Merge remote-tracking branch 'origin/master' into feat/new-es-7

uc-cdis · Nov 6, 2023 · f6ec8c2 · f6ec8c2
2 parents e3f75a5 + 9265477
commit f6ec8c2
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diff --git a/.github/workflows/image_build_and_test.yaml b/.github/workflows/image_build_and_test.yaml
@@ -67,11 +67,6 @@ jobs:
           ls ..
           pwd
 
-      - name: Extract branch name
-        shell: bash
-        run: echo "branch=$(echo $(echo ${GITHUB_REF#refs/heads/} | tr / _))" >> $GITHUB_OUTPUT
-        id: extract_branch
-
       - name: Copy configuration files
         run: |
           cp -f tests/integrated_tests/gen3/tube/etlMapping.yaml ../compose-etl/configs/etlMapping.yaml
@@ -87,8 +82,9 @@ jobs:
       - name: Replace tube branch
         working-directory: ../compose-etl
         run: |
-          BRANCH=${{ steps.extract_branch.outputs.branch }}
-          sed -i "s/tube:master/tube:${BRANCH//\//_}/g" docker-compose.yml
+          BRANCH=${{ github.head_ref || github.ref_name }}
+          BRANCH=$(echo $BRANCH | tr / _)
+          sed -i "s/tube:master/tube:$BRANCH/g" docker-compose.yml
 
       - name: change max_map_count (needed for running Elasticsearch in container)
         working-directory: ../compose-etl

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -21,7 +21,6 @@ gen3datamodel = "3.0.2"
 hdfs = "2.7.0"
 psycopg2-binary="2.9.3"
 psqlgraph = "3.0.1"
-py2neo = "2021.2.3"
 pyspark = "3.3.0"
 urllib3 = "1.26.16"
 requests = "^2.28.1"

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diff --git a/...dgc/dataframe/file__0/part-00000-a6b7025e-5c86-4030-a38e-aa4f2ea0d7f0-c000.snappy.parquet b/...dgc/dataframe/file__0/part-00000-a6b7025e-5c86-4030-a38e-aa4f2ea0d7f0-c000.snappy.parquet
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diff --git a/...e__collected_leaf_dfs/part-00000-3fffcbc8-7378-4b8b-a9a0-d43509c9a5c2-c000.snappy.parquet b/...e__collected_leaf_dfs/part-00000-3fffcbc8-7378-4b8b-a9a0-d43509c9a5c2-c000.snappy.parquet
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diff --git a/...a50-9c8b-15d1b24ebccf-c000.snappy.parquet → ...565-9166-6ebcb25787cb-c000.snappy.parquet b/...a50-9c8b-15d1b24ebccf-c000.snappy.parquet → ...565-9166-6ebcb25787cb-c000.snappy.parquet
diff --git a/...671-bb2d-5f4448bdd262-c000.snappy.parquet → ...968-b23c-2c3685369cdb-c000.snappy.parquet b/...671-bb2d-5f4448bdd262-c000.snappy.parquet → ...968-b23c-2c3685369cdb-c000.snappy.parquet
diff --git a/...4e1-a322-35eb0747d3d7-c000.snappy.parquet → ...438-bd76-8764773746fb-c000.snappy.parquet b/...4e1-a322-35eb0747d3d7-c000.snappy.parquet → ...438-bd76-8764773746fb-c000.snappy.parquet
diff --git a/...714-8e18-ac65369a709b-c000.snappy.parquet → ...fa5-a002-8eef7f0d6566-c000.snappy.parquet b/...714-8e18-ac65369a709b-c000.snappy.parquet → ...fa5-a002-8eef7f0d6566-c000.snappy.parquet
diff --git a/tests/dataframe_tests/test_data/ibdgc/graphs/node_rawsnpgenotype/part-m-00000 b/tests/dataframe_tests/test_data/ibdgc/graphs/node_rawsnpgenotype/part-m-00000
@@ -107,7 +107,6 @@
 "2020-01-17 06:02:21.920928+00","{phs-jenkins,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""9a44404f79dc6f4a703a3c920cb8168d"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""3d9cba6023"", ""file_size"": 82, ""object_id"": ""dg.XXXX/96a8bdbb-ffe6-4b73-85d8-077113ba4cc8"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins"", ""data_format"": ""IDAT"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_089cfcb3b9"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2020-01-17T06:02:21.920928+00:00"", ""updated_datetime"": ""2020-01-17T06:02:21.920928+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 v2.0""}","6ee014e3-08fd-4793-be6d-efceea9f1c85"
 "2020-01-17 06:02:25.486043+00","{phs-jenkins,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""35cc1c62ae485d5fd84d76efe1f1038f"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""374cc8f429"", ""file_size"": 45, ""object_id"": ""dg.XXXX/293ab724-5952-4894-b073-8bf8cdef7187"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins"", ""data_format"": ""Illumina Final Report"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_0f7903f8b1"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2020-01-17T06:02:25.486043+00:00"", ""updated_datetime"": ""2020-01-17T06:02:25.486043+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 v2.0""}","9b43176f-a5ff-449d-8809-98b009e223c6"
 "2020-01-17 06:02:25.996377+00","{phs-jenkins,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""2b08d27ca9f8c701e1683b6cc35bca56"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""6a9bec74b7"", ""file_size"": 73, ""object_id"": ""dg.XXXX/414fc12f-07aa-44a2-a636-5f1b8b7a4d1d"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins"", ""data_format"": ""IDAT"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_0e4a6da4cf"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2020-01-17T06:02:25.996377+00:00"", ""updated_datetime"": ""2020-01-17T06:02:25.996377+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 v2.0""}","b1fe7a37-253b-46d5-8498-17fa2acc34f6"
-"2020-01-17 06:02:27.622894+00","{phs-jenkins,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""1417d7dd12491d2fa2df5dfddf0695f1"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""98454cd64e"", ""file_size"": 43, ""object_id"": ""dg.XXXX/420f68e3-dfc5-40f7-a488-429855128d57"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins"", ""data_format"": ""Illumina Final Report"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_bae932c9b9"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2020-01-17T06:02:27.622894+00:00"", ""updated_datetime"": ""2020-01-17T06:02:27.622894+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 v2.0""}","07ce47b3-e3cf-4449-95e2-cd0f97f63231"
 "2020-02-17 22:11:08.545392+00","{phs-jenkins,jnkns}","{}","{""type"": ""raw_snp_genotype"", ""state"": ""validated"", ""md5sum"": ""61a2dc1880f911805d52873c6d97c793"", ""samples"": [], ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""zoe"", ""file_size"": 21153942804, ""object_id"": ""dg.XXXX/420f68e3-dfc5-40f7-a488-429855128888"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins"", ""data_format"": ""Illumina Final Report"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_bae932ddd9"", ""data_category"": ""SNP Genotypes"", ""state_comment"": ""zoe"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2020-01-13T06:02:27.622894+00:00"", ""updated_datetime"": ""2020-01-13T06:02:27.622894+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 v2.0"", ""core_metadata_collections"": [{""id"": ""df2fcfd1-b591-46af-85fb-3973e2915c60"", ""submitter_id"": ""core_metadata_collection_9f28aa40cc""}]}","07ce47b3-e3cf-4449-95e2-cd0f97f63333"
 "2021-01-08 19:06:21.543558+00","{phs-jenkins2,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""b77ec4ef33b0194bfff84fa84fd1ba17"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""ab3514fb8d"", ""file_size"": 47, ""object_id"": ""dg.XXXX/2540642a-1f7a-429e-941b-01179b46c987"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins2"", ""data_format"": ""PLINK BED File"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_6c8561c54d"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2021-01-08T19:06:21.543558+00:00"", ""updated_datetime"": ""2021-01-08T19:06:21.543558+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 Kit v2.0 BeadChip""}","db5edc3a-9d40-4f0c-98cd-fa81340a800d"
 "2021-01-08 19:06:21.953907+00","{phs-jenkins2,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""ad7d1b0fc5b2d142a49708f5e5e255bb"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""b9473dc19b"", ""file_size"": 38, ""object_id"": ""dg.XXXX/d3f6e0fb-9b14-406d-b7ec-8cfbde1e5f26"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins2"", ""data_format"": ""IDAT"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_87a3cdfdaa"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2021-01-08T19:06:21.953907+00:00"", ""updated_datetime"": ""2021-01-08T19:06:21.953907+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 Kit v2.0 BeadChip""}","a4685a40-9e93-41ca-8282-55ddf0406148"
@@ -159,3 +158,4 @@
 "2021-12-03 17:29:46.819802+00","{phs-jenkins2,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""1934980c70028286e3d0e1dc93fc52c2"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""ab4a7dd26d"", ""file_size"": 38, ""object_id"": ""dg.XXXX/d91d5320-1361-47b5-a621-682a68942017"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins2"", ""data_format"": ""Illumina Final Report"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_94ec1ee267"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2021-12-03T17:29:46.819802+00:00"", ""updated_datetime"": ""2021-12-03T17:29:46.819802+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 Kit v3.0 BeadChip""}","2a771ed5-65f6-4fe3-a495-50a8ba1c3215"
 "2021-12-03 17:29:47.2528+00","{phs-jenkins2,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""7fcab28b2175fe30b96f403fb1e8de67"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""906409e0cd"", ""file_size"": 98, ""object_id"": ""dg.XXXX/4949a7af-45bb-435f-90dd-c1d9f64c5e93"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins2"", ""data_format"": ""Illumina Final Report"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_4c198ea272"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": null, ""created_datetime"": ""2021-12-03T17:29:47.252800+00:00"", ""updated_datetime"": ""2021-12-03T17:29:47.252800+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 Kit v3.0 BeadChip""}","10db8aa1-d1ce-49c8-9b6d-f4d8eaf9a13e"
 "2021-12-03 17:29:47.627038+00","{phs-jenkins2,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""0539888381dc2b0710b5d98a5629c3a3"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""eb846b8e74"", ""file_size"": 91000000000, ""object_id"": ""dg.XXXX/36aa80ae-f382-45a1-9749-bd7f97b0d7c5"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins2"", ""data_format"": ""Illumina Final Report"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_95b1f96f48"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2021-12-03T17:29:47.627038+00:00"", ""updated_datetime"": ""2021-12-03T17:29:47.627038+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 Kit v2.0 BeadChip""}","e6e8f885-e18e-40e5-9602-66b0dea0d09f"
+"2020-01-17 06:02:27.622894+00","{phs-jenkins,jnkns}","{}","{""state"": ""validated"", ""md5sum"": ""1417d7dd12491d2fa2df5dfddf0695f1"", ""data_type"": ""SNP Intensities and/or Called Genotypes"", ""file_name"": ""98454cd64e"", ""file_size"": 43, ""object_id"": ""dg.XXXX/420f68e3-dfc5-40f7-a488-429855128d58"", ""file_state"": ""registered"", ""project_id"": ""jnkns-jenkins"", ""data_format"": ""Illumina Final Report"", ""assay_method"": ""SNP Array"", ""submitter_id"": ""raw_snp_genotype_bae932c9b9"", ""data_category"": ""SNP Genotypes"", ""assay_instrument"": ""Illumina"", ""created_datetime"": ""2020-01-17T06:02:27.622894+00:00"", ""updated_datetime"": ""2023-05-22T18:49:47.758824+00:00"", ""assay_instrument_model"": ""Illumina Infinium Global Screening Array-24 Kit v2.0 BeadChip""}","07ce47b3-e3cf-4449-95e2-cd0f97f63231"
diff --git a/tests/dataframe_tests/test_data/ibdgc/graphs/node_root/part-m-00000 b/tests/dataframe_tests/test_data/ibdgc/graphs/node_root/part-m-00000
@@ -1 +1 @@
-"2020-01-16 19:05:12.953264+00","{}","{}","{""schema_version"": ""-7780338601903350209""}","root"
+"2020-01-16 19:05:12.953264+00","{}","{}","{""schema_version"": ""1879278627024622741""}","root"
diff --git a/...c/dataframe/imaging_data_file__0/_SUCCESS → ...ta/midrc/dataframe/annotation__0/_SUCCESS b/...c/dataframe/imaging_data_file__0/_SUCCESS → ...ta/midrc/dataframe/annotation__0/_SUCCESS
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diff --git a/...__collected_collecting_dfs__case/_SUCCESS → ...anslator.ensure_project_id_exist/_SUCCESS b/...__collected_collecting_dfs__case/_SUCCESS → ...anslator.ensure_project_id_exist/_SUCCESS
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diff --git a/...ng_dfs__core_metadata_collection/_SUCCESS → ...0_Translator.get_direct_children/_SUCCESS b/...ng_dfs__core_metadata_collection/_SUCCESS → ...0_Translator.get_direct_children/_SUCCESS
diff --git a/...r.get_direct_children/part-00000-d09ab2ae-a482-4521-821f-61f85a02bfe5-c000.snappy.parquet b/...r.get_direct_children/part-00000-d09ab2ae-a482-4521-821f-61f85a02bfe5-c000.snappy.parquet
diff --git a/...d_collecting_dfs__cr_series_file/_SUCCESS → ...e_table_to_dataframe__annotation/_SUCCESS b/...d_collecting_dfs__cr_series_file/_SUCCESS → ...e_table_to_dataframe__annotation/_SUCCESS
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diff --git a/...collecting_dfs__cr_series_file_1/_SUCCESS → ...on__1_Translator.translate_final/_SUCCESS b/...collecting_dfs__cr_series_file_1/_SUCCESS → ...on__1_Translator.translate_final/_SUCCESS
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diff --git a/...ator.translate_parent/part-00000-9ee8e625-4483-4444-a2da-a8ed564a63f9-c000.snappy.parquet b/...ator.translate_parent/part-00000-9ee8e625-4483-4444-a2da-a8ed564a63f9-c000.snappy.parquet
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diff --git a/...d_collecting_dfs__ct_series_file/_SUCCESS → ...e_table_to_dataframe__annotation/_SUCCESS b/...d_collecting_dfs__ct_series_file/_SUCCESS → ...e_table_to_dataframe__annotation/_SUCCESS
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diff --git a/...collecting_dfs__ct_series_file_1/_SUCCESS → ...table_to_dataframe__annotation_1/_SUCCESS b/...collecting_dfs__ct_series_file_1/_SUCCESS → ...table_to_dataframe__annotation_1/_SUCCESS
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diff --git a/...ollected_collecting_dfs__dataset/_SUCCESS → ...te_table_to_dataframe__condition/_SUCCESS b/...ollected_collecting_dfs__dataset/_SUCCESS → ...te_table_to_dataframe__condition/_SUCCESS
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		"2020-01-16 19:05:12.953264+00","{}","{}","{""schema_version"": ""1879278627024622741""}","root"