Branch: refs/heads/master
Home: https://github.com/PathwayCommons/factoid
Commit: 5733c0649d2e8e7e66fd8b6d58ae3ff85c8d70e7
https://github.com/PathwayCommons/factoid/commit/5733c0649d2e8e7e66fd8b6d58ae3ff85c8d70e7
Author: Jeffrey <[email protected]>
Date: 2020-10-14 (Wed, 14 Oct 2020)
Changed paths:
M package-lock.json
M package.json
Log Message:
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Merge pull request #878 from PathwayCommons/v0.12.2
0.12.2
Commit: 104f9c2ae2346c243210c046e163cdeabfb43c6d
https://github.com/PathwayCommons/factoid/commit/104f9c2ae2346c243210c046e163cdeabfb43c6d
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-14 (Wed, 14 Oct 2020)
Changed paths:
M src/server/sitemap.js
M test/sitemap/docs2Sitemap.js
Log Message:
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Supplement the sitemap urls with PNG image URL and metadata
Commit: 4992a35fdf1e3dc554de28dfe548389c67098b69
https://github.com/PathwayCommons/factoid/commit/4992a35fdf1e3dc554de28dfe548389c67098b69
Author: Jeffrey <[email protected]>
Date: 2020-10-14 (Wed, 14 Oct 2020)
Changed paths:
M src/server/sitemap.js
M test/sitemap/docs2Sitemap.js
Log Message:
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Merge pull request #880 from PathwayCommons/iss842_sitemap-images
Supplement the sitemap urls with PNG image URL and metadata
Commit: 1c1a2292dd05b344a5e55a9b848968c0ed081c3a
https://github.com/PathwayCommons/factoid/commit/1c1a2292dd05b344a5e55a9b848968c0ed081c3a
Author: metincansiper <[email protected]>
Date: 2020-10-16 (Fri, 16 Oct 2020)
Changed paths:
M src/model/element/interaction-type/deubiquitination.js
Log Message:
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Fixed a typo in effect of deubiquitination interaction type
Commit: 6a0c27a9065f2d7d30e3b5a0bd9999ed29446a3f
https://github.com/PathwayCommons/factoid/commit/6a0c27a9065f2d7d30e3b5a0bd9999ed29446a3f
Author: Max Franz <[email protected]>
Date: 2020-10-21 (Wed, 21 Oct 2020)
Changed paths:
M src/model/element/interaction-type/deubiquitination.js
Log Message:
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Merge pull request #883 from PathwayCommons/deubiquitination_typo
Fixed a typo in effect of deubiquitination interaction type
Commit: 8f63b3883edcf9e4976590ea8cc7f71d975eef4f
https://github.com/PathwayCommons/factoid/commit/8f63b3883edcf9e4976590ea8cc7f71d975eef4f
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-26 (Mon, 26 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
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Friendlier message for editors submit
Commit: 80fffdc11862e99bbdc2a4c764ffb9032333537d
https://github.com/PathwayCommons/factoid/commit/80fffdc11862e99bbdc2a4c764ffb9032333537d
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-26 (Mon, 26 Oct 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
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Warning text
Commit: c3d3712d24d244ff8219868661e097234f81a4f5
https://github.com/PathwayCommons/factoid/commit/c3d3712d24d244ff8219868661e097234f81a4f5
Author: Max Franz <[email protected]>
Date: 2020-10-26 (Mon, 26 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
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Merge pull request #884 from PathwayCommons/iss861_warnings-nicer
Friendlier message for editor Task warnings
Commit: fada0b9721a90f546cf4e7e2ceb179bde232d04d
https://github.com/PathwayCommons/factoid/commit/fada0b9721a90f546cf4e7e2ceb179bde232d04d
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-27 (Tue, 27 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
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- TextEditable component
- Using the new component in the submit done TaskView to set name
Commit: d378c77b98dbb17b610fb8d7cd469d05b6f5d9b6
https://github.com/PathwayCommons/factoid/commit/d378c77b98dbb17b610fb8d7cd469d05b6f5d9b6
Author: metincansiper <[email protected]>
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:
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During bulk export skip the files where the conversion is failing and give an
error message summarizing the case.
Commit: 8be4a1b12b29c38d270dc53ec70c0c399a65778f
https://github.com/PathwayCommons/factoid/commit/8be4a1b12b29c38d270dc53ec70c0c399a65778f
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-27 (Tue, 27 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
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- Drop autofocus
- Emphasize the editing state
Commit: 397f95a519069d94995c86294b88ed93c94bb339
https://github.com/PathwayCommons/factoid/commit/397f95a519069d94995c86294b88ed93c94bb339
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-27 (Tue, 27 Oct 2020)
Changed paths:
M src/client/components/tasks.js
Log Message:
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Add autofocus as option, default to false
Commit: 3476d49939fd0feeacc548b9001b604c0887e808
https://github.com/PathwayCommons/factoid/commit/3476d49939fd0feeacc548b9001b604c0887e808
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-28 (Wed, 28 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
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Using the focus HTML attribute rather than the 'editing' state
Commit: 715ede09df6219cec28ba2f54961d86a2a32bac1
https://github.com/PathwayCommons/factoid/commit/715ede09df6219cec28ba2f54961d86a2a32bac1
Author: Max Franz <[email protected]>
Date: 2020-10-28 (Wed, 28 Oct 2020)
Changed paths:
M src/config.js
M src/model/document/document.js
M src/server/routes/api/document/index.js
M src/util/email.js
Log Message:
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Related papers notification
Details:
- This is currently a prototype.
- A new email template type is defined as `relatedPaperNotification`.
- The emails are triggered whenever the related papers are updated for a
document.
- A new metadata field is available on a document.
`doc.relatedPapersNotified()` can be used to set or get whether the
notifications have been sent. This prevents duplicates.
- Novel interactions are an optional enhancement in the emails: An author can
receive an email whether or not the originating factoid has a novel
interaction. However, if there is a novel interaction, this should be
mentioned in the email.
- Currently, only notifications are sent to the terminal. The emails are
disabled until the template is set up.
- Action items are marked by `// TODO RPM`
Action items:
- [ ] Add a template to Mailjet (@jvwong), based on our email document on
Google Docs.
- [ ] Reuse our Indra querying code to determine whether there is a novel
interaction -- i.e. an interaction that has zero results in Indra
(@metincansiper).
- [ ] Verify that our emails send correctly on unstable. We'll temporary set
unstable to send these notifications to Max and Jeff (@maxkfranz @jvwong).
- [ ] Finalise the email template text (@maxkfranz).
- [ ] Research the feasibility of the bonus 'factoidable' nudge: Can we
determine using AI whether a paper is a good candidate for Biofactoid?
Ref. : Novel interaction notification #858
Commit: 2aede654b7494dd415447d4c1617523681516388
https://github.com/PathwayCommons/factoid/commit/2aede654b7494dd415447d4c1617523681516388
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-28 (Wed, 28 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
make it appear as native text input (persistent border)
Commit: 04e60f5e06b243efd539618a6679af04461bd7bb
https://github.com/PathwayCommons/factoid/commit/04e60f5e06b243efd539618a6679af04461bd7bb
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-28 (Wed, 28 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
-----------
Show a check on save. Don't show check for empty string.
Commit: af776e68211fb38369839950d6736f4ae11c4bd6
https://github.com/PathwayCommons/factoid/commit/af776e68211fb38369839950d6736f4ae11c4bd6
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-29 (Thu, 29 Oct 2020)
Changed paths:
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
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- Fixed bug in placeholder blur/focus
- Add back no transition
Commit: 0e4fd2c162c948291a9c6adc09e9064fd8fcdf03
https://github.com/PathwayCommons/factoid/commit/0e4fd2c162c948291a9c6adc09e9064fd8fcdf03
Author: Jeffrey Wong <[email protected]>
Date: 2020-10-29 (Thu, 29 Oct 2020)
Changed paths:
M src/client/components/editor/submit.js
Log Message:
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Use sticky tippy opt for submit button popover.
Commit: ac70b70206ab37b3c98853b2992efdc0d3b35b25
https://github.com/PathwayCommons/factoid/commit/ac70b70206ab37b3c98853b2992efdc0d3b35b25
Author: Max Franz <[email protected]>
Date: 2020-10-29 (Thu, 29 Oct 2020)
Changed paths:
M src/server/routes/api/document/export.js
M src/util/document.js
Log Message:
-----------
Merge pull request #885 from PathwayCommons/zip_error_handle
During bulk export skip the files where the conversion is failing
Commit: 54313112e94cacad1294ad22f0aacfd46a31eeb1
https://github.com/PathwayCommons/factoid/commit/54313112e94cacad1294ad22f0aacfd46a31eeb1
Author: Jeffrey <[email protected]>
Date: 2020-10-29 (Thu, 29 Oct 2020)
Changed paths:
M src/client/components/editor/submit.js
M src/client/components/tasks.js
M src/styles/tasks.css
Log Message:
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Merge pull request #887 from PathwayCommons/iss729_curator-name
Additional info: Curator name
Commit: e300e9f7f47f80a67a0907126a64db6f35705460
https://github.com/PathwayCommons/factoid/commit/e300e9f7f47f80a67a0907126a64db6f35705460
Author: Max Franz <[email protected]>
Date: 2020-10-29 (Thu, 29 Oct 2020)
Changed paths:
M src/styles/carousel.css
Log Message:
-----------
Remove the date from the carousel entries
Commit: 0a14cdcaa20c6c65cca6994815ec6c933fda7b78
https://github.com/PathwayCommons/factoid/commit/0a14cdcaa20c6c65cca6994815ec6c933fda7b78
Author: Max Franz <[email protected]>
Date: 2020-10-30 (Fri, 30 Oct 2020)
Changed paths:
M src/styles/carousel.css
Log Message:
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Merge pull request #890 from PathwayCommons/carousel-rm-date
Remove the date from the carousel entries
Commit: f78c6115ac73c187afc1e8eee8e44d2ac87b5941
https://github.com/PathwayCommons/factoid/commit/f78c6115ac73c187afc1e8eee8e44d2ac87b5941
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-02 (Mon, 02 Nov 2020)
Changed paths:
M Dockerfile
Log Message:
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Upgrade nodeJS image.
Commit: 182418399e970cc8d13bc0f25d149ffd892828a5
https://github.com/PathwayCommons/factoid/commit/182418399e970cc8d13bc0f25d149ffd892828a5
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-02 (Mon, 02 Nov 2020)
Changed paths:
M src/client/components/element-info/entity-assoc-display.js
Log Message:
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Check for the existence of chemical synonyms and formulae.
Commit: c4ce1a042f100c208be4fa9e693b987b36b5df52
https://github.com/PathwayCommons/factoid/commit/c4ce1a042f100c208be4fa9e693b987b36b5df52
Author: Jeffrey <[email protected]>
Date: 2020-11-02 (Mon, 02 Nov 2020)
Changed paths:
M Dockerfile
Log Message:
-----------
Merge pull request #891 from PathwayCommons/iss889_docker-nodejs
Upgrade nodeJS image.
Commit: 9192dc8fc5abb9a5cb6c385a0e9f91b60ab0edb5
https://github.com/PathwayCommons/factoid/commit/9192dc8fc5abb9a5cb6c385a0e9f91b60ab0edb5
Author: Jeffrey <[email protected]>
Date: 2020-11-03 (Tue, 03 Nov 2020)
Changed paths:
M src/client/components/element-info/entity-assoc-display.js
Log Message:
-----------
Merge pull request #892 from PathwayCommons/iss888_empty-chebi-fields
Chemical synonyms and formulae field labels shown if they exist
Commit: 2f2e4a8c60e6d98e28cf601be91906b83550c576
https://github.com/PathwayCommons/factoid/commit/2f2e4a8c60e6d98e28cf601be91906b83550c576
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-04 (Wed, 04 Nov 2020)
Changed paths:
M package.json
Log Message:
-----------
Declare license .
Commit: 6e972b289a9407f5be792a54ef8043ddcef6313d
https://github.com/PathwayCommons/factoid/commit/6e972b289a9407f5be792a54ef8043ddcef6313d
Author: Max Franz <[email protected]>
Date: 2020-11-04 (Wed, 04 Nov 2020)
Changed paths:
A LICENSE
Log Message:
-----------
Add LICENSE file (MIT)
Commit: 57b5929ccd76cc2b5eb728f9c9c2564c561dd7e9
https://github.com/PathwayCommons/factoid/commit/57b5929ccd76cc2b5eb728f9c9c2564c561dd7e9
Author: Jeffrey <[email protected]>
Date: 2020-11-04 (Wed, 04 Nov 2020)
Changed paths:
A LICENSE
M package.json
Log Message:
-----------
Merge pull request #894 from PathwayCommons/iss893_license
Declare license .
Commit: 1d1a5ed21f6f86ee31b7b32ab9dc315b4f5d2cae
https://github.com/PathwayCommons/factoid/commit/1d1a5ed21f6f86ee31b7b32ab9dc315b4f5d2cae
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-06 (Fri, 06 Nov 2020)
Changed paths:
M src/model/document/document.js
Log Message:
-----------
Attribute for stashing references for the article
Commit: 6dd39ccd92fb39f1c2aabf2af56c2571d4f7b73c
https://github.com/PathwayCommons/factoid/commit/6dd39ccd92fb39f1c2aabf2af56c2571d4f7b73c
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-06 (Fri, 06 Nov 2020)
Changed paths:
M src/server/routes/api/document/pubmed/linkPubmed.js
Log Message:
-----------
- Expose helper function elink2UidList (renamed from data2UidList)
- Accept an optional filter for linknames
Commit: ddfb05c40f3b770abea9ccacd417552def08a892
https://github.com/PathwayCommons/factoid/commit/ddfb05c40f3b770abea9ccacd417552def08a892
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-06 (Fri, 06 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Add a capability for setting the subset of referenced papers inside the
'getRelPprsForDoc'
Commit: dd4b45a2b15dc8ef8754b1cb5b1e78fea9c7a0e2
https://github.com/PathwayCommons/factoid/commit/dd4b45a2b15dc8ef8754b1cb5b1e78fea9c7a0e2
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-06 (Fri, 06 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Use the new set of referenced papers.
Commit: fa2050ac8213e66ee38d664742dc6b7bd3563b15
https://github.com/PathwayCommons/factoid/commit/fa2050ac8213e66ee38d664742dc6b7bd3563b15
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-09 (Mon, 09 Nov 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/index.js
Log Message:
-----------
Add an admin email, use in the relatedPapers emailer.
Commit: 062ee8cd52de38679d4db68c72614f30c761ee3e
https://github.com/PathwayCommons/factoid/commit/062ee8cd52de38679d4db68c72614f30c761ee3e
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-09 (Mon, 09 Nov 2020)
Changed paths:
M src/config.js
M src/server/routes/api/document/index.js
Log Message:
-----------
- emailRelatedPaperAuthors bundled with code for document status being
switched to 'public', following submission
- EMAIL_RELPPRS_CONTACT config that flags whether the relatedPapersEmails
should be sent to contacts (default true)
Commit: d67ad38f17f94cbaaf713bdba36ea696fae9737d
https://github.com/PathwayCommons/factoid/commit/d67ad38f17f94cbaaf713bdba36ea696fae9737d
Author: metincansiper <[email protected]>
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 <[email protected]>
Date: 2020-11-09 (Mon, 09 Nov 2020)
Changed paths:
M src/model/element/interaction.js
Log Message:
-----------
remove a console statement
Commit: 827d70be7be7086dafefa7644def4f0e9af76711
https://github.com/PathwayCommons/factoid/commit/827d70be7be7086dafefa7644def4f0e9af76711
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-09 (Mon, 09 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Tie the relatedPapers contact emailing to the admin refresh
Commit: b6623cf93e3b0bdf1b798efc4d93c5b246bc2eec
https://github.com/PathwayCommons/factoid/commit/b6623cf93e3b0bdf1b798efc4d93c5b246bc2eec
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/util/email.js
Log Message:
-----------
Use `logger` to remove linting warning in preparation for merging
Commit: fbbef392e87797f9b89f7bcf3137af0ea2b4dea1
https://github.com/PathwayCommons/factoid/commit/fbbef392e87797f9b89f7bcf3137af0ea2b4dea1
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Set `doc.relatedPapersNotified()` flag
Commit: bf0f241733ea2bcdfecb1524128a28bea5507d8d
https://github.com/PathwayCommons/factoid/commit/bf0f241733ea2bcdfecb1524128a28bea5507d8d
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/config.js
M src/util/email.js
Log Message:
-----------
Set template ID
Commit: 41b4bfe066fa22338b40993d8c5e5d9f5ebbae2e
https://github.com/PathwayCommons/factoid/commit/41b4bfe066fa22338b40993d8c5e5d9f5ebbae2e
Author: metincansiper <[email protected]>
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 <[email protected]>
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
Commit: 5526dd7d789c0540c3d690a21e57de524f3a002c
https://github.com/PathwayCommons/factoid/commit/5526dd7d789c0540c3d690a21e57de524f3a002c
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Add interactions filter based on `isNovel()` and add guard within
`emailRelatedPaperAuthors()` re. `doc.relatedPapersNotified()`
Commit: 1e75e29f015377fe759b393da5ce1b0f63b7ae3f
https://github.com/PathwayCommons/factoid/commit/1e75e29f015377fe759b393da5ce1b0f63b7ae3f
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Remove the organism dropdown when there are no alternative organism matches :
Removes case where a dropdown with only 'Other' is displayed.
Commit: 3c1fde47b4aa36ec66188ec55f986a3480c28f60
https://github.com/PathwayCommons/factoid/commit/3c1fde47b4aa36ec66188ec55f986a3480c28f60
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Hide the organism entry in the manual match mode for grounding
Commit: bd4df1e41854ecd82aa99f7a418977db736b4501
https://github.com/PathwayCommons/factoid/commit/bd4df1e41854ecd82aa99f7a418977db736b4501
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Change 'Current match' label to 'Selected' in manual match mode for grounding
: Avoids overlap
Commit: 2496c5f459e51b7843b6d34eab91a252b5e3a6ba
https://github.com/PathwayCommons/factoid/commit/2496c5f459e51b7843b6d34eab91a252b5e3a6ba
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
Log Message:
-----------
Use the selected grounding as the top-level organism dropdown ID, if possible
: Removes the case where the dropdown resets to the top entry, when a non-first
'Which p53?' value is selected.
Commit: 96e6d539dbdeb0a893a46ebad02220d4999b1a59
https://github.com/PathwayCommons/factoid/commit/96e6d539dbdeb0a893a46ebad02220d4999b1a59
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/styles/element-info/entity-info.css
Log Message:
-----------
Increase spacing between synonyms : Increases visual separation to ease the
visual identification of where a synonym starts and ends.
Commit: 194043930023f359aac8767b50971f7ec3a5ffd1
https://github.com/PathwayCommons/factoid/commit/194043930023f359aac8767b50971f7ec3a5ffd1
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/client/components/element-info/entity-info.js
M src/styles/element-info/entity-info.css
Log Message:
-----------
Merge pull request #897 from PathwayCommons/org-dropdown-etc
Org dropdown etc.
Commit: bee0cd55849a5b4471cce73c90dfbd00fa67293f
https://github.com/PathwayCommons/factoid/commit/bee0cd55849a5b4471cce73c90dfbd00fa67293f
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
M src/config.js
M src/model/document/document.js
M src/model/element/interaction.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/linkPubmed.js
M src/util/email.js
Log Message:
-----------
Merge pull request #886 from PathwayCommons/email-rel-pprs
Related papers notification
Commit: 7a52c9f90951cf7ebb0b55e8d2e25797ff6aab60
https://github.com/PathwayCommons/factoid/commit/7a52c9f90951cf7ebb0b55e8d2e25797ff6aab60
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
A src/server/email.js
M src/server/routes/api/document/index.js
R src/util/email.js
M src/util/index.js
Log Message:
-----------
Moving email.js util to server-side.
Commit: 7fdf9f2de5de346240cd319bc0bf21bf6db2212e
https://github.com/PathwayCommons/factoid/commit/7fdf9f2de5de346240cd319bc0bf21bf6db2212e
Author: Max Franz <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
R src/client/client-util/file.js
R src/client/client-util/index.js
M src/client/components/carousel.js
M src/client/components/document-management-components.js
M src/client/components/document-management.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
M src/client/components/editor/info-panel.js
M src/client/components/editor/submit.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/progression-stepper.js
M src/client/components/home.js
M src/client/components/notification/base.js
M src/client/components/notification/corner.js
M src/client/components/notification/inline.js
M src/client/components/notification/panel.js
M src/client/components/tasks.js
M src/client/components/twitter-share.js
A src/client/dom.js
M src/client/index.js
A src/server/document-util.js
M src/server/routes/api/document/export.js
R src/util/document.js
R src/util/dom.js
M src/util/index.js
Log Message:
-----------
Move util/dom and util/document
Commit: 5c3b4b5132a4892e31cf218cb871902cfdf942aa
https://github.com/PathwayCommons/factoid/commit/5c3b4b5132a4892e31cf218cb871902cfdf942aa
Author: Jeffrey <[email protected]>
Date: 2020-11-10 (Tue, 10 Nov 2020)
Changed paths:
R src/client/client-util/file.js
R src/client/client-util/index.js
M src/client/components/carousel.js
M src/client/components/document-management-components.js
M src/client/components/document-management.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
M src/client/components/editor/info-panel.js
M src/client/components/editor/submit.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/progression-stepper.js
M src/client/components/home.js
M src/client/components/notification/base.js
M src/client/components/notification/corner.js
M src/client/components/notification/inline.js
M src/client/components/notification/panel.js
M src/client/components/tasks.js
M src/client/components/twitter-share.js
A src/client/dom.js
M src/client/index.js
A src/server/document-util.js
A src/server/email.js
M src/server/routes/api/document/export.js
M src/server/routes/api/document/index.js
R src/util/document.js
R src/util/dom.js
R src/util/email.js
M src/util/index.js
Log Message:
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Merge pull request #898 from PathwayCommons/iss858_move-email-server
Moving email.js util to server-side.
Commit: 52ce17cf396ff4945d8127ad6a399633013f9a60
https://github.com/PathwayCommons/factoid/commit/52ce17cf396ff4945d8127ad6a399633013f9a60
Author: Max Franz <[email protected]>
Date: 2020-11-11 (Wed, 11 Nov 2020)
Changed paths:
M src/server/email.js
M src/util/strings.js
Log Message:
-----------
Related papers emails: strip out final period in title and add
firstAuthorEtAl var
Commit: ebbcdf3d94220fa1cbb5ab9b484efdd7ec592224
https://github.com/PathwayCommons/factoid/commit/ebbcdf3d94220fa1cbb5ab9b484efdd7ec592224
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-11 (Wed, 11 Nov 2020)
Changed paths:
M src/util/pubmed.js
Log Message:
-----------
Provide the individual name parts (if they exist) in the citation attribute.
Commit: 67643f86a783719479d674b3888ab09164010bff
https://github.com/PathwayCommons/factoid/commit/67643f86a783719479d674b3888ab09164010bff
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-11 (Wed, 11 Nov 2020)
Changed paths:
M src/util/pubmed.js
Log Message:
-----------
Add name parts to contact
Commit: ebd0086384bb4f5cae866f438776211a1e45e2a1
https://github.com/PathwayCommons/factoid/commit/ebd0086384bb4f5cae866f438776211a1e45e2a1
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-11 (Wed, 11 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Use the contact ForeName as name for email message
Commit: 430eb1c2064a48a7454b6386505d04218f1c1e3f
https://github.com/PathwayCommons/factoid/commit/430eb1c2064a48a7454b6386505d04218f1c1e3f
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-12 (Thu, 12 Nov 2020)
Changed paths:
M src/util/pubmed.js
Log Message:
-----------
Support citation with ISODate string.
Commit: 94a9bcdc0d447f9fe1c90b1d6a30d4e05485ac29
https://github.com/PathwayCommons/factoid/commit/94a9bcdc0d447f9fe1c90b1d6a30d4e05485ac29
Author: Max Franz <[email protected]>
Date: 2020-11-12 (Thu, 12 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #899 from PathwayCommons/iss858_name-parts
Provide author name parts and use in emails to ref'd paper authors
Commit: 61557c171372f9996e193a171823e8a6297e2d2b
https://github.com/PathwayCommons/factoid/commit/61557c171372f9996e193a171823e8a6297e2d2b
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-12 (Thu, 12 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Add two criteria to sendable papers: not older than (5 years), and isn't a
review.
Commit: b1cde716da67156d85430a4aebf7334ed78e3aaa
https://github.com/PathwayCommons/factoid/commit/b1cde716da67156d85430a4aebf7334ed78e3aaa
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-12 (Thu, 12 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Filter by date first
Commit: 7ab9081bb19f4165b1430049c0aab7014c614526
https://github.com/PathwayCommons/factoid/commit/7ab9081bb19f4165b1430049c0aab7014c614526
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-12 (Thu, 12 Nov 2020)
Changed paths:
M src/util/pubmed.js
Log Message:
-----------
Null out all the date fields be default in case you get a MedlineDate.
Commit: e4e597c9e2188263274b758e72cca0a38d71c3ee
https://github.com/PathwayCommons/factoid/commit/e4e597c9e2188263274b758e72cca0a38d71c3ee
Author: Jeffrey <[email protected]>
Date: 2020-11-13 (Fri, 13 Nov 2020)
Changed paths:
M src/server/routes/api/document/index.js
M src/util/pubmed.js
Log Message:
-----------
Merge pull request #900 from PathwayCommons/iss858_rank-filter-papers
Applying additional selection criteria to emails for related papers
Commit: 43031034d872527da5234f455fd74194e4811bb4
https://github.com/PathwayCommons/factoid/commit/43031034d872527da5234f455fd74194e4811bb4
Author: metincansiper <[email protected]>
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:
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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: 175d5aa558cd4bfc8909f42460993a2ffe875180
https://github.com/PathwayCommons/factoid/commit/175d5aa558cd4bfc8909f42460993a2ffe875180
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-19 (Thu, 19 Nov 2020)
Changed paths:
M docker/docker-compose.yml
Log Message:
-----------
Expose the EMAIL_RELPPRS_CONTACT as a env variable in Docker.
Commit: 49e93ec85f8ceab662c58617570ad240dfff9fb9
https://github.com/PathwayCommons/factoid/commit/49e93ec85f8ceab662c58617570ad240dfff9fb9
Author: Max Franz <[email protected]>
Date: 2020-11-19 (Thu, 19 Nov 2020)
Changed paths:
M docker/docker-compose.yml
Log Message:
-----------
Merge pull request #903 from PathwayCommons/docker-expose-relpprs-email
Expose the EMAIL_RELPPRS_CONTACT as a env variable in Docker.
Commit: 6d07f452dd78fdbde1430ff7da39a98e305c1ba6
https://github.com/PathwayCommons/factoid/commit/6d07f452dd78fdbde1430ff7da39a98e305c1ba6
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-20 (Fri, 20 Nov 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Read the paper link points to preprint
Commit: d1e98c2a813aacea65be5dfd9d47043d4ac9ccdc
https://github.com/PathwayCommons/factoid/commit/d1e98c2a813aacea65be5dfd9d47043d4ac9ccdc
Author: Max Franz <[email protected]>
Date: 2020-11-20 (Fri, 20 Nov 2020)
Changed paths:
M src/client/components/home.js
Log Message:
-----------
Merge pull request #905 from PathwayCommons/iss770_read-the-paper
Read the paper link points to preprint
Commit: 5863744cee5f8c65829ce92a409394a525d34d1b
https://github.com/PathwayCommons/factoid/commit/5863744cee5f8c65829ce92a409394a525d34d1b
Author: Jeffrey Wong <[email protected]>
Date: 2020-11-20 (Fri, 20 Nov 2020)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
0.13.0
Commit: fc71c85eed915fc8b28a702ad2790e745b110586
https://github.com/PathwayCommons/factoid/commit/fc71c85eed915fc8b28a702ad2790e745b110586
Author: Max Franz <[email protected]>
Date: 2020-11-20 (Fri, 20 Nov 2020)
Changed paths:
Log Message:
-----------
Merge master and 0.13 branches together for a clean merge
git merge -s ours master
Commit: e21626db906647fdba4ab07c01209975f3dbf75d
https://github.com/PathwayCommons/factoid/commit/e21626db906647fdba4ab07c01209975f3dbf75d
Author: Jeffrey <[email protected]>
Date: 2020-11-21 (Sat, 21 Nov 2020)
Changed paths:
M Dockerfile
A LICENSE
M docker/docker-compose.yml
M package-lock.json
M package.json
R src/client/client-util/file.js
R src/client/client-util/index.js
M src/client/components/carousel.js
M src/client/components/document-management-components.js
M src/client/components/document-management.js
M src/client/components/editor/help.js
M src/client/components/editor/index.js
M src/client/components/editor/info-panel.js
M src/client/components/editor/submit.js
M src/client/components/element-info/entity-assoc-display.js
M src/client/components/element-info/entity-info.js
M src/client/components/element-info/progression-stepper.js
M src/client/components/home.js
M src/client/components/notification/base.js
M src/client/components/notification/corner.js
M src/client/components/notification/inline.js
M src/client/components/notification/panel.js
M src/client/components/tasks.js
M src/client/components/twitter-share.js
A src/client/dom.js
M src/client/index.js
M src/config.js
M src/model/document/document.js
M src/model/element/interaction-type/deubiquitination.js
M src/model/element/interaction.js
A src/server/document-util.js
A src/server/email.js
M src/server/routes/api/document/export.js
M src/server/routes/api/document/index.js
M src/server/routes/api/document/pubmed/linkPubmed.js
M src/server/sitemap.js
M src/styles/carousel.css
M src/styles/element-info/entity-info.css
M src/styles/tasks.css
R src/util/document.js
R src/util/dom.js
R src/util/email.js
M src/util/index.js
M src/util/pubmed.js
M src/util/strings.js
M test/sitemap/docs2Sitemap.js
Log Message:
-----------
Merge pull request #906 from PathwayCommons/v0.13.0
Version 0.13.0
Compare:
https://github.com/PathwayCommons/factoid/compare/7c1ade50d2df...e21626db9066
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