home: https://github.com/PathwayCommons/factoid Commit: fdf4a3e05f79d98cf187fcfa4f4e528b336b2b59 https://github.com/PathwayCommons/factoid/commit/fdf4a3e05f79d98cf187fcfa4f4e528b336b2b59 Author: metincansiper Date: 2020-11-30 (Mon, 30 Nov 2020) Changed paths: M src/client/components/editor/info-panel.js M src/model/document/document.js M src/server/routes/api/document/index.js Log Message: --- Query orcid urls of authors on server side. Commit: 376b92a854fecde1b0bc65754420b9f3d559fef1 https://github.com/PathwayCommons/factoid/commit/376b92a854fecde1b0bc65754420b9f3d559fef1 Author: metincansiper Date: 2020-11-30 (Mon, 30 Nov 2020) Changed paths: M src/client/components/editor/info-panel.js Log Message: --- Fixed linting errors Compare: https://github.com/PathwayCommons/factoid/compare/52086e53df7d...376b92a854fe -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/author_page_link/52086e-376b92%40github.com.
[PathwayCommons/factoid] 52086e: Automatic connection of researcher profiles #907
Branch: refs/heads/author_page_link Home: https://github.com/PathwayCommons/factoid Commit: 52086e53df7d8398e47a889ec491c1c96fc2da9d https://github.com/PathwayCommons/factoid/commit/52086e53df7d8398e47a889ec491c1c96fc2da9d Author: metincansiper Date: 2020-11-25 (Wed, 25 Nov 2020) Changed paths: M src/client/components/editor/info-panel.js M src/styles/editor/editor.css Log Message: --- Automatic connection of researcher profiles #907 -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/author_page_link/00-52086e%40github.com.
[PathwayCommons/factoid] dc2f32: Added swagger documentation for biopax id mapping ...
Branch: refs/heads/biopax_id_mapping Home: https://github.com/PathwayCommons/factoid Commit: dc2f3245fcdd35d81f0733fb5154f9780a9f1447 https://github.com/PathwayCommons/factoid/commit/dc2f3245fcdd35d81f0733fb5154f9780a9f1447 Author: metincansiper Date: 2020-11-20 (Fri, 20 Nov 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Added swagger documentation for biopax id mapping parameter. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/biopax_id_mapping/5d0984-dc2f32%40github.com.
[PathwayCommons/factoid] 12c42a: Use assoc.dbprefix for mapping ids to uniprot ids.
Branch: refs/heads/biopax_id_mapping Home: https://github.com/PathwayCommons/factoid Commit: 12c42a885a19d568c9c2345c153730055892d0b7 https://github.com/PathwayCommons/factoid/commit/12c42a885a19d568c9c2345c153730055892d0b7 Author: metincansiper Date: 2020-11-19 (Thu, 19 Nov 2020) Changed paths: M src/model/element/entity.js M src/server/routes/api/document/index.js Log Message: --- Use assoc.dbprefix for mapping ids to uniprot ids. Commit: 5d09849bebd8212b43542c499c616f3b6aa13a93 https://github.com/PathwayCommons/factoid/commit/5d09849bebd8212b43542c499c616f3b6aa13a93 Author: metincansiper Date: 2020-11-19 (Thu, 19 Nov 2020) Changed paths: M src/client/components/document-management.js M src/client/components/home.js M src/model/document/document.js M src/server/routes/api/document/index.js Log Message: --- Merge branch 'biopax_id_mapping' of https://github.com/PathwayCommons/factoid into biopax_id_mapping Compare: https://github.com/PathwayCommons/factoid/compare/3b813958936a...5d09849bebd8 -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/biopax_id_mapping/3b8139-5d0984%40github.com.
[PathwayCommons/factoid] 430310: Provide an admin facility to add articles using bi...
Branch: refs/heads/biopax_id_mapping Home: https://github.com/PathwayCommons/factoid Commit: 43031034d872527da5234f455fd74194e4811bb4 https://github.com/PathwayCommons/factoid/commit/43031034d872527da5234f455fd74194e4811bb4 Author: metincansiper Date: 2020-11-18 (Wed, 18 Nov 2020) Changed paths: M src/client/components/document-management.js M src/client/components/home.js M src/config.js M src/model/document/document.js M src/server/routes/api/document/index.js Log Message: --- Provide an admin facility to add articles using biopax file from url (#881) * Working on creating multiple documents from bioapax file through admin panel, nearly done! * Improvements for uploading multiple articles through biopax * Handle association of elements created through biopax urls. * Bug fixes for creating multiple articles * Fix linting error * complete the entities created through biopax files * Updated the non-exising email address specified for submitting multiple articles. * A quick fix * Skip emailing step for multiple article creations. * Fixed linting errors * Set the source of documents as either 'admin' or 'pc' * Use uniprot id while grounding entities coming from biopax url. * Consider other databases than uniprot while grounding entities for loading multiple documents * A queick bug fix to set the elements paramater to an empty array in the service to create a document. Commit: 3b813958936a47c627e1ed0408245362847fbf8f https://github.com/PathwayCommons/factoid/commit/3b813958936a47c627e1ed0408245362847fbf8f Author: metincansiper Date: 2020-11-19 (Thu, 19 Nov 2020) Changed paths: M src/client/components/document-management.js M src/client/components/home.js M src/model/document/document.js M src/server/routes/api/document/index.js Log Message: --- Merge branch 'unstable' into biopax_id_mapping Compare: https://github.com/PathwayCommons/factoid/compare/d2697dc0a26f...3b813958936a -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/biopax_id_mapping/d2697d-3b8139%40github.com.
[PathwayCommons/factoid] d2697d: Use a different file name while downloading the bi...
Branch: refs/heads/biopax_id_mapping Home: https://github.com/PathwayCommons/factoid Commit: d2697dc0a26fb381d144f80f612791e8da48512b https://github.com/PathwayCommons/factoid/commit/d2697dc0a26fb381d144f80f612791e8da48512b Author: metincansiper Date: 2020-11-19 (Thu, 19 Nov 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Use a different file name while downloading the biopax zip files if the idMapping is desired. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/biopax_id_mapping/91ebbd-d2697d%40github.com.
[PathwayCommons/factoid] 91ebbd: A little code reorganization for mapping ncbi ids ...
Branch: refs/heads/biopax_id_mapping Home: https://github.com/PathwayCommons/factoid Commit: 91ebbd154cb96634be666a633a2d5ba361d13bb0 https://github.com/PathwayCommons/factoid/commit/91ebbd154cb96634be666a633a2d5ba361d13bb0 Author: metincansiper Date: 2020-11-19 (Thu, 19 Nov 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- A little code reorganization for mapping ncbi ids to uniprot ids. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/biopax_id_mapping/35229b-91ebbd%40github.com.
[PathwayCommons/factoid] 35229b: Query ncbi to uniprot id mappings chunk by chunk.
Branch: refs/heads/biopax_id_mapping Home: https://github.com/PathwayCommons/factoid Commit: 35229b1633b4c767e067b07dfcb88822c403fc2b https://github.com/PathwayCommons/factoid/commit/35229b1633b4c767e067b07dfcb88822c403fc2b Author: metincansiper Date: 2020-11-19 (Thu, 19 Nov 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Query ncbi to uniprot id mappings chunk by chunk. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/biopax_id_mapping/4f04a1-35229b%40github.com.
[PathwayCommons/factoid] 4f04a1: Extended biopax zip download service with id mappi...
Branch: refs/heads/biopax_id_mapping Home: https://github.com/PathwayCommons/factoid Commit: 4f04a1d2839f160d94f2d318902faa21ff57485c https://github.com/PathwayCommons/factoid/commit/4f04a1d2839f160d94f2d318902faa21ff57485c Author: metincansiper Date: 2020-11-18 (Wed, 18 Nov 2020) Changed paths: M src/config.js M src/model/document/document.js M src/model/element/entity.js M src/model/element/interaction-type/binding.js M src/model/element/interaction-type/demethylation.js M src/model/element/interaction-type/dephosphorylation.js M src/model/element/interaction-type/deubiquitination.js M src/model/element/interaction-type/interaction-type.js M src/model/element/interaction-type/interaction.js M src/model/element/interaction-type/methylation.js M src/model/element/interaction-type/modification.js M src/model/element/interaction-type/phosphorylation.js M src/model/element/interaction-type/transcription-translation.js M src/model/element/interaction-type/ubiquitination.js M src/model/element/interaction.js M src/server/document-util.js M src/server/routes/api/document/export.js M src/server/routes/api/document/index.js Log Message: --- Extended biopax zip download service with id mapping parameter -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/biopax_id_mapping/00-4f04a1%40github.com.
[PathwayCommons/factoid] 430310: Provide an admin facility to add articles using bi...
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: 43031034d872527da5234f455fd74194e4811bb4 https://github.com/PathwayCommons/factoid/commit/43031034d872527da5234f455fd74194e4811bb4 Author: metincansiper Date: 2020-11-18 (Wed, 18 Nov 2020) Changed paths: M src/client/components/document-management.js M src/client/components/home.js M src/config.js M src/model/document/document.js M src/server/routes/api/document/index.js Log Message: --- Provide an admin facility to add articles using biopax file from url (#881) * Working on creating multiple documents from bioapax file through admin panel, nearly done! * Improvements for uploading multiple articles through biopax * Handle association of elements created through biopax urls. * Bug fixes for creating multiple articles * Fix linting error * complete the entities created through biopax files * Updated the non-exising email address specified for submitting multiple articles. * A quick fix * Skip emailing step for multiple article creations. * Fixed linting errors * Set the source of documents as either 'admin' or 'pc' * Use uniprot id while grounding entities coming from biopax url. * Consider other databases than uniprot while grounding entities for loading multiple documents * A queick bug fix to set the elements paramater to an empty array in the service to create a document. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/e4e597-430310%40github.com.
[PathwayCommons/factoid] 9f0c34: A queick bug fix to set the elements paramater to ...
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: 9f0c34f2ae74d8338a69c07ccf678ab9561d6d7c https://github.com/PathwayCommons/factoid/commit/9f0c34f2ae74d8338a69c07ccf678ab9561d6d7c Author: metincansiper Date: 2020-11-16 (Mon, 16 Nov 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- A queick bug fix to set the elements paramater to an empty array in the service to create a document. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/c77303-9f0c34%40github.com.
[PathwayCommons/factoid] 4b70ba: Take into account `lastEditedDate` in the document...
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: 4b70bad414ba3f9c9d7cf1bb3bdc536e6d1ec984 https://github.com/PathwayCommons/factoid/commit/4b70bad414ba3f9c9d7cf1bb3bdc536e6d1ec984 Author: Max Franz Date: 2020-10-08 (Thu, 08 Oct 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Take into account `lastEditedDate` in the document image cache Refs. : Document post-mortem: Missing metadata and misc problems #851 Commit: e370d3392bf09eeb14357418e2b52bf9fe60d282 https://github.com/PathwayCommons/factoid/commit/e370d3392bf09eeb14357418e2b52bf9fe60d282 Author: Max Franz Date: 2020-10-08 (Thu, 08 Oct 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Remove logs Commit: 605163b93797984bbae27f7b20c114c9aff14b92 https://github.com/PathwayCommons/factoid/commit/605163b93797984bbae27f7b20c114c9aff14b92 Author: Max Franz Date: 2020-10-08 (Thu, 08 Oct 2020) Changed paths: M src/server/routes/api/document/indra.js Log Message: --- More aggressive Indra retries - Increase the number of retries. - Add a random delta so that different queries don't tend to come in at the same time. Refs. : Document post-mortem: Missing metadata and misc problems #851 Commit: 2cdb267547d8b70061ea24b6a777826ec30194de https://github.com/PathwayCommons/factoid/commit/2cdb267547d8b70061ea24b6a777826ec30194de Author: Max Franz Date: 2020-10-08 (Thu, 08 Oct 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Merge pull request #864 from PathwayCommons/clear-img-cache-851 Take into account `lastEditedDate` in the document image cache Commit: 4def92b647b003cc1fdecaa2ffeb7442e820a01b https://github.com/PathwayCommons/factoid/commit/4def92b647b003cc1fdecaa2ffeb7442e820a01b Author: Max Franz Date: 2020-10-08 (Thu, 08 Oct 2020) Changed paths: M src/client/components/element-info/entity-info.js M src/model/document/document.js M src/model/element/entity.js M src/model/organism.js Log Message: --- More salient organism in entity grounding popover - Make the organism name salient (at the top) in the grounding popover. - Add `ent.organism()` shortcut function to get the `Organism` an `Entity` is grounded to (may be null for chemical). - Add `doc.commonOrganism()` to get the most common `Organism` in a `Document` -- may be null in the case of a tie. - Add `doc.irregularOrganismEntities()` to get an array of entities that are grounded to an organism other than the common one. Refs. : - Grounding: Entity organism preference / mixed organisms for genes #861 - Block users from submitting empty documents #860 Commit: 47c3f163325086e71ddd1f75ea8c1c809ad11308 https://github.com/PathwayCommons/factoid/commit/47c3f163325086e71ddd1f75ea8c1c809ad11308 Author: Jeffrey Date: 2020-10-08 (Thu, 08 Oct 2020) Changed paths: M src/client/components/element-info/entity-info.js M src/model/document/document.js M src/model/element/entity.js M src/model/organism.js Log Message: --- Merge pull request #866 from PathwayCommons/organism-validation More salient organism in entity grounding popover Commit: 636a1b628d5d0e5178fbeee630d3ccd39bf88e98 https://github.com/PathwayCommons/factoid/commit/636a1b628d5d0e5178fbeee630d3ccd39bf88e98 Author: Jeffrey Wong Date: 2020-10-08 (Thu, 08 Oct 2020) Changed paths: M src/client/components/tasks.js M src/model/element/entity.js M src/styles/tasks.css Log Message: --- - Warn if organisms are different - Create task list component Commit: c5dc3e0e66b25d6842500690b113f5b8e1889102 https://github.com/PathwayCommons/factoid/commit/c5dc3e0e66b25d6842500690b113f5b8e1889102 Author: Jeffrey Wong Date: 2020-10-08 (Thu, 08 Oct 2020) Changed paths: M src/client/components/tasks.js Log Message: --- Make the message for organisms more generic Commit: 9d7bfe4a1b1437a55497595b0d0e9150a14f9a45 https://github.com/PathwayCommons/factoid/commit/9d7bfe4a1b1437a55497595b0d0e9150a14f9a45 Author: Jeffrey Wong Date: 2020-10-09 (Fri, 09 Oct 2020) Changed paths: M src/client/components/tasks.js Log Message: --- Irregular organism message and list text Commit: ff88cfa44ad873528dffd50dd52580ab1b079db7 https://github.com/PathwayCommons/factoid/commit/ff88cfa44ad873528dffd50dd52580ab1b079db7 Author: Jeffrey Wong Date: 2020-10-09 (Fri, 09 Oct 2020) Changed paths: M src/client/components/editor/submit.js M src/client/components/tasks.js Log Message: --- - Add warning for no entity in submit - Add components for closing tooltip on click Commit: 6f188549f20ca283f9fc0f198081059f353f56a8 https://github.com/Pathw
[PathwayCommons/factoid] d67ad3: Mark novel interactios.
Branch: refs/heads/email-rel-pprs Home: https://github.com/PathwayCommons/factoid Commit: d67ad38f17f94cbaaf713bdba36ea696fae9737d https://github.com/PathwayCommons/factoid/commit/d67ad38f17f94cbaaf713bdba36ea696fae9737d Author: metincansiper Date: 2020-11-09 (Mon, 09 Nov 2020) Changed paths: M src/model/element/interaction.js M src/server/routes/api/document/index.js Log Message: --- Mark novel interactios. Commit: fc92759ac2af1a68a654639d0eb5e01b3e8dc297 https://github.com/PathwayCommons/factoid/commit/fc92759ac2af1a68a654639d0eb5e01b3e8dc297 Author: metincansiper Date: 2020-11-09 (Mon, 09 Nov 2020) Changed paths: M src/model/element/interaction.js Log Message: --- remove a console statement Commit: 41b4bfe066fa22338b40993d8c5e5d9f5ebbae2e https://github.com/PathwayCommons/factoid/commit/41b4bfe066fa22338b40993d8c5e5d9f5ebbae2e Author: metincansiper Date: 2020-11-10 (Tue, 10 Nov 2020) Changed paths: M src/model/element/interaction.js Log Message: --- Set the default novel value of interactions as false. Commit: 88fab26f744599b994472e5cc3037fb01ec7089e https://github.com/PathwayCommons/factoid/commit/88fab26f744599b994472e5cc3037fb01ec7089e Author: metincansiper Date: 2020-11-10 (Tue, 10 Nov 2020) Changed paths: M src/model/element/interaction.js M src/server/routes/api/document/index.js Log Message: --- Merge branch 'novel_intn' into email-rel-pprs Compare: https://github.com/PathwayCommons/factoid/compare/bf0f241733ea...88fab26f7445 -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/email-rel-pprs/bf0f24-88fab2%40github.com.
[PathwayCommons/factoid] 41b4bf: Set the default novel value of interactions as false.
Branch: refs/heads/novel_intn Home: https://github.com/PathwayCommons/factoid Commit: 41b4bfe066fa22338b40993d8c5e5d9f5ebbae2e https://github.com/PathwayCommons/factoid/commit/41b4bfe066fa22338b40993d8c5e5d9f5ebbae2e Author: metincansiper Date: 2020-11-10 (Tue, 10 Nov 2020) Changed paths: M src/model/element/interaction.js Log Message: --- Set the default novel value of interactions as false. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/novel_intn/fc9275-41b4bf%40github.com.
[PathwayCommons/factoid] d67ad3: Mark novel interactios.
Branch: refs/heads/novel_intn Home: https://github.com/PathwayCommons/factoid Commit: d67ad38f17f94cbaaf713bdba36ea696fae9737d https://github.com/PathwayCommons/factoid/commit/d67ad38f17f94cbaaf713bdba36ea696fae9737d Author: metincansiper Date: 2020-11-09 (Mon, 09 Nov 2020) Changed paths: M src/model/element/interaction.js M src/server/routes/api/document/index.js Log Message: --- Mark novel interactios. Commit: fc92759ac2af1a68a654639d0eb5e01b3e8dc297 https://github.com/PathwayCommons/factoid/commit/fc92759ac2af1a68a654639d0eb5e01b3e8dc297 Author: metincansiper Date: 2020-11-09 (Mon, 09 Nov 2020) Changed paths: M src/model/element/interaction.js Log Message: --- remove a console statement Compare: https://github.com/PathwayCommons/factoid/compare/d67ad38f17f9%5E...fc92759ac2af -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/novel_intn/00-fc9275%40github.com.
[PathwayCommons/factoid] d60bcd: Consider other databases than uniprot while ground...
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: d60bcd22bea7f580b6eae6b27d05b2cb94116caf https://github.com/PathwayCommons/factoid/commit/d60bcd22bea7f580b6eae6b27d05b2cb94116caf Author: metincansiper Date: 2020-11-03 (Tue, 03 Nov 2020) Changed paths: M src/config.js M src/server/routes/api/document/index.js M src/server/routes/api/element-association/grounding-search.js Log Message: --- Consider other databases than uniprot while grounding entities for loading multiple documents -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/c5160e-d60bcd%40github.com.
[PathwayCommons/factoid] c5160e: Use uniprot id while grounding entities coming fro...
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: c5160ec489eb41f3bd5bc4e7f614dc7a86f27b7f https://github.com/PathwayCommons/factoid/commit/c5160ec489eb41f3bd5bc4e7f614dc7a86f27b7f Author: metincansiper Date: 2020-10-29 (Thu, 29 Oct 2020) Changed paths: M src/server/routes/api/document/index.js M src/server/routes/api/element-association/grounding-search.js Log Message: --- Use uniprot id while grounding entities coming from biopax url. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/98cdbe-c5160e%40github.com.
[PathwayCommons/factoid] d378c7: During bulk export skip the files where the conver...
Branch: refs/heads/zip_error_handle Home: https://github.com/PathwayCommons/factoid Commit: d378c77b98dbb17b610fb8d7cd469d05b6f5d9b6 https://github.com/PathwayCommons/factoid/commit/d378c77b98dbb17b610fb8d7cd469d05b6f5d9b6 Author: metincansiper Date: 2020-10-27 (Tue, 27 Oct 2020) Changed paths: M src/server/routes/api/document/export.js M src/util/document.js Log Message: --- During bulk export skip the files where the conversion is failing and give an error message summarizing the case. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/zip_error_handle/00-d378c7%40github.com.
[PathwayCommons/factoid] 1c1a22: Fixed a typo in effect of deubiquitination interac...
Branch: refs/heads/deubiquitination_typo Home: https://github.com/PathwayCommons/factoid Commit: 1c1a2292dd05b344a5e55a9b848968c0ed081c3a https://github.com/PathwayCommons/factoid/commit/1c1a2292dd05b344a5e55a9b848968c0ed081c3a Author: metincansiper Date: 2020-10-16 (Fri, 16 Oct 2020) Changed paths: M src/model/element/interaction-type/deubiquitination.js Log Message: --- Fixed a typo in effect of deubiquitination interaction type -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/deubiquitination_typo/00-1c1a22%40github.com.
[PathwayCommons/factoid] 98cdbe: Set the source of documents as either 'admin' or 'pc'
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: 98cdbe12c915b43a19ca65965115d6cb81661cfe https://github.com/PathwayCommons/factoid/commit/98cdbe12c915b43a19ca65965115d6cb81661cfe Author: metincansiper Date: 2020-10-15 (Thu, 15 Oct 2020) Changed paths: M src/client/components/home.js M src/model/document/document.js M src/server/routes/api/document/index.js Log Message: --- Set the source of documents as either 'admin' or 'pc' -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/e87409-98cdbe%40github.com.
[PathwayCommons/factoid] e87409: Fixed linting errors
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: e874092f05950b5a98a4e831ea9da224555a3933 https://github.com/PathwayCommons/factoid/commit/e874092f05950b5a98a4e831ea9da224555a3933 Author: metincansiper Date: 2020-10-15 (Thu, 15 Oct 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Fixed linting errors -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/81bf82-e87409%40github.com.
[PathwayCommons/factoid] 81bf82: Skip emailing step for multiple article creations.
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: 81bf82e4663c2460120b2e563aa5ca2de5d299f4 https://github.com/PathwayCommons/factoid/commit/81bf82e4663c2460120b2e563aa5ca2de5d299f4 Author: metincansiper Date: 2020-10-15 (Thu, 15 Oct 2020) Changed paths: M src/client/components/home.js M src/server/routes/api/document/index.js Log Message: --- Skip emailing step for multiple article creations. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/af3ca6-81bf82%40github.com.
[PathwayCommons/factoid] af3ca6: A quick fix
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: af3ca65b791dd802df4551ca373a05ca9ed5c0d0 https://github.com/PathwayCommons/factoid/commit/af3ca65b791dd802df4551ca373a05ca9ed5c0d0 Author: metincansiper Date: 2020-10-15 (Thu, 15 Oct 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- A quick fix -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/eb1564-af3ca6%40github.com.
[PathwayCommons/factoid] eb1564: Updated the non-exising email address specified fo...
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: eb1564d801195107c728905d90b8d1475bae837a https://github.com/PathwayCommons/factoid/commit/eb1564d801195107c728905d90b8d1475bae837a Author: metincansiper Date: 2020-10-14 (Wed, 14 Oct 2020) Changed paths: M src/client/components/home.js Log Message: --- Updated the non-exising email address specified for submitting multiple articles. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/2f0082-eb1564%40github.com.
[PathwayCommons/factoid] 2f0082: complete the entities created through biopax files
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: 2f0082d64cc4343fd8f17d69e8ccf05d46391071 https://github.com/PathwayCommons/factoid/commit/2f0082d64cc4343fd8f17d69e8ccf05d46391071 Author: metincansiper Date: 2020-10-14 (Wed, 14 Oct 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- complete the entities created through biopax files -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/815275-2f0082%40github.com.
[PathwayCommons/factoid] 815275: Fix linting error
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: 81527567520f41c68187fec7e70868a3032c5ebd https://github.com/PathwayCommons/factoid/commit/81527567520f41c68187fec7e70868a3032c5ebd Author: metincansiper Date: 2020-10-14 (Wed, 14 Oct 2020) Changed paths: M src/server/routes/api/document/index.js Log Message: --- Fix linting error -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/e2f26c-815275%40github.com.
[PathwayCommons/factoid] e2f26c: Bug fixes for creating multiple articles
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: e2f26c485b0b63bbddefca6cf812e8da15342c23 https://github.com/PathwayCommons/factoid/commit/e2f26c485b0b63bbddefca6cf812e8da15342c23 Author: metincansiper Date: 2020-10-14 (Wed, 14 Oct 2020) Changed paths: M src/client/components/home.js M src/server/routes/api/document/index.js Log Message: --- Bug fixes for creating multiple articles -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/d5835c-e2f26c%40github.com.
[PathwayCommons/factoid] d5835c: Handle association of elements created through bio...
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: d5835c9052067153d21f868d1b3b7830d66d4cac https://github.com/PathwayCommons/factoid/commit/d5835c9052067153d21f868d1b3b7830d66d4cac Author: metincansiper Date: 2020-10-14 (Wed, 14 Oct 2020) Changed paths: M src/client/components/home.js M src/server/routes/api/document/index.js Log Message: --- Handle association of elements created through biopax urls. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/295a8f-d5835c%40github.com.
[PathwayCommons/factoid] 295a8f: Improvements for uploading multiple articles throu...
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: 295a8f0fe6224260a799f080aecc424da53af56d https://github.com/PathwayCommons/factoid/commit/295a8f0fe6224260a799f080aecc424da53af56d Author: metincansiper Date: 2020-10-13 (Tue, 13 Oct 2020) Changed paths: M src/client/components/home.js M src/server/routes/api/document/index.js Log Message: --- Improvements for uploading multiple articles through biopax -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/4baaa5-295a8f%40github.com.
[PathwayCommons/factoid] 4baaa5: Working on creating multiple documents from bioapa...
Branch: refs/heads/pc2_data Home: https://github.com/PathwayCommons/factoid Commit: 4baaa5758e3a1a35657bd79541eb9fe72c36859d https://github.com/PathwayCommons/factoid/commit/4baaa5758e3a1a35657bd79541eb9fe72c36859d Author: metincansiper Date: 2020-10-12 (Mon, 12 Oct 2020) Changed paths: M src/client/components/document-management.js M src/client/components/home.js M src/server/routes/api/document/index.js Log Message: --- Working on creating multiple documents from bioapax file through admin panel, nearly done! -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/pc2_data/00-4baaa5%40github.com.
[PathwayCommons/factoid] 4da0d6: Exclude junk documents from bulk download #828 (#831)
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: 4da0d6e95644c883c95f7a497cb877b80efcf537 https://github.com/PathwayCommons/factoid/commit/4da0d6e95644c883c95f7a497cb877b80efcf537 Author: metincansiper Date: 2020-09-15 (Tue, 15 Sep 2020) Changed paths: M src/server/routes/api/document/export.js Log Message: --- Exclude junk documents from bulk download #828 (#831) -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/4f90c6-4da0d6%40github.com.
[PathwayCommons/factoid] 4f90c6: In biopax export constantly use citation() and do ...
Branch: refs/heads/unstable Home: https://github.com/PathwayCommons/factoid Commit: 4f90c6aa71ae0fae0dd4723ebf4db4e4d853cb11 https://github.com/PathwayCommons/factoid/commit/4f90c6aa71ae0fae0dd4723ebf4db4e4d853cb11 Author: metincansiper Date: 2020-09-15 (Tue, 15 Sep 2020) Changed paths: M src/model/document/document.js Log Message: --- In biopax export constantly use citation() and do not set publication fieldd when pmid is missing. (#830) -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-cvs+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-cvs/PathwayCommons/factoid/push/refs/heads/unstable/c73aa6-4f90c6%40github.com.
