song-docker-1.0.2

• updated song-server, song-client and db schema to song-1.0.2
• updated minio to RELEASE.2018-05-11T00-29-24Z
• update score to 1.1.1

song-1.0.2

Summary:

Bug Fixes:

• reverted jsonb type to json for Info table

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Downloads

Song-Client-1.0.2 Distribution

Song-Server-1.0.2 Distribution

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Details

Full Changelog

Merged pull requests:

• fix(Revert): changed back to json type instead of jsonb #275 (rtisma)

song-1.0.1

Summary

Bug Fixes:

• fixed endpoint security for the export service

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Downloads

Song-Client-1.0.1 Distribution

Song-Server-1.0.1 Distribution

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Details

Full Changelog

Merged pull requests:

• fix(Security): secured export endpoint #274 (rtisma)
• updated python sdk to 1.0.0 #273 (rtisma)

song-1.0.0

Full Changelog

Summary

Bug Fixes:

• Info fields for some entities are not created
• Some entities do not implement Equals, HashCode and ToString properly
• Python-SDK StudyClient errors when trying to read a study
• Incorrect setting order for Study organization and description
• Incorrect message context for Analysis errors
• Python-SDK Dataclasses 0.4

New Features/Enhancements:

• Export service to generate payloads for SONG data, used for mirroring SONG instances
• Improved error handling
• Doubled the amount of tests, with significantly increased coverage
• Improved Swagger UI descriptions
• Improved song-docker documentation (README.md)

Transitioning from 0.x.x to 1.0.0

The following schema definitions must be added to the production database

DROP VIEW IF EXISTS BusinessKeyView;
CREATE VIEW BusinessKeyView AS
  SELECT
    S.id as study_id,
    SP.id AS specimen_id,
    SP.submitter_id AS specimen_submitter_id,
    SA.id AS sample_id,
    SA.submitter_id AS sample_submitter_id
  FROM Study S
    INNER JOIN Donor D ON S.id = D.study_id
    INNER JOIN Specimen SP ON D.id = SP.donor_id
    INNER JOIN Sample SA ON SP.id = SA.specimen_id;

DROP VIEW IF EXISTS InfoView;
CREATE VIEW InfoView AS
  SELECT
    A.id as analysis_id,
    I_STUDY.info as study_info,
    I_DONOR.info as donor_info,
    I_SP.info as specimen_info,
    I_SA.info as sample_info,
    I_A.info as analysis_info,
    I_F.info as file_info
    FROM Study S
      INNER JOIN Info I_STUDY ON I_STUDY.id = S.id and I_STUDY.id_type = 'Study'
      INNER JOIN Donor D ON S.id = D.study_id
      INNER JOIN Info I_DONOR ON I_DONOR.id = D.id and I_DONOR.id_type = 'Donor'
      INNER JOIN Specimen SP ON D.id = SP.donor_id
      INNER JOIN Info I_SP ON I_SP.id = SP.id and I_SP.id_type = 'Specimen'
      INNER JOIN Sample SA ON SP.id = SA.specimen_id
      INNER JOIN Info I_SA ON I_SA.id = SA.id and I_SA.id_type = 'Sample'
      INNER JOIN SampleSet SS on SA.id = SS.sample_id
      INNER JOIN Analysis A on  SS.analysis_id = A.id
      INNER JOIN Info I_A ON I_A.id = A.id and I_A.id_type = 'Analysis'
      INNER JOIN File F on  A.id = F.analysis_id
      INNER JOIN Info I_F ON I_F.id = F.id and I_F.id_type = 'File';

DROP VIEW IF EXISTS IdView;
CREATE VIEW IdView AS
  SELECT DISTINCT
    A.id as analysis_id,
    A.type as analysis_type,
    A.state as analysis_state,
    A.study_id as study_id,
    D.id as donor_id,
    SP.id as specimen_id,
    SA.id as sample_id,
    F.id as object_id
  FROM Donor D
    INNER JOIN Specimen SP on D.id = SP.donor_id
    INNER JOIN Sample as SA on SP.id = SA.specimen_id
    INNER JOIN SampleSet as SAS on SA.id = SAS.sample_id
    INNER JOIN File as F on SAS.analysis_id = F.analysis_id
    INNER JOIN Analysis as A on SAS.analysis_id = A.id;

Misc:

• Removed song-importer since JDBI is no longer being used
• Replaced JDBI with Hibernate

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Downloads

Song-Client-1.0.0 Distribution

Song-Server-1.0.0 Distribution

Song-Python-SDK-1.0.0 PyPi Distribution

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Details

Implemented enhancements:

• Replace JBDI with Hibernate #258
• EGO/SONG Support - Tag new JWT based strategy #239
• EGO/SONG Support - Create JWT Strategy #238
• Add DB logging configuration #216
• Update Docker README #202
• Add Certs and TLS to song-aws server #192
• Improve error handling for all endpoints #168
• [SONG-PYTHON-SDK] Release song python sdk 0.3.9 #163
• Song on amazon #160
• Add documentation to song-python-sdk #148
• [SONG-SERVER] update Swagger with aliased names #102
• Pom cleanup #242 (rtisma)
• song-191-update-dataclases #212 (rtisma)
• Feature/song 148 sdk instructions #206 (rtisma)
• Feature/song 148 python sdk documentation #203 (rtisma)
• Feature/song 196 aws importer2 #201 (rtisma)
• Feature/read me update docker #200 (rtisma)

Fixed bugs:

• Specimen and Donor info fields not created after payload upload #244
• Missing index files from song.collab for FI206869 #199
• Update to dataclasses 0.4 #191
• StudyClient does not work #188
• Modelling of Normal Submitted Sample ID is incorrect #183
• Publish command not working #182
• Specimen and Donor is not required for a Sample in VariantCall JsonSchema #173
• [SONG-SERVER] Connection pool closes when subsequent infoSearch requests are made #169
• [SONG-SERVER] Duplicate Random Unique AnalysisId created when payload does not contain submittedAnalysisId #167
• Fix Postgres cache lookup issue #125
• Feature/song 183 incorrect normal submitted sample #208 (rtisma)

Closed issues:

• Generate payloads for DKFZ #255
• EGO/SONG Support - Unit Tests for Existing and New Security #237
• Add publish test using WireMock #231
• Build Circle-CI for Song #223
• Collect .meta files for DKFZ #221
• Database dump for DKFZ #196
• Prepare second batch of metadata for DKFZ PCAWG data objects #166

Merged pull requests:

• Feature/song 258 replace jdbi with hibernate #270 (rtisma)
• refactor: Removed includeOtherIds feature. #268 (rtisma)
• Feature/random cleanup #267 (rtisma)
• Feature/song 188 study client fix #265 (rtisma)
• fix: Fixed export client and typos #264 (rtisma)
• Feature/song 255 dkfz payloads #2 #262 (rtisma)
• ExportService #261 (rtisma)
• Add Circle Ci build job #248 (jonathanganesh)
• Feature/song 244 missing info payload fix #246 (rtisma)
• Feature/song 231 publish test wiremock #233 (rtisma)
• Feature/song 182 sdk publish command fix #218 (rtisma)
• song-173-json-schema-update #217 (rtisma)
• song-168-fix-read-status-codes #215 (rtisma)
• Feature/song 183 refactored filtering #211 (rtisma)
• updated versions to 0.3.9 #187 (rtisma)

song-0.3.9

New

1. Song Python SDK 0.3.9 Release (Issue #133, #149, #153, #154 and PR #152)
   • Available on PyPi (refer to Downloads sections below)
   • Compatible with song-server 0.3.9
   • Created ReadTheDocs with tutorials and an sdk reference: https://song-docs.readthedocs.io/en/develop/index.html

Enhancements

1. Issue #165 and #102: [SONG-SERVER] Updated swagger documentation (PR #177)
   • Enabled authorization only for endpoints doing PUT, POST or DELETE operations
   • added basic api info
   • added api-docs redirect to swagger-ui.html

Bug Fixes

1. Issue #167: [SONG-SERVER] Duplicate random AnalysisId created when payload does not contain submittedAnalysisId (PR #179)
2. Issue #169: [SONG-SERVER] Connection pool closes when subsequent infoSearch requests are made (PR #180)

Breaking Changes

1. PR #177: getStudy no longer returns a list of studies, but a single study if it exists, or null if it does not

Downloads

Song-Client-0.3.9 Distribution

Song-Server-0.3.9 Distribution

Song-Python-SDK-0.3.9 PyPi Distribution

song-0.3.8

song-0.3.8 (2018-01-19)

Full Changelog

Implemented enhancements:

• SONG - Update to support manifest ID downloads #139

Fixed bugs:

• FI9995 not searchable in song-client #129

Closed issues:

• Support multiple studies in SONG configuration #140
• 6 - Rethink CLI client #137
• 2 - Python Song SDK #133
• Update JsonSchemas and Postrgres Schemas for optional fields #127
• Multiple save error #124

Merged pull requests:

• fixed failing tests due to more than expected entries in test_db #156 (rtisma)
• fixed bug and added test #155 (rtisma)
• Feature/add entity endpoint #143 (rtisma)
• fixed-duplicate-info-id-bug #131 (rtisma)
• Feature/db index optimize #130 (rtisma)
• Feature/docker update example #119 (rtisma)
• updated docker with song-0.3.7 and id-5.1.4 #118 (rtisma)
• updated since analysisSubmitterId no longer exists #117 (rtisma)

song-0.3.7

song-0.3.7 (2017-12-04)

Full Changelog

Implemented enhancements:

• Change server error logs to be actual stacktrace #95

Merged pull requests:

• Feature/dcc 5752 optional schema2 #116 (rtisma)
• Bugfix: Swapped parameters of call to idService, as per ticket. #115 (KevinFHartmann)
• Feature/dcc 5749 song study id configuration and payload usage #114 (KevinFHartmann)
• Feature/update dcc id 5.1.4 #113 (rtisma)
• updated release versions #112 (rtisma)
• feature/dcc-5726-disable-entity-endpoints #111 (rtisma)
• updated to dcc-id release version 5.1.3 #110 (rtisma)
• Feature/file id bug #109 (rtisma)
• Feature/update object storage #108 (rtisma)
• Feature/dcc 5738 customizable scope prefix #107 (rtisma)
• detect-missing-study-id #106 (rtisma)
• Minor code cleanup. Death to mutating loops. #100 (andricDu)
• Kafka Support #93 (andricDu)
• Docker for Song - Configuration1 #92 (rtisma)
• fixed swagger issue #91 (rtisma)
• updated validation delay for prod to be fast by default and slow for … #90 (rtisma)
• dcc-5707-multiple-save-error #89 (rtisma)
• dcc-5688-info-object #88 (rtisma)
• added-tabs-to-manifest.txt #87 (rtisma)
• updated client dist package #86 (rtisma)
• removed analysisAccess, added fileAccess #85 (rtisma)
• Feature/add access analysis #84 (rtisma)