Code

Neo4jv5#92

Code

Merged

yuanzhou merged 112 commits intodev-integratex-atlas-consortia/ubkg-api:dev-integratefrom neo4jv5x-atlas-consortia/ubkg-api:neo4jv5Copy head branch name to clipboardApr 12, 2024

+10,016-772

Commits

Commits on Dec 11, 2023

• Branch created as per ubkg-api#87

  ChuckKollar

  committed
  042d109

Commits on Jan 23, 2024

• Updated project.toml to reflect V5 of neo4j

  ChuckKollar

  committed
  6e4d3f6

Commits on Jan 24, 2024

• Updated the minor version in pyproject.toml

  ChuckKollar

  committed
  a678fdb

Commits on Jan 25, 2024

• 1. Updated README.md to synchronize instructions with those for hs-ontology-api, especially developer instructions.

  Show description for ec35fed
  AlanSimmons

  committed
  ec35fed

• Removed artifacts from .gitignore

  AlanSimmons

  committed
  0818ea1

• Removed artifacts from .gitignore

  AlanSimmons

  committed
  c4e6bd1

Commits on Jan 26, 2024

• Corrected query for codes_code_id_codes_get function so that it accepts list of SABs and includes the specified code in the response (i.e., if code_id = X, the response includes X).

  AlanSimmons

  committed
  4234f9e

• Corrected query for codes_code_id_codes_get function so that it accepts list of SABs and includes the specified code in the response (i.e., if code_id = X, the response includes X).

  AlanSimmons

  committed
  d50cfa9

• updated spec yaml for codes/{code-id}/codes endpoint and response object

  AlanSimmons

  committed
  4bfd833

Commits on Jan 30, 2024

• Added 404 error handling to endpoints that we want to keep; updated spec YAML

  AlanSimmons

  committed
  cef29f0

• Added 404 error handling to endpoints that we want to keep; updated spec YAML; started archive of deprecated code

  AlanSimmons

  committed
  71b91a9

• Deprecated semantics and tui routes. Added 404 error checks to endpoints.

  AlanSimmons

  committed
  eb61586

Commits on Jan 31, 2024

• Deprecated semantics and tui routes. Added 404 error checks to endpoints. Updated documentation.

  AlanSimmons

  committed
  76ca3c0

Commits on Feb 1, 2024

• Converted 2 of 4 POST endpoints in the concepts routes into GETS.

  AlanSimmons

  committed
  67801f8

• Converted all POST endpoints to GET; new test script.

  AlanSimmons

  committed
  988225b

• 1. Cleaned up ubkg-api-spec.yaml.

  AlanSimmons

  committed
  8579ac3

Commits on Feb 5, 2024

• New route: concepts/<concept-id>/paths/expand, using new code. New configuration to limit payload size.

  AlanSimmons

  committed
  825369d

Commits on Feb 6, 2024

• Added origin object to path-related responses.

  AlanSimmons

  committed
  8ed3525

• Fixed size calcuation of payload in check_payload_size; use ROWLIMIT in app.cfg only to set the default for LIMIT.

  AlanSimmons

  committed
  549f036

• Refactored /concept/<concept_id>/paths/shortestpath endpoint

  AlanSimmons

  committed
  cd4c7e2

• Refactored /concept/<concept_id>/paths/trees endpoint

  AlanSimmons

  committed
  31936d1

Commits on Feb 7, 2024

• New /concepts/subgraphs endpoint

  AlanSimmons

  committed
  b2a2a95

• Updated test script for revised paths endpoints; Started Release notes; bumped version to 2.

  AlanSimmons

  committed
  6885b6f

• New version of semantics/semantictypes endpoint.

  AlanSimmons

  committed
  eaa0b5a

• New version of semantics/semantictypes endpoint.

  AlanSimmons

  committed
  5667c91

Commits on Feb 8, 2024

• Changed shortestpath route to include terminus_concept_id as a path parameter instead of a query parameter. Renamed concept_id (query_concept_id) to origin_concept_id and target_concept_id to termi…

  Show description for 3d6bd5b
  AlanSimmons

  committed
  3d6bd5b

• Reorganized endpoints, moving shortestpath.

  AlanSimmons

  committed
  2e1917c

• Refactored semantics/<identifier>/semantic_types endpoint to use a path parameter.

  AlanSimmons

  committed
  db87583

• New semantics/semantic_types endpoint

  AlanSimmons

  committed
  33d11e1

Commits on Feb 9, 2024

• New concepts/<identifier>/nodes endpoint

  AlanSimmons

  committed
  a75af8c

• New concepts/<search>/nodes endpoint

  AlanSimmons

  committed
  e12fbeb

• New database/info/server endpoint; new compatibility checking function, which currently is used for the concepts/subgraph endpoint.

  AlanSimmons

  committed
  f42ae07

• release note update

  AlanSimmons

  committed
  2d38d93

• Initial commit of ubkg_api Dockerization for Data Distillary

  

  kburke

  committed
  149102a

Commits on Feb 10, 2024

• Revised endpoints for semantic_types into semantic_types and semantic_subtypes

  AlanSimmons

  committed
  a378e23

Commits on Feb 11, 2024

• Removed name property from database/server endpoint.

  AlanSimmons

  committed
  9281110

• Rearranged path for semantics/semantic_types/{identifier} and semantics/semantic_subtypes/{identifier}

  AlanSimmons

  committed
  b346b48

• Updated release notes

  AlanSimmons

  committed
  bcb848b

Commits on Feb 12, 2024

• New node_types routes

  AlanSimmons

  committed
  7814e6e

• Test for node_types routes; refinement to semantic_types and semantic_subtype routes.

  AlanSimmons

  committed
  2c43928

• New property_types endpoint; updated release notes

  AlanSimmons

  committed
  4f2637e

• New relationship_types endpoint; updated release notes

  AlanSimmons

  committed
  b44278b

• updated test

  AlanSimmons

  committed
  f566d04

• new sabs/codes/counts and sabs/codes/details endpoints

  AlanSimmons

  committed
  5c5e1ba

Commits on Feb 13, 2024

• Updates to test script; revision of paths in controllers to conform to DevOps guidelines; updates to release notes.

  AlanSimmons

  committed
  82da56b

Commits on Feb 14, 2024

• Cleanup of code (whitespace, etc.)

  AlanSimmons

  committed
  c81bc6a

• Corrections to test script

  AlanSimmons

  committed
  deb70e3

• Split semantics/semantic_types and semantics/subtypes code; corrected yaml and corresponding routes; improved iserr logic for missing sub-class data in returns

  AlanSimmons

  committed
  be10f66

• Code review changes per Joe

  

  kburke

  committed
  6933b89

• Code review change per Joe, rename Docker network

  

  kburke

  committed
  778fa60

• Improved test script; improved 404 error responses for some endpoints.

  AlanSimmons

  committed
  a65fe83

• Revision to release notes

  AlanSimmons

  committed
  6d6b33e

• Revision to release notes

  AlanSimmons

  committed
  4339513

Commits on Feb 15, 2024

• Match networks: entry for network name with services:ubkg-api:networks: entry.

  

  kburke

  committed
  c06d8be

Commits on Feb 16, 2024

• Bug fix for /paths/trees endpoint that checks for mindepth value for case of no mindepth specified in query.

  AlanSimmons

  committed
  a18cd66

• Bug fix for /paths/trees endpoint that checks for mindepth value for case of no mindepth specified in query.

  AlanSimmons

  committed
  f77500e

• Bug fix for /paths/trees endpoint that checks for mindepth value for case of no mindepth specified in query.

  AlanSimmons

  committed
  c442d78

• .gitignore

  AlanSimmons

  committed
  afe0357

• .gitignore

  AlanSimmons

  committed
  b6c800e

• .gitignore

  AlanSimmons

  committed
  206568a

• .gitignore

  AlanSimmons

  committed
  f25281c

• Replacing underscores with hyphens

  AlanSimmons

  committed
  bfb9c25

• Replacing underscores with hyphens

  AlanSimmons

  committed
  d7dfb27

• Replacing underscores with hyphens; release notes

  AlanSimmons

  committed
  45c31f6

• Merge pull request #97 from x-atlas-consortia/simmons/neo4jv5

  Show description for 5e610cf
  yuanzhou

  authored
  5e610cf

• Resolved merge conflicts from Alan's latest work

  

  kburke

  committed
  018fb58

• Merge pull request #96 from x-atlas-consortia/karlburke/DataDistilleryDockerizationOfubkg_api

  Show description for 6988b83
  yuanzhou

  authored
  6988b83

Commits on Feb 20, 2024

• Separate copy of DD API spec YAML.

  AlanSimmons

  committed
  03aba8f

• Configuration of Docker network

  

  kburke

  committed
  306b20e

• Separate copy of DD API spec YAML.

  AlanSimmons

  committed
  83153e2

• Merge pull request #98 from x-atlas-consortia/simmons/19FEB2024/neo4jv5

  Show description for e6d36b5
  yuanzhou

  authored
  e6d36b5

Commits on Feb 23, 2024

• Placedholder for logs directory to avoid permission issues during deployment

  

  kburke

  committed
  d3bf1c0

• Rename logging directory to log, aligned with docker-compose.yml and uwsgi.config

  

  kburke

  committed
  80908eb

• Remove unused logs directory

  

  kburke

  committed
  015523c

• Merge pull request #99 from x-atlas-consortia/karlburke/DataDistilleryDockerizationOfubkg_api

  Show description for 34a859c
  yuanzhou

  authored
  34a859c

• Ignore config

  yuanzhou

  authored
  a187b29

Commits on Feb 26, 2024

• Updated SmartAPI YAMLs for both ubkg and dd to add explicit schemas for array responses from /concepts/{id}/codes and terms/{term_id}/concepts

  AlanSimmons

  committed
  a15d072

• Merge pull request #100 from x-atlas-consortia/simmons/19FEB2024/neo4jv5

  Show description for 1285d0c
  yuanzhou

  authored
  1285d0c

Commits on Feb 27, 2024

• Status endpoint code

  ChuckKollar

  committed
  3d41fde

Commits on Feb 28, 2024

• Added API key documentation

  AlanSimmons

  committed
  a6f453c

• Added API key documentation

  AlanSimmons

  committed
  8472340

• Added API key documentation

  AlanSimmons

  committed
  bd56a2d

• api.key

  AlanSimmons

  committed
  47c73d3

• api.key

  AlanSimmons

  committed
  18f709d

Commits on Feb 29, 2024

• api.key

  AlanSimmons

  committed
  c4c4c7b

• Merge pull request #102 from x-atlas-consortia/simmons/28feb/neo4jv5

  Show description for 63359d7
  shirey

  authored
  63359d7

Commits on Mar 4, 2024

• Set up nginx to accept X-API-KEY header

  

  kburke

  committed
  7e60987

• Fix nginx to accept X-API-KEY header

  

  kburke

  committed
  00c7e54

• remove errant X-API-KEY line

  

  kburke

  committed
  110eddc

• Merge pull request #101 from x-atlas-consortia/add_status_endpoint

  Show description for 9d47d4f
  yuanzhou

  authored
  9d47d4f

• Merge pull request #103 from x-atlas-consortia/karlburke/EnableXAPIKeyHeader

  Show description for 4f967f0
  yuanzhou

  authored
  4f967f0

Commits on Mar 7, 2024

• Bug fixes: 1. semantics_controller.py: rearranged URL order for semantics/semantic-types/<semantic_type> and semantics/<semantic_type>/subtypes 2. Corrected test scripts.

  AlanSimmons

  committed
  0c7413c

Commits on Mar 8, 2024

• Merge pull request #104 from x-atlas-consortia/simmons/07mar/neo4jv5

  Show description for 60f798a
  yuanzhou

  authored
  60f798a

Commits on Mar 11, 2024

• Bug fixes: 1. Corrected controller for path for semantics/<semantic_type>/subtypes 2. Corrected test scripts.

  AlanSimmons

  committed
  bf20e45

• Merge pull request #106 from x-atlas-consortia/simmons/11mar/neo4jv5

  Show description for f1189dd
  yuanzhou

  authored
  f1189dd

• Bug fixes: 1. Corrected controller for path for semantics/<semantic_type>/subtypes 2. Corrected test scripts.

  AlanSimmons

  committed
  edb1f16

Commits on Mar 12, 2024

• Merge pull request #108 from x-atlas-consortia/simmons/11mar/neo4jv5

  Show description for 4688bba
  yuanzhou

  authored
  4688bba

• Create python-app.yml

  DerekFurstPitt

  authored
  c20af3e

• fixed path to requirements doc to align with ubkg-api's format

  DerekFurstPitt

  committed
  35a3a8a

Commits on Mar 19, 2024

• Refactored concepts/{id}/paths/expand to return in paths/nodes/edges format.

  AlanSimmons

  committed
  ff1ac25

Commits on Mar 22, 2024

• Refactored concepts/{id}/paths/expand to return in paths/nodes/edges format; removed "convenience" endpoint descriptions from spec yamls; updated ubkg-api-spec.yaml to differ from dd-api-spec.yaml

  AlanSimmons

  committed
  1f0c324

Commits on Mar 25, 2024

• Refactored concepts/{id}/paths/expand to return in Table result frame (paths/nodes/edges) format; removed "convenience" endpoint descriptions from spec yamls; updated ubkg-api-spec.yaml to differ f…

  Show description for 4f1caba
  AlanSimmons

  committed
  4f1caba

Commits on Mar 26, 2024

• Supply a package_base_dir when instantiating UbkgAPI

  ChuckKollar

  committed
  a3a18f6

Commits on Apr 2, 2024

• Reconciled differences in app.py between branches simmons/14mar2024/neo4jv5 and neo4jv5.

  AlanSimmons

  committed
  a42731c

• Bumped version in pyproject.toml

  AlanSimmons

  committed
  d758f57

Commits on Apr 3, 2024

• Reverted version in pyproject.toml

  AlanSimmons

  committed
  5875cc1

• Merge pull request #111 from x-atlas-consortia/Derek-Furst/setup-python3.9

  Show description for 7357a73
  yuanzhou

  authored
  7357a73

• Fix typo

  yuanzhou

  authored
  f759715

Commits on Apr 4, 2024

• Merge pull request #112 from x-atlas-consortia/simmons/14mar2024/neo4jv5

  Show description for 9d2fc6a
  yuanzhou

  authored
  9d2fc6a

Commits on Apr 10, 2024

• Specify Path object for BULD/VERSION base package

  yuanzhou

  authored
  ae9f9c3

• Bump version to 2.1.1

  yuanzhou

  authored
  50fea55

• Merge pull request #115 from x-atlas-consortia/yuanzhou/fix-status-uwsgi

  Show description for 25cc0ce
  yuanzhou

  authored
  25cc0ce