- Emojis: ? x2
- Categories: Other Changes x2
- #696 - 📝 add new experiment strategy - a05c799c by HuangXiaoyan0106
- #695 - 🐛 Force Tag info in GH action - 479c409f by haynescd
- Emojis: ? x2
- Categories: Other Changes x2
- #693 - ✅ update workflow_type and data_tyep enum - b0efce4e by HuangXiaoyan0106
- #691 - ⬆️ Upgrade actions/checkout to v4 - 20b64b4c by haynescd
- Emojis: ? x1
- Categories: Other Changes x1
- Emojis: ? x3, ✨ x3, 👨🏻💻 x1, ⬆️ x1
- Categories: Additions x3, Ops x1, Other Changes x4
- #688 - 🐛 Update Tag of dataservice image - ae8831e7 by haynescd
- #686 - 🐛 Update GH Action to use correct branch - 4646d950 by haynescd
- #679 - ✨ AD-2303 add amount and amount_units - 1ac116a9 by chris-s-friedman
- #680 - ✨ Add has_matched_normal and collection_id - f3da17b1 by chris-s-friedman
- #685 - 👷 Add Github Action to build and deploy dev image when merged to master - 56cd60cc by haynescd
- #684 - 👨🏻💻 Always bind all interfaces when app runs in docker-compose - 7370bbd6 by znatty22
- #681 - ✨ D3B-674 Add cavatica related gf fields - 182f4b2b by chris-s-friedman
- #682 - ⬆️ Bump Werkzeug from 0.15.3 to 0.15.5 - 645d888b by chris-s-friedman
- Emojis: ✨ x1
- Categories: Additions x1
- Emojis: 🐛 x1
- Categories: Fixes x1
- Emojis: ♻️ x1
- Categories: Additions x1
- Emojis: ♻️ x1, ✨ x1
- Categories: Additions x2
- #670 - ♻️ Refactor biobank_contact to be two columns - ef9eb9e5 by znatty22
- #668 - ✨ Add biobank_contact to Study table - a470710f by znatty22
- Emojis: ♻️ x1, ✨ x2, ? x1
- Categories: Additions x3, Other Changes x1
- #667 - ♻️ Don't delete samples with 0 biospecimens - 6eddc7c7 by znatty22
- #665 - ✨ New sample-relationships API - 51995c37 by znatty22
- #661 - 🗃️ Migration for Biospecimen.specimen_status - 83e2ed49 by znatty22
- #660 - ✨ Add Biospecimen.specimen_status - 0d3f1aab by znatty22
- Emojis: ? x1
- Categories: Other Changes x1
- Emojis: ♻️ x1, ✨ x3
- Categories: Additions x4
- #656 - ♻️ Rename GenomicFile.release_status - 6352c4d1 by znatty22
- #655 - ✨ Modify GenomicFile release_status, data_type enums - 8462709f by znatty22
- #653 - ✨ Track parent studies - 40a4a7a9 by znatty22
- #650 - ✨ Add new SE, GF columns for Bix - 4ae8899b by znatty22
- Emojis: 🔥 x1
- Categories: Removals x1
- Emojis: ✨ x2
- Categories: Additions x2
- #646 - ✨ Add new Sample table and API - 76cbf79f by znatty22
- #642 - ✨ Add preservation method to biospecimen - f68ba490 by znatty22
- Emojis: ? x1
- Categories: Other Changes x1
- Emojis: ? x1
- Categories: Other Changes x1
- Emojis: ? x1
- Categories: Other Changes x1
- Emojis: ⬆️ x1, ? x1, ✨ x1
- Categories: Additions x1, Ops x1, Other Changes x1
- #633 - ⬆️ update builder from alpine 3.7 -> 3.18 - 2391bf51 by devbyaccident
- #632 - 🐛 Loosen ACL restriction - 7cf4f80b by znatty22
- #624 - ✨ Store ACL in new authz field - bf13d28c by znatty22
- Emojis: 🔧 x1
- Categories: Ops x1
- Emojis: ? x4, 📝 x1, 🐛 x1, 🔥 x1
- Categories: Documentation x1, Removals x1, Fixes x1, Other Changes x4
- #627 - ✨ add snRNAseq experiment strategy - cf23ffe8 by calkinsh
- #621 - ✨ Add Saliva Kit to SAMPLE_PROCUREMENT_ENUM for Letra - 18ad0315 by r3m0chop
- #625 - 🐛 Fix port mapping in docker-compose - 634ffca7 by znatty22
- #614 - 📝 point documentation at the kidsfirstdrc.org domain, not kids-first.io - b080a869 by chris-s-friedman
- #622 - 🐛 Fix indexd POST error handling - 73755b5c by znatty22
- #623 - 👥 Add codeowners - 232cc46e by znatty22
- #620 - 🔥 Remove existing .DS_Store files and update .gitignore - 3903b983 by r3m0chop
- Emojis: ✨ x1, ? x1, 🐛 x2
- Categories: Additions x1, Fixes x2, Other Changes x1
- #618 - ✨ add scRNA as enumeration for experiment strategy - a3c29bc6 by calkinsh
- #611 - ⬆️ Upgrade to latest psycopg2 - 0f2f247b by znatty22
- #616 - 🐛 Fix dev setup again - 52ab9f11 by znatty22
- #610 - 🐛 Fix local dev setup and instructions - 7705f2b7 by znatty22
- Emojis: 👩💻 x1, ✨ x1
- Categories: Additions x1, Other Changes x1
- #605 - 👩💻 Improve developer setup - cb55bd56 by znatty22
- #604 - ✨ Add visibility reason and comment columns - e1be5564 by znatty22
- Emojis: ✅ x1, 🔥 x1, ✨ x2, 🔧 x1
- Categories: Additions x3, Removals x1, Ops x1
- #602 - ✅ update tests based on new sequencing_exp enums - 245e2829 by chris-s-friedman
- #600 - 🔥 remove polya_stranded library_prep - cc47b9e3 by chris-s-friedman
- #599 - ✨ Add ONT platform - 6c41ed87 by Christina-J-Diaz
- #598 - 🔧 add more data types from bix pipeline outputs - 688c1cb4 by chris-s-friedman
- #594 - ✨ Update enum values for sequencing_experiment - 8b3bf07e by youngnm
- Emojis: ✨ x1
- Categories: Additions x1
- #589 - ✨ add data_type enums of bix workflows - ebcc507e by chris-s-friedman
- Emojis: ✨ x1, 👷♀️ x1
- Categories: Additions x1, Other Changes x1
- #587 - ✨ Add Predisposition to DIAGNOSIS_CATEGORY_ENUM - 20eb95af by youngnm
- #583 - 👷♀️ Automate tagging and release generation - 846cfb92 by znatty22
- Emojis: 📝 x1, ✨ x2, 📌 x1
- Categories: Additions x2, Documentation x1, Ops x1
- #582 - 📝 Update project ID in link to codacy badge - 137aff2d by znatty22
- #581 - ✨ Add Methylation to EXPERIMENT_STRATEGY_ENUM - 3b484b8c by youngnm
- #550 - ✨ Add study fields: short_code, program, domain - d074e9bf by znatty22
- #577 - 📌 Pin PyYAML to avoid apispec breaking - e34e284f by znatty22
- Emojis: 🐛 x1
- Categories: Fixes x1
- #575 - 🐛 Fix Homo sapiens casing - 97ea96d9 by liberaliscomputing
- Emojis: ✨ x1, 🐛 x1, 📝 x1
- Categories: Additions x1, Documentation x1, Fixes x1
- #572 - ✨ Add Fly and 🐭 - 8980e6b6 by liberaliscomputing
- #565 - 🐛 Allow larger values for SE total_reads - 98f69e74 by fiendish
- #566 - 📝 Update development init instructions - 99d4dcff by fiendish
- Emojis: 💬 x2, 🐛 x1
- Categories: Fixes x3
- #562 - 💬 Add familial collection labels - b48f88c9 by fiendish
- #560 - 🐛 Added CIDR for prd - 01f5eb2d by alubneuski
- #559 - 💬 Add procurement string for marrow - 2fa31e22 by fiendish
- Emojis: 🐳 x1, ⏪ x1, ✨ x1, ? x1
- Categories: Ops x1, Removals x1, Additions x1, Other Changes x1
- #554 - 🔧 Migrated to the standard deploy - ccb5b36b by alubneuski
- #551 - 🐳 Publish port for postgres database - b4d8983f by chris-s-friedman
- #548 - ⏪ Revert authz changes - 665fb538 by dankolbman
- #539 - ✨ Add Indexd authz field - e76c79c2 by dankolbman
Adds new fields to entities.
Feature Emojis: ⬆️x2 ✨x1 📝x1 Feature Labels: data model x1 feature x1 documentation x1 bug x1 devops x1
- (#543) ✨ Add new attributes to participant, biospecimen, seq exp - @znatty22
- (#545) 📝 Update README w new ERAlchemy install instruction - @znatty22
- (#544) ⬆️ Bump pytest to 5.2.0 - @znatty22
- (#534) ⬆️ Bump werkzeug from 0.14.1 to 0.15.3 - @dependabot[bot]
Fixes issue with pagination potentially skipping entries with similiar creation dates.
Feature Emojis: ✨x1 Feature Labels: bug x1 feature x1 refactor x1
- (#529) ✨ Add pagination by uuid - @dankolbman
Feature Emojis: ✨x1 🐛x1 Feature Labels: feature x1 bug x1
- (#526) ✨ Add New Data Type Enums for Somatic Mutation Analysis - @liberaliscomputing
- (#522) 🐛 Add missing groupby for sequencing center - @dankolbman
Hot fix to the dockerfile build.
Feature Emojis: ♻️x1 Feature Labels: refactor x1
- (#519) ♻️ Make Dockerfile follow best practices - @znatty22
Minor operations changes.
Feature Emojis: 🔊x2 🐳x1 ⬆️x1 ✨x1 Feature Labels: devops x4 refactor x1
- (#515) 🐳 Remove venv from docker - @dankolbman
- (#516) 🔊 Move log formatting to nginx.conf - @dankolbman
- (#512) ⬆️ Bump postgres to 11.1 - @dankolbman
- (#514) 🔊 Add response timing to logs - @dankolbman
- (#511) ✨ Exclude fkey lists from genomic-files and biospecimens results - @parimalak
Adds index to created_at column for better pagination performance.
Feature Emojis: ⬆️x1 🗃x1 ✏️x1 🐳x1 x1 Feature Labels: refactor x2 data model x1 devops x1
- (#508) ⬆️ Bump webargs version - @dankolbman
- (#507) 🗃 Add indices to created_at - @dankolbman
- (#505) ✏️ SG doc typo - @fiendish
- (#501) 🐳 Add dataservice to kf-data-stack network - @znatty22
- (#500) 💬 add linked longread 10x sequencing strategy - @fiendish
Feature Emojis: 🐛🗃x1 ♻️x1 Feature Labels: data model x1 feature x1
- (#497) 🐛🗃 Migration - Fix sequencing_experiment_genomic_file KF ID prefixes - @znatty22
- (#492) ♻️ Make Seq Exp and Genomic File Many to Many - @znatty22
Feature Emojis: ✨x1 Feature Labels: data model x1 feature x1
- (#486) ✨ Add access_urls to indexd models to point to gen3 locations - @dankolbman
Feature Emojis: x1 🐛x1 ✨x1 🎨x1 🚚x1 Feature Labels: feature x2 bug x2 refactor x2 documentation x1
- (#473) ✨Add biospecimen_id and genomic_file_id for genomic file and biospecimen endpoint - @parimalak
- (#480) 🐛 Do not include 'None' in rollup arrays - @dankolbman
- (#478) ✨ Summarize sequencing experiment fields on genomic file - @dankolbman
- (#476) 🎨 Make capitalization consistent for resources - @dankolbman
- (#474) 🚚 Mass rename of CavaticaTask and relationships - @dankolbman
Feature Emojis: 🐛x1 🔧x1 ✨x1 Feature Labels: feature x2 bug x1 data model x1
- (#471) 🐛 Fix typo in license badge link - @znatty22
- (#469) 🔧 Update Biospecimen method_of_sample_procurement enum - @znatty22
- (#468) ✨ Add method_of_sample_procurement col to biospec - @znatty22
Feature Emojis: ♻️x2 ⬆️x1 🐛x1 🔥x1 Feature Labels: refactor x1
- (#458) ⬆️ Upgrade dependencies - @dankolbman
- (#459) 🐛 Fix down rev in migration - @znatty22
- (#455) ♻️ Standardize biospecimen_diagnosis entity - @znatty22
- (#453) ♻️ Standardize read_group_genomic_file entity - @znatty22
- (#456) 🔥 Remove cascade delete genomic file on sequencing-experiment delete - @znatty22
Patches breaking change for Indexd and moves consent field from participant to biospecimen.
Feature Emojis: x1 ♻️x1 Feature Labels: refactor x2 data model x1 bug x1
- (#447) ✨Move consent_type from participant to biospecimen - @parimalak
- (#443) ♻️ Don't use rev in indexd requests - @dankolbman
Feature Emojis: 🐛x1 Feature Labels: bug x1
- (#439) 🐛 Remove duplicates from join results - @dankolbman
- (#437) 🐛 Fix join for genomic files study filter - @dankolbman
Feature Emojis: ✨x5 🐛x2 🔧x1 Feature Labels: feature x3 bug x2 refactor x2 data model x1
- (#436) ✨update outcome enum to deceased - @parimalak
- (#420) 🐛 fix parsing of uniqueness constraint error - @fiendish
- (#435) 🔧 Update read group quality scale enum - @znatty22
- (#430) ✨ Update analyte_type enum to support imaging files - @parimalak
- (#427) 🐛 Fix filtering in biospecimen, diagnosis GET all endpoint - @znatty22
- (#412) ✨ Refactor ReaGroup GenomicFile Relation - @znatty22
- (#426) ✨ Update data_type enum to support image files - @parimalak
- (#422) ✨Rename field volume_ml to volume_ul - @parimalak
Adds several new fields in the datamodel in #408:
family_typeon Familysource_text_noteson FamilyRelationshipaffected_statuson Participantdiagnosis_categoryon Participantvisibleon all tables
Feature Emojis: ✨x4 👷x1 🔧x1 🐛x1 Feature Labels: data model x4 devops x3 feature x3
- (#416) 🐛 Fix biospecimens and diagnoses links by diagnosis_id and biospecimen_id - @parimalak
- (#413) 👷 Load bucket url from vault - @dankolbman
- (#401) ✨ Add biospecimen_diagnosis association table - @parimalak
- (#410) 🔧 Increase nginx proxy_buffer size to stop truncating repsonses - @dankolbman
- (#408) ✨Data model changes - @parimalak
- (#407) ✨ Add visible to base model - @parimalak
- (#394) ✨ Add biospecimen_genomic_file association table and endpoints - @parimalak
Feature Emojis: ✨x3 🐛x3 👷x1 Feature Labels: bug x3 data model x2 data-import x1 devops x1 documentation x1
- (#389) ✨ Add More than One Race to race enum - @parimalak
- (#386) 🐛 Fix sns mocks - @dankolbman
- (#384) 👷 Added new jenkinsfile - @alubneuski
- (#359) ✨ Add relation from biospecimen to diagnosis - @dankolbman
- (#352) ✨ Read groups - @dankolbman
- (#373) 🐛 Fix 500 error on /studies?study_id - @znatty22
- (#380) 🐛 Update API docs - correct version of code - @znatty22
Feature Emojis: ✨x17 🐛x10 🗃x5 🔧x3 📝x2 ⚡x2 👷x1 💄x1 🚑x1 🏷x1 ♻️x1 Feature Labels: data model x17 feature x12 bug x12 Ready for review x5 refactor x3 documentation x2 devops x1
- (#316) 🔧 Bucket secret default - @dankolbman
- (#317) ✨ Basic Filter Params - @znatty22
- (#324) ♻️ Refactor child links - @znatty22
- (#331) 🔧Fix reverse family relationships - @znatty22
- (#333) 🐛 Fix case sensitivity of family relationships - @znatty22
- (#299) ✨ Add enum validators for entities - @parimalak
- (#279) ✨ Add SNS events for data changes - @dankolbman
- (#334) ✏️ Update genomic file data type enum - @dankolbman
- (#335) 🐛 Default SNS ARN to None - @dankolbman
Feature Emojis: ✨x14 🐛x8 🗃x5 📝x2 ⚡x2 👷x1 💄x1 🔧x1 🚑x1 Feature Labels: data model x16 bug x10 feature x9 Ready for review x2 documentation x2 refactor x1
- (#145) ✨ Genomic file resource - @dankolbman
- (#196) ✨ Alias Group Model (for participant aliases) - @znatty22
- (#204) ✨Model updates - @parimalak
- (#218) ✨ Merging participant and demographic - @parimalak
- (#219) 👪 Family model and resources - @dankolbman
- (#223) 📝 Update API docs to include 400, 404 responses - @znatty22
- (#225) 👷 moving to the new deployment process - @alubneuski
- (#228) ✨Biospecimen model - @parimalak
- (#230) ✨ Filter Resources by Study - @znatty22
- (#235) 🐛 fix backref's for diagnoses, outcomes, phenotypes in participant model - @parimalak
- (#238) 🗃 Add missing alias_group migration - @znatty22
- (#244) ✨ Sequencing Center entity - @parimalak
- (#247) 🗃 Fix migration heads - @parimalak
- (#250) ⚡️Optimize loading of children in default pagination - @znatty22
- (#252) 💄 Center logo and badges - @dankolbman
- (#253) 🗃 Study file integration with Indexd - @dankolbman
- (#255) 🐛 Use correct schema for study file resources - @dankolbman
- (#256) 📝 Update entity relationship diagram - @znatty22
- (#258) 🐛Delete parent orphans - @znatty22
- (#261) ✨ Relation links - @znatty22
- (#262) ✨Model Changes - @parimalak
- (#263) ✨ Add integration with bucket service - @dankolbman
- (#268) 🔧 Update indexd required fields with required flag in schema - @znatty22
- (#270) ✨ Add availabilty to study_file - @parimalak
- (#281) 🗃 Squash migrations - @dankolbman
- (#283) 🐛 Change modified_at field on update - @dankolbman
- (#284) ⚡️ Faster tests - @dankolbman
- (#289) ✨ Update sequencing_experiment_id to be nullable in genomic_file - @parimalak
- (#290) ✨ Cavatica Models and Endpoints - @znatty22
- (#300) 🐛 Fix bug w shipment_date = null - @znatty22
- (#302) 🗃 Remove null constraint on biospecimen_id in genomic file - @dankolbman
- (#304) 🐛 Fix bug w experiment_date = null - @znatty22
- (#305) ✨ Move acl to root document - @dankolbman
- (#308) 🐛 Use the db session by default in all base schemas - @dankolbman
- (#309) 🐛 Ignore mime type when parsing request body - @dankolbman
- (#312) 🚑 Remove datamodel and migration version from status - @dankolbman
Feature Emojis: ✨x38 👷x10 🐛x10 ♻️x6 📝x5 🗃x3 🐳x2 🔧x2 Nonex2 💥x1 🐘x1 🖼x1 🔥x1 🚢x1 🏷x1 🕷x1 Feature Labels: feature x24 data model x22 refactor x9 bug x9 devops x8 documentation x3 Epic x1
- (#10) ✨ Create person entity - @dankolbman
- (#15) 👷 Add Jenkinsfile - @dankolbman
- (#17) 🐳 Add docker file - @dankolbman
- (#23) 🗃 Add base mixin for the data model - @dankolbman
- (#26) 🔧 Refactor code base to be modular for additional entities - @znatty22
- (#27) ✨ Kids First Ids - @dankolbman
- (#30) ♻️ Formatting responses and abstracting out some of the models - @dankolbman
- (#31) 📝 Update readme with information - @dankolbman
- (#33) 👷 Add CircleCI tests - @dankolbman
- (#34) 👷 Add badge for CircleCI - @dankolbman
- (#37) 🐛 Fix circleci - @dankolbman
- (#38) 🐛 Update/fix Base class in models.py - @znatty22
- (#49) 🔧 Update sqlalchemy config w foreign key constraint for sqlite - @znatty22
- (#54) 🐛 Initialize database on start - @dankolbman
- (#56) ✨ Status page and rerouting - @dankolbman
- (#60) ♻️ Rename Person to Participant in all relevant files - @znatty22
- (#61) ✨ Add ERD generator - @dankolbman
- (#62) ✨ Demographic resource and tests - @znatty22
- (#64) ✨ Add Demographic db model - @znatty22
- (#65) 💥 Nuke and pave™ - @dankolbman
- (#66) ✨ Sample db model - @parimalak
- (#67) ✨ Add Diagnosis db model and tests - @znatty22
- (#72) ✨ Deserialize objects - @dankolbman
- (#73) 📝 swagger docs - @dankolbman
- (#74) ✨ Aliquot model with Tests - @parimalak
- (#75) ✨ Diagnosis resource and tests - @znatty22
- (#77) ✨ Add pagination - @dankolbman
- (#78) 🐘 Postgres - @dankolbman
- (#79) ✨ Genomic file model and tests - @znatty22
- (#81) ✨ Add Sequencing experiment model with tests - @parimalak
- (#82) ✨ Sample resource and tests - @znatty22
- (#84) ✨ Aliquot resource - @znatty22
- (#85) ♻️ Refactor pg exceptions to flask error handler - @dankolbman
- (#88) ♻️ Refactor dummy data generator - @znatty22
- (#89) ✨ Dummy data generator - @parimalak
- (#91) 👷 Fix dependency bug for CircleCI - @dankolbman
- (#96) 🐛 Change hvac requirement back to http - @dankolbman
- (#97) 👷 Update deploy to QA in Jenkinsfile - @dankolbman
- (#98) 🐛 Fix typo in Jenkins file - @dankolbman
- (#99) 🐛 Add line break - @dankolbman
- (#100) 🐛 Fix Jenkinsfile typo - @dankolbman
- (#102) 👷 Feature/simplifying jenkinsfile - @alubneuski
- (#103) 📝 Update README with how to generate mock data - @dankolbman
- (#105) 🗃 Remove postgres id and use kf_id as primary key - @dankolbman
- (#107) 🗃 Change uuid field to Postgres UUID - @dankolbman
- (#109) ✨ Add Controlled Access field to Genomic file entity - @parimalak
- (#114) ✨ Family relationship model - @znatty22
- (#121) ✨ Phenotype model - @parimalak
- (#125) ✨ Add Outcome Entity to Model - @parimalak
- (#126) ✨ Workflow model - @znatty22
- (#130) ✨ Study model - @znatty22
- (#131) ✨ Add fields to diagnosis Entity - @parimalak
- (#132) ✨ Add fields to Partcipant Entity - @parimalak
- (#135) ✨ Kf id prefix - @dankolbman
- (#139) 👷 Feature/add clean before checkout - @alubneuski
- (#144) 👷 Removed clean before checkout - @alubneuski
- (#146) ✨ Add Investigator model - @parimalak
- (#149) ✨ Study file model - @parimalak
- (#155) ✨ Add file_size to GenomicFile model - @znatty22
- (#157) 🖼 Readme image - @dankolbman
- (#158) 🐛 Fix self links - @dankolbman
- (#159) 📝 add NOTICE - @allisonheath
- (#170) 👷 Add codacy integration - @dankolbman
- (#173) ✨ ⚡️Change PUT to PATCH in all resource APIs and minor updates - @znatty22
- (#174) ✨ Add pagination to resources - @dankolbman
- (#175) ✨ Study resource - @dankolbman
- (#176) ✨ Investigator resource - @dankolbman
- (#177) 🔒 Avoid system calls during status request - @dankolbman
- (#178) ♻️ Rename participant tests to conform to naming convention - @dankolbman
- (#179) 🔥 Remove SQLite configuration - @dankolbman
- (#180) ✨ Add phenotype endpoint - @parimalak
- (#181) 👷 Added jenkins webhook property - @alubneuski
- (#183) ♻️ Fix self links - @dankolbman
- (#186) 📝 Docs branding - @dankolbman
- (#189) ✨Add outcome endpoint - @parimalak
- (#190) ✨ Sequencing Experiment Resource - @znatty22
- (#194) ✨Family relationship resource - @znatty22
- (#195) 🚢 Added prd deployment step without tagging - @alubneuski
- (#197) ✨Study file resource - @parimalak
- (#200) 🐳 Use nginx for main proxy - @dankolbman
- (#203) 🏷 Feature/adding tagging - @alubneuski
- (#206) ☁️ Added cloud region - @alubneuski
- (#214) 🕷fixing - @alubneuski
- (#215) 🐛 Put back dockerfile command - @dankolbman
- (#216) 🐛 Use run script to upgrade db before supervisor - @dankolbman