v1.0.0: First release of CCDI Prefect codebase

23 Aug 2024

• This release is compatible with CCDI data model 1.9.1

What's Changed

• Add files by @qiongL910 in #1
• fixed a bug in catcherr by @qiongL910 in #2
• ccdi prefect workflow by @qiongL910 in #3
• Ccdidc 725 add synonym by @qiongL910 in #4
• Updated readme by @qiongL910 in #5
• Update README.md by @qiongL910 in #6
• fixed s3_catcherry bug of handling missing value by @qiongL910 in #7
• fixed sys exit bug in sra script by @qiongL910 in #8
• Update s3_ccdi_to_cds.py by @svburke in #9
• Update s3_ccdi_to_cds.py by @svburke in #10
• Add tabbreaker by @qiongL910 in #11
• fixed a bug in tabbreaker by @qiongL910 in #12
• Update README.md by @qiongL910 in #13
• Update s3_catcherry.py by @svburke in #14
• Validationry testing by @svburke in #15
• CCDIDC-741 Add updater workflow by @qiongL910 in #16
• CCDIDC-757 by @svburke in #17
• CCDIDC-750 added unittests for update_ccdi_template.py by @qiongL910 in #18
• Update s3_catcherry.py by @svburke in #19
• CCDIDC-746 allow subflow fail by @qiongL910 in #20
• Ccdidc 749 bucket reader by @qiongL910 in #21
• Update s3_ccdi_to_sra.py by @qiongL910 in #22
• fixed an sra subflow bug by @qiongL910 in #23
• Fix runner id key error by @qiongL910 in #24
• Allow runner id slash by @qiongL910 in #25
• Update s3_ccdi_to_sra.py by @qiongL910 in #26
• Ccdidc 770 template exampler by @qiongL910 in #27
• Ccdidc 789 bucket subdirectory by @qiongL910 in #28
• Ccdidc 809 hard code sra value by @qiongL910 in #29
• CCDIDC-813 resort files sharing the same library ID by @qiongL910 in #30
• Ccdidc 765 812 by @svburke in #31
• Ccdidc 790 add pre sra dbgap input by @qiongL910 in #32
• Ccdidc 747 by @svburke in #33
• CCDIDC-822 SRA bug fix by @qiongL910 in #34
• CCDIDC-833 fixed ccdi to sra bug, alignment software str replacement by @qiongL910 in #35
• fixed a bug ccdi_to_sra, function concatenate_library_id by @qiongL910 in #36
• CCDIDC-828 fixed the time dependent file name bug by @qiongL910 in #37
• Ccdidc 850 add sra contact by @qiongL910 in #38
• Ccdidc 792 model to submission by @qiongL910 in #39
• Ccdidc 791 file mover by @qiongL910 in #40
• Ccdidc 859 keep header style by @qiongL910 in #41
• Update s3_ccdi_to_sra.py by @qiongL910 in #43
• Update bucket_reader.py by @qiongL910 in #44
• Update s3_catcherry.py by @svburke in #42
• Update bucket_reader.py by @qiongL910 in #45
• Update bucket_reader.py by @qiongL910 in #46
• Update bucket_reader.py by @qiongL910 in #47
• Update bucket_reader.py by @qiongL910 in #48
• handle empty bucket in bucket-reader by @qiongL910 in #49
• bucket-reader reports empty bucket and better exception handle by @qiongL910 in #50
• Update s3_ccdi_to_index.py by @svburke in #51
• CCDIDC-861 CCDIDC-862 pulling neo4j data and validation by @qiongL910 in #52
• modified get aws parameter flow by @qiongL910 in #54
• pd_loc_issue by @svburke in #55
• memory_levels by @svburke in #57
• Neo4j validate patch by @qiongL910 in #58
• Update bucket_reader.py by @qiongL910 in #60
• CCDIDC-906 by @svburke in #59
• Added error message by @qiongL910 in #61
• allows workflow to conitnue without latest template version info by @qiongL910 in #62
• CCDIDC-914 Make github API call with token headers by @qiongL910 in #63
• CCDIDC-901 Remove duplicates in dbgap output by @qiongL910 in #65
• 60gb_workpool by @svburke in #64
• reformat sra instrument model value by @qiongL910 in #67
• Update s3_ccdi_to_sra.py by @svburke in #68
• Ccdidc 936 md5sum cal by @qiongL910 in #69
• Merge changes of main into branch by @qiongL910 in #70
• CCDIDC 897 file mover parallel by @qiongL910 in #56
• Ccdidc 948 dcf indexing by @qiongL910 in #71
• CCDIDC-952 folder downloading error fixing by @qiongL910 in #72
• Ccdidc 915 submission cruncher by @qiongL910 in #73
• Ccdidc 886 file remover by @qiongL910 in #74
• Ccdidc 964 join tsvs by @qiongL910 in #75
• Overnight flow bug by @qiongL910 in #76
• Update prefect.yaml by @svburke in #77
• Update s3_ccdi_to_sra.py by @svburke in #78
• Guid checker, CCDIDC-956 by @svburke in #79
• Update model_to_submission.py by @svburke in #80
• Update model_to_submission.py by @qiongL910 in #81
• Modify hard coded sheet order by @qiongL910 in #82
• CCDIDC 978 refactor validation by @qiongL910 in #83
• Update new_model_validation.py by @qiongL910 in #84
• Update s3-Prefect-Pipeline.py by @qiongL910 in #85
• Ccdidc 1092 sra filter filetypes by @qiongL910 in #86
• Update guid_checker.py by @svburke in #87
• CCDIDC-1115 file remover bug by @qiongL910 in #88
• CCDIDC-1094 bucket reader bug by @qiongL910 in #89
• CCDIDC-1148 add missing guid by @qiongL910 in #90
• Fix to acl by @svburke in #91
• Update neo4j_data_tools.py by @svburke in #92
• Update neo4j_data_tools.py by @svburke in #93
• CCDIDC 1115 file remover bug by @qiongL910 in #94
• CCDIDC-1144 mci prefect by @qiongL910 in #95
• CCDIDC-1171 liftover template by @qiongL910 in #96
• CCDIDC 1177 sra and validatioin fix for new model by @qiongL910 in #97
• Update s3_ccdi_to_sra.py by @qiongL910 in #98
• Update guid_checker.py by @svburke in #99
• Update mci_release_run.py by @qiongL910 in #100
• Update mci_release_run.py by @qiongL910 in #101
• CCDIDC-1186 ccdi curation update by @qiongL910 in #102
• Update template_exampler.py by @svburke in #103
• Update template_exampler.py by @svburke in #104
• Update create_submission.py by @svburke in #105
• 1.9.0 fixes by @svburke in #106
• CCDIDC-1206 dcf index update by @qiongL910 in #108
• CCDIDC 1139 dir level size md5sum by @qiongL910 in #109
• CCDIDC 1254 validation report error by @qiongL910 in #110
• CCDIDC 1253 sra duplicated filename fix by @qiongL910 in #111
• CCDIDC-1259 no break space removal by @qiongL910 in #112
• Create model_mapping_maker.py by @svburke in #107
• CCDIDC-1166 sra metadata by @qiongL910 in #113
• CCDIDC 1266 validation key id bug by @qiongL910 in #114
• Ccdidc 1274 by @svburke in #115
• CCDIDC-1273 by @svburke in #116
• CCDIDC-1298 catcherry fail by @qiongL910 in #117
• Update neo4j_data_tools.py by @svburke in #118
• Update neo4j_data_tools.py by @svburke in #119
• CCDIDC-1301 neo4j bug by @qiongL910 in #120

New Contributors

• @qiongL910 made their first contribution in #1
• @svburke made their first contribution in #9

Full Changelog: https://github.com/CBIIT/ChildhoodCancerDataInitiative-Prefect_Pipeline/commits/1.0.0