Branch: refs/heads/master
Home: https://github.com/PathwayCommons/factoid
Commit: 27938781827d1a9906896abd0d8a7906adbdad19
https://github.com/PathwayCommons/factoid/commit/27938781827d1a9906896abd0d8a7906adbdad19
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-16 (Thu, 16 Feb 2023)
Changed paths:
R neo4j-test/connect-neo4j.js
A neo4j-test/init-driver.js
Log Message:
-----------
init driver test works
Commit: 6108a68e856050f1b2d75b04e0916c399dc2fe7f
https://github.com/PathwayCommons/factoid/commit/6108a68e856050f1b2d75b04e0916c399dc2fe7f
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-16 (Thu, 16 Feb 2023)
Changed paths:
M src/neo4j/query-strings.js
Log Message:
-----------
added new query strings to aid with testing
Commit: a6f427560bd308b9b54cff3def368a23f7994959
https://github.com/PathwayCommons/factoid/commit/a6f427560bd308b9b54cff3def368a23f7994959
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-16 (Thu, 16 Feb 2023)
Changed paths:
M neo4j-test/init-driver.js
M src/neo4j/neo4j-functions.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
integrated initDriver, closeDriver differently for testing
Commit: d0c446205dfe66e39921d0325d9af6f23bd2b28d
https://github.com/PathwayCommons/factoid/commit/d0c446205dfe66e39921d0325d9af6f23bd2b28d
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-17 (Fri, 17 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
Log Message:
-----------
new getter function for articleTitle
Commit: e8c4f827fbec534ddd8e26c0ccb90450cf67cfc1
https://github.com/PathwayCommons/factoid/commit/e8c4f827fbec534ddd8e26c0ccb90450cf67cfc1
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-17 (Fri, 17 Feb 2023)
Changed paths:
M README.md
M neo4j-test/init-driver.js
M src/config.js
M src/neo4j/neo4j-driver.js
Log Message:
-----------
Merge branch 'unstable' into testing-neo4j
Commit: 8d017b3a1e23a7f715c9ce5b0cd014a82a166f26
https://github.com/PathwayCommons/factoid/commit/8d017b3a1e23a7f715c9ce5b0cd014a82a166f26
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-17 (Fri, 17 Feb 2023)
Changed paths:
A neo4j-test/connect-neo4j.js
R neo4j-test/init-driver.js
Log Message:
-----------
fixing merge conflict connect-neo4j.js
Commit: 85e0d079404cd51c74649bd95ba830972613164a
https://github.com/PathwayCommons/factoid/commit/85e0d079404cd51c74649bd95ba830972613164a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-17 (Fri, 17 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
deleteAll does not work yet, getNumNodes does
Commit: 0fd067b6257ba8d72a9d116a88129056ee8b11ed
https://github.com/PathwayCommons/factoid/commit/0fd067b6257ba8d72a9d116a88129056ee8b11ed
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-17 (Fri, 17 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/neo4j-functions.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
deleteAll (renamed) function now works
Commit: 5db09d42cf93945f8e99aee9a37d406d60381f55
https://github.com/PathwayCommons/factoid/commit/5db09d42cf93945f8e99aee9a37d406d60381f55
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-17 (Fri, 17 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/neo4j-functions.js
A src/neo4j/test-functions.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
put functions only used in testing in a new file
Commit: 4b4cdf1ee629a7482cc30aae2ec64ffa9294d62c
https://github.com/PathwayCommons/factoid/commit/4b4cdf1ee629a7482cc30aae2ec64ffa9294d62c
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-21 (Tue, 21 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/test-functions.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
getGeneNameById works, test for addNode now works
Commit: f1215754ca251be1cda5f7b1a2a4a02f0718a256
https://github.com/PathwayCommons/factoid/commit/f1215754ca251be1cda5f7b1a2a4a02f0718a256
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-21 (Tue, 21 Feb 2023)
Changed paths:
M src/config.js
Log Message:
-----------
Merge branch 'unstable' of github.com:PathwayCommons/factoid into
testing-neo4j
Commit: f1667eb70392e97232398d26f2489fe7db89bad9
https://github.com/PathwayCommons/factoid/commit/f1667eb70392e97232398d26f2489fe7db89bad9
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-21 (Tue, 21 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/query-strings.js
M src/neo4j/test-functions.js
Log Message:
-----------
starting implementation of addEdge test
Commit: 3be031723b968980b59d488083a4b0fceaf9b47f
https://github.com/PathwayCommons/factoid/commit/3be031723b968980b59d488083a4b0fceaf9b47f
Author: Jeffrey <[email protected]>
Date: 2023-02-21 (Tue, 21 Feb 2023)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
Merge pull request #1128 from PathwayCommons/v0.22.1
Update version tag
Commit: 0294d39774cddb1b3e8a83783f0214452dfe88c6
https://github.com/PathwayCommons/factoid/commit/0294d39774cddb1b3e8a83783f0214452dfe88c6
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-21 (Tue, 21 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/query-strings.js
M src/neo4j/test-functions.js
Log Message:
-----------
finished addEdge test. Deleted unnecessary function and query strings
Commit: 496f584fa6dae92780fcb68255d7fddc8503922e
https://github.com/PathwayCommons/factoid/commit/496f584fa6dae92780fcb68255d7fddc8503922e
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-21 (Tue, 21 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/test-functions.js
Log Message:
-----------
checking for duplicates testing completed
Commit: cc8f46cf4ec9bc270ad35bdd7f1ba536194be651
https://github.com/PathwayCommons/factoid/commit/cc8f46cf4ec9bc270ad35bdd7f1ba536194be651
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-21 (Tue, 21 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/neo4j-functions.js
Log Message:
-----------
searchByGeneId test completed
Commit: 3c02e831e4cd5d18edf19d07c7611be575fbf134
https://github.com/PathwayCommons/factoid/commit/3c02e831e4cd5d18edf19d07c7611be575fbf134
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-21 (Tue, 21 Feb 2023)
Changed paths:
M neo4j-test/example.js
Log Message:
-----------
updated addEdge test: formatting
Commit: 712b09b6e915ee83493ecd00490435e5121c5e67
https://github.com/PathwayCommons/factoid/commit/712b09b6e915ee83493ecd00490435e5121c5e67
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-22 (Wed, 22 Feb 2023)
Changed paths:
M neo4j-test/example.js
Log Message:
-----------
deleteAllNodeandEdges before each test
Commit: 7aca7b0bf38968498c97fd174d609cc4d797f13d
https://github.com/PathwayCommons/factoid/commit/7aca7b0bf38968498c97fd174d609cc4d797f13d
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-22 (Wed, 22 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/test-functions.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
rename getGeneNameById to getGeneName
Commit: 4e16b6c8ba4d8d993cca8b34586eb4c09b2f2659
https://github.com/PathwayCommons/factoid/commit/4e16b6c8ba4d8d993cca8b34586eb4c09b2f2659
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-22 (Wed, 22 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/neo4j-functions.js
Log Message:
-----------
made high-level functions related to searchByGeneId
Commit: abdae8bd268332e82a62dcf11d0ddd02cf2300f2
https://github.com/PathwayCommons/factoid/commit/abdae8bd268332e82a62dcf11d0ddd02cf2300f2
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-22 (Wed, 22 Feb 2023)
Changed paths:
M neo4j-test/example.js
Log Message:
-----------
added test case for searching in an empty database
Commit: 10823db8c9494138421bfd3f203323a9338537c4
https://github.com/PathwayCommons/factoid/commit/10823db8c9494138421bfd3f203323a9338537c4
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-22 (Wed, 22 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/test-functions.js
Log Message:
-----------
rename getEdgeById to getEdge
Commit: bdbba9733a6b9986012107e47befbb3c653f476d
https://github.com/PathwayCommons/factoid/commit/bdbba9733a6b9986012107e47befbb3c653f476d
Author: Jeffrey Wong <[email protected]>
Date: 2023-02-23 (Thu, 23 Feb 2023)
Changed paths:
M src/neo4j/.env
M src/neo4j/docker-compose.yml
Log Message:
-----------
Add RethinkDB instance.
Commit: 0adfce2f19b0c857ae856df1df9b9f352a3ec810
https://github.com/PathwayCommons/factoid/commit/0adfce2f19b0c857ae856df1df9b9f352a3ec810
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-24 (Fri, 24 Feb 2023)
Changed paths:
M src/neo4j/starting-neo4j.js
Log Message:
-----------
added comment
Commit: fee908d2b36ec75387f9316e0760b7d144bb5c9a
https://github.com/PathwayCommons/factoid/commit/fee908d2b36ec75387f9316e0760b7d144bb5c9a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-24 (Fri, 24 Feb 2023)
Changed paths:
M src/neo4j/neo4j-functions.js
Log Message:
-----------
documentation
Commit: 32d81bfc6efce2b276cfb0b19cb7ae260e067dcf
https://github.com/PathwayCommons/factoid/commit/32d81bfc6efce2b276cfb0b19cb7ae260e067dcf
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-24 (Fri, 24 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/query-strings.js
M src/neo4j/test-functions.js
Log Message:
-----------
made getNode and turned getGeneName into a derivative of getNode
Commit: 7a221406fa8f2dba7102fb65d28bbba9f9634804
https://github.com/PathwayCommons/factoid/commit/7a221406fa8f2dba7102fb65d28bbba9f9634804
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-24 (Fri, 24 Feb 2023)
Changed paths:
A src/neo4j/index.js
Log Message:
-----------
made index.js draft
Commit: bdd7a0d936573b2510140eb5351fd096532d77bb
https://github.com/PathwayCommons/factoid/commit/bdd7a0d936573b2510140eb5351fd096532d77bb
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-24 (Fri, 24 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/neo4j-functions.js
Log Message:
-----------
get rid of unused vars
Commit: 13f061f9a284b8a22469708e98acd19d2642f4ec
https://github.com/PathwayCommons/factoid/commit/13f061f9a284b8a22469708e98acd19d2642f4ec
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-27 (Mon, 27 Feb 2023)
Changed paths:
M neo4j-test/example.js
M src/neo4j/.env
M src/neo4j/docker-compose.yml
A src/neo4j/index.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
M src/neo4j/starting-neo4j.js
M src/neo4j/test-functions.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
Merge pull request #1129 from PathwayCommons/testing-neo4j-v2
Neo4j Testing (Part 2)
Commit: 2c794f62a7bc0bc65eeff22dfb26a6658d6c78bc
https://github.com/PathwayCommons/factoid/commit/2c794f62a7bc0bc65eeff22dfb26a6658d6c78bc
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-28 (Tue, 28 Feb 2023)
Changed paths:
M src/neo4j/index.js
A src/neo4j/neo4j-document.js
Log Message:
-----------
make skeleton for addDocumentToNeo4j
Commit: 06da70df310a08ef7aacbefb8ccd996ef19fd80f
https://github.com/PathwayCommons/factoid/commit/06da70df310a08ef7aacbefb8ccd996ef19fd80f
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-02-28 (Tue, 28 Feb 2023)
Changed paths:
M src/neo4j/neo4j-document.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
test successful with dummy data, fixed bug
Commit: cb289f72ced798e5068b164658e0660dda8b2076
https://github.com/PathwayCommons/factoid/commit/cb289f72ced798e5068b164658e0660dda8b2076
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-02 (Thu, 02 Mar 2023)
Changed paths:
M src/neo4j/get-doc-functions.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
basic code with getAllDocs runs but does not terminate
Commit: dc0792930489888453867b40d066d1db57c0d548
https://github.com/PathwayCommons/factoid/commit/dc0792930489888453867b40d066d1db57c0d548
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-02 (Thu, 02 Mar 2023)
Changed paths:
A neo4j-test/add-nodes-edges.js
A neo4j-test/doc-tests.js
R neo4j-test/example.js
A neo4j-test/testDoc.json
M src/neo4j/get-doc-functions.js
Log Message:
-----------
Can create and delete documents with doc-tests. Database deletion required
first
Commit: 5a596437cb28b5211bc407f29c4e545e9e082b42
https://github.com/PathwayCommons/factoid/commit/5a596437cb28b5211bc407f29c4e545e9e082b42
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-03 (Fri, 03 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
citation field is not populating (fields are null)
Commit: 4cfd84c7667f5ee2e00c64c24b75a1ba90cea8fc
https://github.com/PathwayCommons/factoid/commit/4cfd84c7667f5ee2e00c64c24b75a1ba90cea8fc
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-06 (Mon, 06 Mar 2023)
Changed paths:
M src/neo4j/test-functions.js
Log Message:
-----------
fixed bug in testing functions
Commit: ab43fcfd728f524099fb96abca2a28b4d974a8c3
https://github.com/PathwayCommons/factoid/commit/ab43fcfd728f524099fb96abca2a28b4d974a8c3
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-06 (Mon, 06 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
M src/neo4j/neo4j-document.js
Log Message:
-----------
tests are in place (works only for hardcoded data right now)
Commit: 49af3894713418ce42cf6469d7d3c5cc9c7f49e0
https://github.com/PathwayCommons/factoid/commit/49af3894713418ce42cf6469d7d3c5cc9c7f49e0
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-06 (Mon, 06 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
addDocumentToNeo4j works with a few hard coded parts
Commit: cdb7440272ac85faf2b2253d728c4c28a2b5f7c0
https://github.com/PathwayCommons/factoid/commit/cdb7440272ac85faf2b2253d728c4c28a2b5f7c0
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-06 (Mon, 06 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
made function convertUUIDtoId, less hard coding
Commit: 0826e6881392ad62622e5617b16305d1cf5249f5
https://github.com/PathwayCommons/factoid/commit/0826e6881392ad62622e5617b16305d1cf5249f5
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-07 (Tue, 07 Mar 2023)
Changed paths:
A test/data/document.json
M test/document.js
Log Message:
-----------
Add test for article info in Document fromJson
Commit: a6fc2f5b5eacea50d795603f6c889401d18dbff7
https://github.com/PathwayCommons/factoid/commit/a6fc2f5b5eacea50d795603f6c889401d18dbff7
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-07 (Tue, 07 Mar 2023)
Changed paths:
M src/model/document/document.js
Log Message:
-----------
Distinct fields for json deserialization
Commit: cd97f0ad8ab8563f37b02e15794cebaa0a050b0e
https://github.com/PathwayCommons/factoid/commit/cd97f0ad8ab8563f37b02e15794cebaa0a050b0e
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
commented out code regarding rdb
Commit: 5a530438933dfad108a7b9f6aa5e469bfa1d047a
https://github.com/PathwayCommons/factoid/commit/5a530438933dfad108a7b9f6aa5e469bfa1d047a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
M src/neo4j/neo4j-document.js
Log Message:
-----------
workaround for null citation fields
Commit: 628bcfca82281bdd22adb8d92b03151d54a2cd1a
https://github.com/PathwayCommons/factoid/commit/628bcfca82281bdd22adb8d92b03151d54a2cd1a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
A neo4j-test/add-nodes-edges.js
A neo4j-test/doc-tests.js
R neo4j-test/example.js
A neo4j-test/testDoc.json
M src/neo4j/get-doc-functions.js
M src/neo4j/index.js
A src/neo4j/neo4j-document.js
M src/neo4j/test-functions.js
M src/neo4j/test-temp-run.js
Log Message:
-----------
Merge pull request #1132 from PathwayCommons/neo4j-document
Make function addDocumentToNeo4j
Commit: ab6e60e4ee1d78acfbc45590c870df1d21cf5e81
https://github.com/PathwayCommons/factoid/commit/ab6e60e4ee1d78acfbc45590c870df1d21cf5e81
Author: Jeffrey <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M src/model/document/document.js
A test/data/document.json
M test/document.js
Log Message:
-----------
Merge pull request #1134 from PathwayCommons/iss1133_doc-fromJson-article
Document from JSON: article
Commit: 29597c72574d9988b8d98b30c4ef85ad98db40d8
https://github.com/PathwayCommons/factoid/commit/29597c72574d9988b8d98b30c4ef85ad98db40d8
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
M neo4j-test/testDoc.json
Log Message:
-----------
cleanup doc-level tests. Commented out failing tests. Related to #135
Commit: 1497b1e67f8e01efa13fee3ae99fd02370e1061f
https://github.com/PathwayCommons/factoid/commit/1497b1e67f8e01efa13fee3ae99fd02370e1061f
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
fixed bug regarding duplicating doi
Commit: 3306899f9597b18632b00a36a1dd9b43b01dd65e
https://github.com/PathwayCommons/factoid/commit/3306899f9597b18632b00a36a1dd9b43b01dd65e
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
remove test for document fields, keep neo4j test
Commit: d9f5d9b0597e8c8e76bc4c5e34866b7ed1b1c4e6
https://github.com/PathwayCommons/factoid/commit/d9f5d9b0597e8c8e76bc4c5e34866b7ed1b1c4e6
Author: Jeffrey <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
M neo4j-test/testDoc.json
M src/neo4j/neo4j-document.js
Log Message:
-----------
Merge pull request #1136 from PathwayCommons/iss1135_add-article-testdoc
Add article to test document JSON
Commit: 5d1a213c51f6e33eec2332f5370b0455a237a896
https://github.com/PathwayCommons/factoid/commit/5d1a213c51f6e33eec2332f5370b0455a237a896
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
makes and drops a db, not fully configured yet
Commit: eee4fb58ce5ce8a5a501353fc7fe6cbc92a7ffa5
https://github.com/PathwayCommons/factoid/commit/eee4fb58ce5ce8a5a501353fc7fe6cbc92a7ffa5
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-08 (Wed, 08 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
M neo4j-test/testDoc.json
M src/model/document/document.js
M src/neo4j/neo4j-document.js
A test/data/document.json
M test/document.js
Log Message:
-----------
Merge branch 'unstable' into iss1135-rdb-testing-clean-delete
Commit: 25e61f86997045c6217c177b6c5a1f623848e392
https://github.com/PathwayCommons/factoid/commit/25e61f86997045c6217c177b6c5a1f623848e392
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-09 (Thu, 09 Mar 2023)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
Add package rethinkdb-fixtures
Commit: 148e810c26af83727726772419319467927e52a5
https://github.com/PathwayCommons/factoid/commit/148e810c26af83727726772419319467927e52a5
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-09 (Thu, 09 Mar 2023)
Changed paths:
M neo4j-test/testDoc.json
Log Message:
-----------
Replace testDoc JSON with a semi-edited db dump of doc and elements
Commit: a99d91de00be0e790e3f235236e4495a7de7cbb2
https://github.com/PathwayCommons/factoid/commit/a99d91de00be0e790e3f235236e4495a7de7cbb2
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-09 (Thu, 09 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
Use isolated db instance for tests.
Commit: cfafb829ed8a0bc082687c22e9aeb26778e67863
https://github.com/PathwayCommons/factoid/commit/cfafb829ed8a0bc082687c22e9aeb26778e67863
Author: Jeffrey <[email protected]>
Date: 2023-03-09 (Thu, 09 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
M neo4j-test/testDoc.json
M package-lock.json
M package.json
Log Message:
-----------
Merge pull request #1137 from PathwayCommons/iss1135-rdb-testing-clean-delete
Iss1135: Ensure clean deletion of RethinkDB database for Testing
Commit: eef8de77f938a4ca9c4ad4dc2d9304b96eb614cd
https://github.com/PathwayCommons/factoid/commit/eef8de77f938a4ca9c4ad4dc2d9304b96eb614cd
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-09 (Thu, 09 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
M src/neo4j/neo4j-document.js
Log Message:
-----------
addDocumentToNeo4j now uses a document instance without error
Commit: e972fcc1550936546ca868c6bf2b5ae3214a6162
https://github.com/PathwayCommons/factoid/commit/e972fcc1550936546ca868c6bf2b5ae3214a6162
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-09 (Thu, 09 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
better way of determining if element is Entity
Commit: 9e9b7d040d0e8fdd3884f9e0bd5ee125afb21d1d
https://github.com/PathwayCommons/factoid/commit/9e9b7d040d0e8fdd3884f9e0bd5ee125afb21d1d
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-09 (Thu, 09 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
better way of determining source/target pt 1
Commit: 82e980914bb4d59570997e779ce5222e4ea94b1b
https://github.com/PathwayCommons/factoid/commit/82e980914bb4d59570997e779ce5222e4ea94b1b
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-09 (Thu, 09 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
better way of determining source/target pt 2, finished
Commit: 8740c748a2cd41fa66ac40943b08a16f33ac9c78
https://github.com/PathwayCommons/factoid/commit/8740c748a2cd41fa66ac40943b08a16f33ac9c78
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-10 (Fri, 10 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
tidy up the for loops
Commit: 5eb87e5485cbdf6fc2baffa0d365e7f5ec461539
https://github.com/PathwayCommons/factoid/commit/5eb87e5485cbdf6fc2baffa0d365e7f5ec461539
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-10 (Fri, 10 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
remove hard code from tests (commented out)
Commit: 05a92c9539c0543f5e3dc1e3483c1f712b4770f3
https://github.com/PathwayCommons/factoid/commit/05a92c9539c0543f5e3dc1e3483c1f712b4770f3
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-10 (Fri, 10 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
M src/neo4j/neo4j-document.js
Log Message:
-----------
Merge pull request #1140 from PathwayCommons/iss1138-adddocumenttoneo4j
addDocumentToNeo4j now uses Document instance
Commit: d2f5e670efcc1c80f3e8f615f51f638d63514dcd
https://github.com/PathwayCommons/factoid/commit/d2f5e670efcc1c80f3e8f615f51f638d63514dcd
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-10 (Fri, 10 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
delete commented out lines from test suite
Commit: 0ce518fa3753e4d394f1d12546b1f8acac2767f6
https://github.com/PathwayCommons/factoid/commit/0ce518fa3753e4d394f1d12546b1f8acac2767f6
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-13 (Mon, 13 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
better documentation in neo4j-document.js
Commit: e3471dd50d02a727dd870984c29f4d2c6742c83f
https://github.com/PathwayCommons/factoid/commit/e3471dd50d02a727dd870984c29f4d2c6742c83f
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-13 (Mon, 13 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
A neo4j-test/goultDoc1.json
Log Message:
-----------
run doc-tests.js with simple Goult JSON. Unsuccessful
Commit: 303b09099682b4a3a949ae011f89081ec9dc65df
https://github.com/PathwayCommons/factoid/commit/303b09099682b4a3a949ae011f89081ec9dc65df
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-13 (Mon, 13 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
reorganize test suite, comment out breaking test
Commit: 3c6b91e916d6bae506c35998222299009340a681
https://github.com/PathwayCommons/factoid/commit/3c6b91e916d6bae506c35998222299009340a681
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-13 (Mon, 13 Mar 2023)
Changed paths:
A neo4j-test/fixtures.js
Log Message:
-----------
Script to generate test fixtures.
Commit: eeb0423a4592a54d41601dc9347566245c7a401f
https://github.com/PathwayCommons/factoid/commit/eeb0423a4592a54d41601dc9347566245c7a401f
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-13 (Mon, 13 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
Merge origin/1141-neo4j-testing into 1141-neo4j-testing
Commit: d38b18dfc91f381a162da664c90c80fb026dfdac
https://github.com/PathwayCommons/factoid/commit/d38b18dfc91f381a162da664c90c80fb026dfdac
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
A neo4j-test/doct_tests_1.json
R neo4j-test/goultDoc1.json
Log Message:
-----------
Goult 1 test (undirect binary interaction) added
Commit: 1596b54363ddfc0c0046a0bacdae49d38f71d324
https://github.com/PathwayCommons/factoid/commit/1596b54363ddfc0c0046a0bacdae49d38f71d324
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
bug in addDocumentToNeo4j for undirected interactions fixed
Commit: 8178880e55562e23d0dec46f03bcd763c1bff59b
https://github.com/PathwayCommons/factoid/commit/8178880e55562e23d0dec46f03bcd763c1bff59b
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
A neo4j-test/doct_tests_2.json
Log Message:
-----------
Goult 2 test (3 nodes, 2 edges) added
Commit: 88a0b7d5cda705c4c1470beb4ccd6395f32f1fd1
https://github.com/PathwayCommons/factoid/commit/88a0b7d5cda705c4c1470beb4ccd6395f32f1fd1
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
A neo4j-test/doct_tests_3.json
Log Message:
-----------
Goult 3 test (2 nodes, 2 edges) added
Commit: 73089f01082aec6cc93545fa0b9177e9de624ac1
https://github.com/PathwayCommons/factoid/commit/73089f01082aec6cc93545fa0b9177e9de624ac1
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
A neo4j-test/doct_tests_4.json
Log Message:
-----------
Goult 4 test (4 nodes, 4 edges) added
Commit: 7e88ba4a6a83a31fe439ef74821221ad40f91482
https://github.com/PathwayCommons/factoid/commit/7e88ba4a6a83a31fe439ef74821221ad40f91482
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
A neo4j-test/doct_tests_5.json
Log Message:
-----------
Goult 5 test (5/6 nodes, 5 edges) added.
Commit: 035bc8e41726c6b524432e729e47b7784b6d2bb4
https://github.com/PathwayCommons/factoid/commit/035bc8e41726c6b524432e729e47b7784b6d2bb4
Author: Max Franz <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M README.md
M src/config.js
M src/server/routes/api/document/index.js
A src/server/routes/api/document/p-limit.js
Log Message:
-----------
Add controls for max. number of images to generate in parallel
- Use `DOCUMENT_IMAGE_PLL_LIMIT` to set the number of images that can be
generated at once.
- It should be as high as the hardware can support to keep things fast.
- It's set at 1 by default. This always works, but it's not as fast as it
could/should be.
- Also add `DOCUMENT_IMAGE_CACHE_SIZE` to the readme. This was undocumented.
Commit: cfad33b5fc299e5f4a0684617da92a26889740d6
https://github.com/PathwayCommons/factoid/commit/cfad33b5fc299e5f4a0684617da92a26889740d6
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
use filter instead of loop for arrNodes, arrEdges
Commit: f31810b30c59158153d0b19500ffc3853f360fbd
https://github.com/PathwayCommons/factoid/commit/f31810b30c59158153d0b19500ffc3853f360fbd
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
update test suite for undirected interactions
Commit: 34c3f3c52212101c6d9023e5182e5d02e69a63c3
https://github.com/PathwayCommons/factoid/commit/34c3f3c52212101c6d9023e5182e5d02e69a63c3
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
A neo4j-test/doct_tests_1.json
A neo4j-test/doct_tests_2.json
A neo4j-test/doct_tests_3.json
A neo4j-test/doct_tests_4.json
A neo4j-test/doct_tests_5.json
A neo4j-test/fixtures.js
M src/neo4j/neo4j-document.js
Log Message:
-----------
Merge pull request #1142 from PathwayCommons/1141-neo4j-testing
Iss1141: Adding more Neo4j Tests
Commit: 55ac7e79d73f1b8f92bb6ee3fc1267d4b1b8c2e3
https://github.com/PathwayCommons/factoid/commit/55ac7e79d73f1b8f92bb6ee3fc1267d4b1b8c2e3
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-14 (Tue, 14 Mar 2023)
Changed paths:
A neo4j-test/search-tests.js
Log Message:
-----------
successfully added all 5 Goult docs
Commit: 76bb3a6c8bac41f193db4ad9229213fcda54e500
https://github.com/PathwayCommons/factoid/commit/76bb3a6c8bac41f193db4ad9229213fcda54e500
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M src/neo4j/neo4j-functions.js
Log Message:
-----------
searchByGeneId update, returns null appropriately
Commit: 5e6fba220c90a58f53afb73efa7f3c988ab60afe
https://github.com/PathwayCommons/factoid/commit/5e6fba220c90a58f53afb73efa7f3c988ab60afe
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M neo4j-test/search-tests.js
Log Message:
-----------
mapk6 test added
Commit: 2c598a23cc667296f67acba2e2982c42623317a6
https://github.com/PathwayCommons/factoid/commit/2c598a23cc667296f67acba2e2982c42623317a6
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M neo4j-test/search-tests.js
M src/neo4j/neo4j-functions.js
Log Message:
-----------
fix getInteractions and getNeighbouringNodes to return null
Commit: 4029dd3d21c6c5c955d8bdb20f61e6c91424f34f
https://github.com/PathwayCommons/factoid/commit/4029dd3d21c6c5c955d8bdb20f61e6c91424f34f
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M src/neo4j/neo4j-functions.js
Log Message:
-----------
update getNeighbouringNodes, getInteractions to return properties
Commit: eaf8bb7d31d5a55563f20c1a50135a255711e9be
https://github.com/PathwayCommons/factoid/commit/eaf8bb7d31d5a55563f20c1a50135a255711e9be
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M neo4j-test/search-tests.js
Log Message:
-----------
KANK1 test added
Commit: 417694681236a4569761a71c22f58988c091482a
https://github.com/PathwayCommons/factoid/commit/417694681236a4569761a71c22f58988c091482a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M src/neo4j/neo4j-functions.js
Log Message:
-----------
filter out duplicate interactions & neighbouring nodes
Commit: 0f70d8505b0a0dc7825453e3cae3d9521b6bb3e2
https://github.com/PathwayCommons/factoid/commit/0f70d8505b0a0dc7825453e3cae3d9521b6bb3e2
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M neo4j-test/search-tests.js
Log Message:
-----------
TLN1 test added
Commit: a4565d42328ab1a71fef85ce79d249296358e451
https://github.com/PathwayCommons/factoid/commit/a4565d42328ab1a71fef85ce79d249296358e451
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M neo4j-test/search-tests.js
Log Message:
-----------
TLNRD1 test added
Commit: eb796446287dabb1df504e6d9b8e1951c307b9f3
https://github.com/PathwayCommons/factoid/commit/eb796446287dabb1df504e6d9b8e1951c307b9f3
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-15 (Wed, 15 Mar 2023)
Changed paths:
M neo4j-test/search-tests.js
Log Message:
-----------
add a doi field to tests
Commit: cc2edc086e05b89208394435437ba93c8bd3932d
https://github.com/PathwayCommons/factoid/commit/cc2edc086e05b89208394435437ba93c8bd3932d
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-17 (Fri, 17 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M neo4j-test/search-tests.js
M src/neo4j/index.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
Log Message:
-----------
renaming Gene to Molecule
Commit: 82dbd99d3291eeb7fe482edd6037a90d1b5865ea
https://github.com/PathwayCommons/factoid/commit/82dbd99d3291eeb7fe482edd6037a90d1b5865ea
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-17 (Fri, 17 Mar 2023)
Changed paths:
M src/neo4j/neo4j-functions.js
R src/neo4j/starting-neo4j.js
M src/neo4j/test-functions.js
R src/neo4j/test-temp-run.js
Log Message:
-----------
fix lint warnings. Delete unused files
Commit: eca68a131632c259a52f895741a9f8b406755cbb
https://github.com/PathwayCommons/factoid/commit/eca68a131632c259a52f895741a9f8b406755cbb
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-17 (Fri, 17 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
A neo4j-test/search-tests.js
M src/neo4j/index.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
R src/neo4j/starting-neo4j.js
M src/neo4j/test-functions.js
R src/neo4j/test-temp-run.js
Log Message:
-----------
Merge pull request #1145 from PathwayCommons/iss1144-neo4j-searchbygeneid
Iss1144: Neo4j Add Tests for searchbyGeneId()
Commit: bd085411f956768ffeae67a884fa926072946190
https://github.com/PathwayCommons/factoid/commit/bd085411f956768ffeae67a884fa926072946190
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-17 (Fri, 17 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M src/neo4j/neo4j-document.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
Log Message:
-----------
add participantTypes field to edges, make 'ToDo's
Commit: 778ed801ef820b4da1854bd477be0b522e2760e1
https://github.com/PathwayCommons/factoid/commit/778ed801ef820b4da1854bd477be0b522e2760e1
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-17 (Fri, 17 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
M src/neo4j/neo4j-functions.js
Log Message:
-----------
addComplexEdge (untested)
Commit: 6526d7042d0280877d979d5222d04771e6b930c4
https://github.com/PathwayCommons/factoid/commit/6526d7042d0280877d979d5222d04771e6b930c4
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-20 (Mon, 20 Mar 2023)
Changed paths:
M src/neo4j/neo4j-functions.js
Log Message:
-----------
add function to make Complex edge id
Commit: 3ed6db485e4dec22bd0af7b27b78006deb8a06b1
https://github.com/PathwayCommons/factoid/commit/3ed6db485e4dec22bd0af7b27b78006deb8a06b1
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-21 (Tue, 21 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M src/neo4j/neo4j-document.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
Log Message:
-----------
get rid of participantTypes, add new fields to addEdge
Commit: 0619f8ee2d0f5df01fc4e2a38ab7c4bf54451951
https://github.com/PathwayCommons/factoid/commit/0619f8ee2d0f5df01fc4e2a38ab7c4bf54451951
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-21 (Tue, 21 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
Log Message:
-----------
update doc-tests.js with new fields
Commit: 53eb150a693b097e76232e7bc09dbc3635832bb3
https://github.com/PathwayCommons/factoid/commit/53eb150a693b097e76232e7bc09dbc3635832bb3
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-21 (Tue, 21 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
add capability to "make" complexes. Untested
Commit: 34ec845721434d90fa1e027089e558f7121b6af6
https://github.com/PathwayCommons/factoid/commit/34ec845721434d90fa1e027089e558f7121b6af6
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-21 (Tue, 21 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
Handle interactions between complex and non-complex (untested)
Commit: 326fd47434aa9306cd9eab88286e736f16d9c04f
https://github.com/PathwayCommons/factoid/commit/326fd47434aa9306cd9eab88286e736f16d9c04f
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-21 (Tue, 21 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
fix minor errors with interaction handling
Commit: cddda96316a89f801967ca653152088f66d0c878
https://github.com/PathwayCommons/factoid/commit/cddda96316a89f801967ca653152088f66d0c878
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
Handle interactions between 2 complexes (untested)
Commit: 8af40ffbf23b4ef31b339f6be3d1a26ebf3caa47
https://github.com/PathwayCommons/factoid/commit/8af40ffbf23b4ef31b339f6be3d1a26ebf3caa47
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
fix bug in complexEdgesMaker
Commit: b52e3c4471df3a12e3931e85e3b0cb388cd6705a
https://github.com/PathwayCommons/factoid/commit/b52e3c4471df3a12e3931e85e3b0cb388cd6705a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
typo
Commit: 2e6e13fc20399e8511e7b27eeb7727443bf5398a
https://github.com/PathwayCommons/factoid/commit/2e6e13fc20399e8511e7b27eeb7727443bf5398a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
fix bug with complexEdgesMaker
Commit: 95e2422f0ccd47d91db498c7f93702a829ae35de
https://github.com/PathwayCommons/factoid/commit/95e2422f0ccd47d91db498c7f93702a829ae35de
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
delete complexEdgesMaker, integrate into addDocumentsToNeo4j
Commit: 5511c839a1bac344f0c0d8636f14533d2563ba7d
https://github.com/PathwayCommons/factoid/commit/5511c839a1bac344f0c0d8636f14533d2563ba7d
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
change type:'complex' to type:'binding'
Commit: daa4894457e30621f8cbd3e88749565a42cdc092
https://github.com/PathwayCommons/factoid/commit/daa4894457e30621f8cbd3e88749565a42cdc092
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M neo4j-test/search-tests.js
M src/neo4j/index.js
M src/neo4j/neo4j-functions.js
Log Message:
-----------
rename searchByMoleculeId to neighbourhood
Commit: 229eee64d954558883feb653d339b1927217ec6a
https://github.com/PathwayCommons/factoid/commit/229eee64d954558883feb653d339b1927217ec6a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
.element() typo
Commit: a9eb2989290f31b0479d12b0d962692d13a9eec2
https://github.com/PathwayCommons/factoid/commit/a9eb2989290f31b0479d12b0d962692d13a9eec2
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M neo4j-test/doc-tests.js
M src/neo4j/neo4j-document.js
Log Message:
-----------
replace 'N/A' with ''
Commit: a9c80528d3f67088f44dc591ed43ea307e1adb97
https://github.com/PathwayCommons/factoid/commit/a9c80528d3f67088f44dc591ed43ea307e1adb97
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
change complex nested loop indexing (more readable)
Commit: 618c1f8391f093071f381cfecdb778aee595ba70
https://github.com/PathwayCommons/factoid/commit/618c1f8391f093071f381cfecdb778aee595ba70
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-22 (Wed, 22 Mar 2023)
Changed paths:
M neo4j-test/add-nodes-edges.js
M neo4j-test/doc-tests.js
M neo4j-test/search-tests.js
M src/neo4j/index.js
M src/neo4j/neo4j-document.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
Log Message:
-----------
Merge pull request #1147 from PathwayCommons/iss1146-neo4j-complexes
Iss1146: Neo4j Handling Complexes
Commit: 7546a833226ff98cad770f1bb878bede3c6f2105
https://github.com/PathwayCommons/factoid/commit/7546a833226ff98cad770f1bb878bede3c6f2105
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-23 (Thu, 23 Mar 2023)
Changed paths:
M neo4j-test/doc-tests.js
R neo4j-test/doct_tests_2.json
R neo4j-test/doct_tests_3.json
R neo4j-test/doct_tests_4.json
R neo4j-test/doct_tests_5.json
A neo4j-test/document/doct_tests_1.json
A neo4j-test/document/doct_tests_2.json
A neo4j-test/document/doct_tests_3.json
A neo4j-test/document/doct_tests_4.json
A neo4j-test/document/doct_tests_5.json
A neo4j-test/document/testDoc.json
M neo4j-test/search-tests.js
R neo4j-test/testDoc.json
Log Message:
-----------
put json files in separate folder within neo4j-test
Commit: 1024761b6f2c37f5fd3a55e7a9daf23e05373edc
https://github.com/PathwayCommons/factoid/commit/1024761b6f2c37f5fd3a55e7a9daf23e05373edc
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-23 (Thu, 23 Mar 2023)
Changed paths:
A neo4j-test/document/complex_tests_1.json
A neo4j-test/document/complex_tests_2.json
A neo4j-test/document/complex_tests_3.json
A neo4j-test/document/complex_tests_4.json
A neo4j-test/document/complex_tests_5.json
A neo4j-test/document/complex_tests_6.json
Log Message:
-----------
make all complex test json files
Commit: 751d9ceffa917e48ebee7c84153109279d47298c
https://github.com/PathwayCommons/factoid/commit/751d9ceffa917e48ebee7c84153109279d47298c
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-23 (Thu, 23 Mar 2023)
Changed paths:
A neo4j-test/doc-tests-complex.js
Log Message:
-----------
begin test suite, bug discovered for test 1
Commit: b532f35bedf050ef826a869f7f19bda8174fe2a6
https://github.com/PathwayCommons/factoid/commit/b532f35bedf050ef826a869f7f19bda8174fe2a6
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-23 (Thu, 23 Mar 2023)
Changed paths:
M src/neo4j/neo4j-document.js
Log Message:
-----------
fixed bug for first test case
Commit: f8b02a9f0d08e5930ffcdb45bcfcd5ba6d08828b
https://github.com/PathwayCommons/factoid/commit/f8b02a9f0d08e5930ffcdb45bcfcd5ba6d08828b
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-23 (Thu, 23 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
M neo4j-test/doc-tests.js
Log Message:
-----------
test case 1 added
Commit: 6021b03a05a3068897b29858166465f63f88f189
https://github.com/PathwayCommons/factoid/commit/6021b03a05a3068897b29858166465f63f88f189
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-23 (Thu, 23 Mar 2023)
Changed paths:
M neo4j-test/document/complex_tests_2.json
M src/neo4j/neo4j-document.js
Log Message:
-----------
test case 2 changed
Commit: 5b383287c357803688c1a5f1932754e78bd61a96
https://github.com/PathwayCommons/factoid/commit/5b383287c357803688c1a5f1932754e78bd61a96
Author: Jeffrey Wong <[email protected]>
Date: 2023-03-23 (Thu, 23 Mar 2023)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Expire from cache according to time since last edit.
Commit: 18e5054891f40a1cfd0e9c276d45e620588fb292
https://github.com/PathwayCommons/factoid/commit/18e5054891f40a1cfd0e9c276d45e620588fb292
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-24 (Fri, 24 Mar 2023)
Changed paths:
M src/neo4j/query-strings.js
M src/neo4j/test-functions.js
Log Message:
-----------
add testing function getComplexEdge
Commit: 2620ae97fb4e88c68495c967bf1aa424af1fcd94
https://github.com/PathwayCommons/factoid/commit/2620ae97fb4e88c68495c967bf1aa424af1fcd94
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-24 (Fri, 24 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
Log Message:
-----------
test case 2 added
Commit: d3a29e0bedba6d5324281b98f232b1b47b12d23e
https://github.com/PathwayCommons/factoid/commit/d3a29e0bedba6d5324281b98f232b1b47b12d23e
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-24 (Fri, 24 Mar 2023)
Changed paths:
M neo4j-test/document/complex_tests_3.json
M neo4j-test/document/complex_tests_4.json
Log Message:
-----------
test case 3 and 4 changed
Commit: e5bbaf39915ef55837b5877aa41c83a532e39696
https://github.com/PathwayCommons/factoid/commit/e5bbaf39915ef55837b5877aa41c83a532e39696
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-24 (Fri, 24 Mar 2023)
Changed paths:
M neo4j-test/document/complex_tests_4.json
Log Message:
-----------
test case 4 changed
Commit: b4c87777a6c770b1c29f7ed39a09aca0e69a2e7e
https://github.com/PathwayCommons/factoid/commit/b4c87777a6c770b1c29f7ed39a09aca0e69a2e7e
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-24 (Fri, 24 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
Log Message:
-----------
test case 3 added
Commit: 8346f0dc015fceebf8238cd3b11bfb69a8ab9c91
https://github.com/PathwayCommons/factoid/commit/8346f0dc015fceebf8238cd3b11bfb69a8ab9c91
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-24 (Fri, 24 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
Log Message:
-----------
test case 4 added
Commit: fa5eb715aa8b9c47a64b9376c1e9cc975f7b8a7d
https://github.com/PathwayCommons/factoid/commit/fa5eb715aa8b9c47a64b9376c1e9cc975f7b8a7d
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-24 (Fri, 24 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
M src/neo4j/neo4j-document.js
Log Message:
-----------
fixed bug with loop conditionals, test case 5 added
Commit: 457264b614b559df62e8365e63ebbcaaca2ac36e
https://github.com/PathwayCommons/factoid/commit/457264b614b559df62e8365e63ebbcaaca2ac36e
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-24 (Fri, 24 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
M src/neo4j/neo4j-document.js
Log Message:
-----------
fixed bug in addDocumentToNeo4j, test case 5 added
Commit: 5338e07c0bae14821771b259a9e8519ce9211a2a
https://github.com/PathwayCommons/factoid/commit/5338e07c0bae14821771b259a9e8519ce9211a2a
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-27 (Mon, 27 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
M src/neo4j/test-functions.js
Log Message:
-----------
rename getComplexEdge to getEdgeByIdAndEndpoints
Commit: 28d70a61e72f8bf512ad4336836187af6ca608da
https://github.com/PathwayCommons/factoid/commit/28d70a61e72f8bf512ad4336836187af6ca608da
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-27 (Mon, 27 Mar 2023)
Changed paths:
A neo4j-test/doc-tests-complex.js
M neo4j-test/doc-tests.js
R neo4j-test/doct_tests_2.json
R neo4j-test/doct_tests_3.json
R neo4j-test/doct_tests_4.json
R neo4j-test/doct_tests_5.json
A neo4j-test/document/complex_tests_1.json
A neo4j-test/document/complex_tests_2.json
A neo4j-test/document/complex_tests_3.json
A neo4j-test/document/complex_tests_4.json
A neo4j-test/document/complex_tests_5.json
A neo4j-test/document/complex_tests_6.json
A neo4j-test/document/doct_tests_1.json
A neo4j-test/document/doct_tests_2.json
A neo4j-test/document/doct_tests_3.json
A neo4j-test/document/doct_tests_4.json
A neo4j-test/document/doct_tests_5.json
A neo4j-test/document/testDoc.json
M neo4j-test/search-tests.js
R neo4j-test/testDoc.json
M src/neo4j/neo4j-document.js
M src/neo4j/query-strings.js
M src/neo4j/test-functions.js
Log Message:
-----------
Merge pull request #1150 from PathwayCommons/iss1149-neo4j-testing-complexes
Neo4j: Testing Complexes
Commit: f21fbc211d8baacc05796e777c8c9dc99b54aed0
https://github.com/PathwayCommons/factoid/commit/f21fbc211d8baacc05796e777c8c9dc99b54aed0
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-27 (Mon, 27 Mar 2023)
Changed paths:
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
Log Message:
-----------
remove old complex edge function
Commit: ad4967c1cd7df4346c88517c18ce3e1496bb48e5
https://github.com/PathwayCommons/factoid/commit/ad4967c1cd7df4346c88517c18ce3e1496bb48e5
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-28 (Tue, 28 Mar 2023)
Changed paths:
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
Log Message:
-----------
made neighbourhoodWithoutComplexes(id)
Commit: 906ce07f089578f35c20e6a627e61bc70ee9bea2
https://github.com/PathwayCommons/factoid/commit/906ce07f089578f35c20e6a627e61bc70ee9bea2
Author: Max Franz <[email protected]>
Date: 2023-03-28 (Tue, 28 Mar 2023)
Changed paths:
M src/server/routes/api/document/index.js
Log Message:
-----------
Merge pull request #1152 from PathwayCommons/iss1151_img-cache
Image cache: Don't load doc
Commit: e9f9db5357971557f2f1c29c85fa7cde4b2cbeda
https://github.com/PathwayCommons/factoid/commit/e9f9db5357971557f2f1c29c85fa7cde4b2cbeda
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-28 (Tue, 28 Mar 2023)
Changed paths:
M src/neo4j/query-strings.js
Log Message:
-----------
change Molecule to Entity
Commit: 226c484c6f79d1a1cd3124620b3a8f573e9ebf63
https://github.com/PathwayCommons/factoid/commit/226c484c6f79d1a1cd3124620b3a8f573e9ebf63
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-28 (Tue, 28 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
Log Message:
-----------
test case 1 and test case 5 added
Commit: eea202f88eeacae8b4c960fdab1dd90edd269cf1
https://github.com/PathwayCommons/factoid/commit/eea202f88eeacae8b4c960fdab1dd90edd269cf1
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-28 (Tue, 28 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
Log Message:
-----------
test case 2 added
Commit: 7543c257bf99d748bfe2f1ff4974d00b0353a238
https://github.com/PathwayCommons/factoid/commit/7543c257bf99d748bfe2f1ff4974d00b0353a238
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-03-28 (Tue, 28 Mar 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
Log Message:
-----------
test cases 3, 4 and 6 added
Commit: f2fb506af59468a88b0352b1fbef0caa4348b059
https://github.com/PathwayCommons/factoid/commit/f2fb506af59468a88b0352b1fbef0caa4348b059
Author: Jeffrey Wong <[email protected]>
Date: 2023-04-03 (Mon, 03 Apr 2023)
Changed paths:
A neo4j-test/add-nodes-edges.js
A neo4j-test/doc-tests-complex.js
A neo4j-test/doc-tests.js
A neo4j-test/doct_tests_1.json
A neo4j-test/document/complex_tests_1.json
A neo4j-test/document/complex_tests_2.json
A neo4j-test/document/complex_tests_3.json
A neo4j-test/document/complex_tests_4.json
A neo4j-test/document/complex_tests_5.json
A neo4j-test/document/complex_tests_6.json
A neo4j-test/document/doct_tests_1.json
A neo4j-test/document/doct_tests_2.json
A neo4j-test/document/doct_tests_3.json
A neo4j-test/document/doct_tests_4.json
A neo4j-test/document/doct_tests_5.json
A neo4j-test/document/testDoc.json
R neo4j-test/example.js
A neo4j-test/fixtures.js
A neo4j-test/search-tests.js
M package-lock.json
M package.json
M src/model/document/document.js
M src/neo4j/get-doc-functions.js
M src/neo4j/index.js
A src/neo4j/neo4j-document.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
R src/neo4j/starting-neo4j.js
M src/neo4j/test-functions.js
R src/neo4j/test-temp-run.js
M src/server/routes/api/document/index.js
A test/data/document.json
M test/document.js
Log Message:
-----------
Merge branch 'unstable' into imgspd
# Conflicts:
# src/server/routes/api/document/index.js
Commit: 57cd4b12c16fd16b998edd4a5e3af08fa2918bfe
https://github.com/PathwayCommons/factoid/commit/57cd4b12c16fd16b998edd4a5e3af08fa2918bfe
Author: Jeffrey <[email protected]>
Date: 2023-04-03 (Mon, 03 Apr 2023)
Changed paths:
M README.md
M src/config.js
M src/server/routes/api/document/index.js
A src/server/routes/api/document/p-limit.js
Log Message:
-----------
Merge pull request #1143 from PathwayCommons/imgspd
Add controls for max. number of images to generate in parallel
Commit: 3f50da9bc365369e77922f491c9c0bb63ba3fc84
https://github.com/PathwayCommons/factoid/commit/3f50da9bc365369e77922f491c9c0bb63ba3fc84
Author: Linda (Jia Wen) Li <[email protected]>
Date: 2023-04-03 (Mon, 03 Apr 2023)
Changed paths:
M neo4j-test/doc-tests-complex.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
Log Message:
-----------
Merge pull request #1154 from PathwayCommons/iss1153-neo4j-filter-complexes
Neo4j: Complex filter for neighbourhood()
Commit: 872f46e578cd95649d8da3bc55cd8688a5fba0d0
https://github.com/PathwayCommons/factoid/commit/872f46e578cd95649d8da3bc55cd8688a5fba0d0
Author: Jeffrey Wong <[email protected]>
Date: 2023-04-03 (Mon, 03 Apr 2023)
Changed paths:
M .eslintignore
Log Message:
-----------
Ignore file with class fields.
Commit: 73b345292b7412e8a7d017f477bbcf5ab5b4c779
https://github.com/PathwayCommons/factoid/commit/73b345292b7412e8a7d017f477bbcf5ab5b4c779
Author: Jeffrey <[email protected]>
Date: 2023-04-03 (Mon, 03 Apr 2023)
Changed paths:
M .eslintignore
Log Message:
-----------
Merge pull request #1160 from PathwayCommons/iss1158_ignore-p-limit
Ignore file with class fields.
Commit: 6c247f7772a38ba7b06fbb6824fb47339f3908af
https://github.com/PathwayCommons/factoid/commit/6c247f7772a38ba7b06fbb6824fb47339f3908af
Author: Jeffrey Wong <[email protected]>
Date: 2023-04-03 (Mon, 03 Apr 2023)
Changed paths:
M package-lock.json
M package.json
Log Message:
-----------
0.23.0
Commit: e10d418adbe68a5268027637672a76fecfea5318
https://github.com/PathwayCommons/factoid/commit/e10d418adbe68a5268027637672a76fecfea5318
Author: Jeffrey <[email protected]>
Date: 2023-04-03 (Mon, 03 Apr 2023)
Changed paths:
M .eslintignore
M README.md
A neo4j-test/add-nodes-edges.js
M neo4j-test/connect-neo4j.js
A neo4j-test/doc-tests-complex.js
A neo4j-test/doc-tests.js
A neo4j-test/doct_tests_1.json
A neo4j-test/document/complex_tests_1.json
A neo4j-test/document/complex_tests_2.json
A neo4j-test/document/complex_tests_3.json
A neo4j-test/document/complex_tests_4.json
A neo4j-test/document/complex_tests_5.json
A neo4j-test/document/complex_tests_6.json
A neo4j-test/document/doct_tests_1.json
A neo4j-test/document/doct_tests_2.json
A neo4j-test/document/doct_tests_3.json
A neo4j-test/document/doct_tests_4.json
A neo4j-test/document/doct_tests_5.json
A neo4j-test/document/testDoc.json
R neo4j-test/example.js
A neo4j-test/fixtures.js
A neo4j-test/search-tests.js
M package-lock.json
M package.json
M src/config.js
M src/model/document/document.js
M src/neo4j/.env
M src/neo4j/docker-compose.yml
M src/neo4j/get-doc-functions.js
A src/neo4j/index.js
A src/neo4j/neo4j-document.js
M src/neo4j/neo4j-functions.js
M src/neo4j/query-strings.js
R src/neo4j/starting-neo4j.js
A src/neo4j/test-functions.js
R src/neo4j/test-temp-run.js
M src/server/routes/api/document/index.js
A src/server/routes/api/document/p-limit.js
A test/data/document.json
M test/document.js
Log Message:
-----------
Merge pull request #1162 from PathwayCommons/v0.23.0
V0.23.0
Compare:
https://github.com/PathwayCommons/factoid/compare/449dddac33ac...e10d418adbe6
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