From bd01ae23cf9f39fceecbfb7e006283a9c3a631be Mon Sep 17 00:00:00 2001 From: David Michaels Date: Mon, 18 Nov 2024 23:31:45 -0500 Subject: [PATCH 01/10] fixed up some inserts data to match 4dn/data/staging --- CHANGELOG.rst | 6 ++++++ poetry.lock | 10 +++++----- pyproject.toml | 4 ++-- src/encoded/tests/data/inserts/award.json | 2 +- src/encoded/tests/data/inserts/bio_feature.json | 4 ++-- src/encoded/tests/data/inserts/biosource.json | 6 +++--- src/encoded/tests/data/inserts/experiment_seq.json | 4 ++-- src/encoded/tests/data/inserts/gene.json | 6 +++--- src/encoded/tests/data/inserts/lab.json | 4 ++-- src/encoded/tests/data/inserts/ontology_term.json | 2 +- src/encoded/tests/data/master-inserts/award.json | 2 +- .../tests/data/master-inserts/experiment_type.json | 2 +- src/encoded/tests/data/master-inserts/ontology.json | 4 ++-- 13 files changed, 31 insertions(+), 25 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 8731399ac2..f17b5b9ddf 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,12 @@ Change Log ---------- +8.4.5 +===== +* 2024-11-18/dmichaels +* Fixed up some inserts data to match 4dn/data/staging. + + 8.4.4 ===== diff --git a/poetry.lock b/poetry.lock index fef4730abd..7ae146daf4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. [[package]] name = "apipkg" @@ -1173,13 +1173,13 @@ xlrd = ">=1.0.0,<2.0.0" [[package]] name = "dcicutils" -version = "8.16.1" +version = "8.16.3" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" optional = false python-versions = "<3.13,>=3.8.1" files = [ - {file = "dcicutils-8.16.1-py3-none-any.whl", hash = "sha256:6bd36178154b18b29ab1a10cedeaae695af6ccd4ee807233bc7e1a2874529ec5"}, - {file = "dcicutils-8.16.1.tar.gz", hash = "sha256:9f588cf39081e46e6f47f2762b50d25eb85907dff121bedf6f6aace99b8d752d"}, + {file = "dcicutils-8.16.3-py3-none-any.whl", hash = "sha256:94c80322a2eb3e77220e7eb32017bc2a138cd1bc772be38a8ddc16876fc374a9"}, + {file = "dcicutils-8.16.3.tar.gz", hash = "sha256:1241682a4fceca8e17d2ea5d336937afa9ba1e1ca09ed0ec44618e5d873d6f9a"}, ] [package.dependencies] @@ -4482,4 +4482,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "577f70bedbe2751290c954a416990f5cee6b0c96087ea81235db3021bb2dfb6d" +content-hash = "609b63a076ea13ec3032ff4d0a59aba39e685105d6587664d896317e93027b9b" diff --git a/pyproject.toml b/pyproject.toml index 5b34cd575d..dbf59fac33 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "fourfront". name = "encoded" -version = "8.4.4" +version = "8.4.5" description = "4DN-DCIC Fourfront" authors = ["4DN-DCIC Team "] license = "MIT" @@ -50,7 +50,7 @@ colorama = "0.3.3" # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. # cryptography = "39.0.2" dcicsnovault = "^11.22.0" -dcicutils = "^8.16.1" +dcicutils = "^8.16.3" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses execnet = "1.4.1" diff --git a/src/encoded/tests/data/inserts/award.json b/src/encoded/tests/data/inserts/award.json index 54bcd62d09..159efe29bf 100644 --- a/src/encoded/tests/data/inserts/award.json +++ b/src/encoded/tests/data/inserts/award.json @@ -40,7 +40,7 @@ "status": "current", "title": "EXPLORING HOW THE GENOME FOLDS THROUGH PROXIMITY LIGATION AND SEQUENCING", "url": "https://projectreporter.nih.gov/project_info_details.cfm?aid=8146738&icde=30734626", - "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334c", + "uuid": "36a06537-7831-494d-b10d-3e9fea931021", "project": "External" }, { diff --git a/src/encoded/tests/data/inserts/bio_feature.json b/src/encoded/tests/data/inserts/bio_feature.json index d35c13cbd5..df3d740854 100644 --- a/src/encoded/tests/data/inserts/bio_feature.json +++ b/src/encoded/tests/data/inserts/bio_feature.json @@ -5,7 +5,7 @@ "feature_type": "0231da78-1adc-4b8a-89b9-4f91908412a3", "uuid": "a8ab8bca-4840-41b7-88d7-04cc19a54657", "genome_location": ["d1115d5e-40aa-43bc-b81c-32c70c9afb01"], - "relevant_genes": ["3f3496f7-31bf-429f-8da7-7f1fdf840dcc"], + "relevant_genes": ["594e3125-a9cb-4ffa-bc2b-17870c1690f0"], "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", @@ -17,7 +17,7 @@ "description": "A protein feature", "feature_type": "91f427e6-5246-4992-8123-b4f8fa9eef01", "uuid": "5a5b6f55-0b54-441c-86bf-292d41e443a0", - "relevant_genes": ["d5ee3bf3-63b0-4032-b133-314173b3cc4d"], + "relevant_genes": ["a093769c-d596-4a26-8916-06ae491575ba"], "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", diff --git a/src/encoded/tests/data/inserts/biosource.json b/src/encoded/tests/data/inserts/biosource.json index 58eeec2339..705246b2be 100644 --- a/src/encoded/tests/data/inserts/biosource.json +++ b/src/encoded/tests/data/inserts/biosource.json @@ -4,7 +4,7 @@ "description": "GM12878 test cells 1", "biosource_type": "immortalized cell line", "individual":"4DNINOOOAAQ1", - "cell_line": "530036bc-8535-4448-903e-854af460b24c", + "cell_line": "b9668b9a-be39-47de-8eab-5bf1b0854417", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", @@ -16,7 +16,7 @@ "description": "GM12878 test cells 2", "biosource_type": "immortalized cell line", "individual":"4DNINOOOAAQ1", - "cell_line": "530036bc-8535-4448-903e-854af460b24c", + "cell_line": "b9668b9a-be39-47de-8eab-5bf1b0854417", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", @@ -39,7 +39,7 @@ "description": "test modified cells", "biosource_type": "immortalized cell line", "individual":"4DNINOOOAAQ1", - "cell_line": "530036bc-8535-4448-903e-854af460b24c", + "cell_line": "b9668b9a-be39-47de-8eab-5bf1b0854417", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", diff --git a/src/encoded/tests/data/inserts/experiment_seq.json b/src/encoded/tests/data/inserts/experiment_seq.json index f756e628e2..580e3996e6 100644 --- a/src/encoded/tests/data/inserts/experiment_seq.json +++ b/src/encoded/tests/data/inserts/experiment_seq.json @@ -2,7 +2,7 @@ { "accession":"4DNEXO6777A1", "biosample":"234411bc-8535-4448-903e-854af460b255", - "experiment_type": "e27b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "47a593da-c458-422a-a974-82b3302e89cb", "files": ["4DNFIN232JB1", "4DNFIN232JB2"], "description": "Biorep 1 Techrep 1 ChIP-seq on GM12878 batch 1", "award": "1U01CA200059-01", @@ -23,7 +23,7 @@ { "accession":"4DNEXO6777B1", "biosample":"234511bc-8535-4448-903e-854af460b255", - "experiment_type": "e27b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "47a593da-c458-422a-a974-82b3302e89cb", "files": ["4DNFIN232JB3"], "description": "Biorep 1 Techrep 2 ChIP-seq on GM12878 batch 1", "award": "1U01CA200059-01", diff --git a/src/encoded/tests/data/inserts/gene.json b/src/encoded/tests/data/inserts/gene.json index 79f4cb9a86..4dc48f8cf7 100644 --- a/src/encoded/tests/data/inserts/gene.json +++ b/src/encoded/tests/data/inserts/gene.json @@ -3,13 +3,13 @@ "geneid": "10664", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", - "uuid": "3f3496f7-31bf-429f-8da7-7f1fdf840dcc" + "uuid": "594e3125-a9cb-4ffa-bc2b-17870c1690f0" }, { "geneid": "5885", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", - "uuid": "d5ee3bf3-63b0-4032-b133-314173b3cc4d", - "preferred_symbol": "YFG" + "uuid": "a093769c-d596-4a26-8916-06ae491575ba", + "preferred_symbol": "RAD21" } ] diff --git a/src/encoded/tests/data/inserts/lab.json b/src/encoded/tests/data/inserts/lab.json index c27b2031cb..3c15fac965 100644 --- a/src/encoded/tests/data/inserts/lab.json +++ b/src/encoded/tests/data/inserts/lab.json @@ -42,8 +42,8 @@ "phone1": "713-798-4897", "postal_code": "77030", "state": "TX", - "title": "Erez Lieberman Aiden Lab, BCM", - "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc98a" + "title": "Erez Lieberman Aiden, BCM", + "uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503" }, { "awards": ["Test-4DN", "1U01CA200059-01", "Test-NOT-4DN"], diff --git a/src/encoded/tests/data/inserts/ontology_term.json b/src/encoded/tests/data/inserts/ontology_term.json index 18c2778b2a..91c3a19744 100644 --- a/src/encoded/tests/data/inserts/ontology_term.json +++ b/src/encoded/tests/data/inserts/ontology_term.json @@ -1,6 +1,6 @@ [ { - "uuid": "530036bc-8535-4448-903e-854af460b24c", + "uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "preferred_name": "GM12878", "term_name": "GM12878", "term_id": "EFO:0002784", diff --git a/src/encoded/tests/data/master-inserts/award.json b/src/encoded/tests/data/master-inserts/award.json index 8b6d135c9d..e3b1b7df0c 100644 --- a/src/encoded/tests/data/master-inserts/award.json +++ b/src/encoded/tests/data/master-inserts/award.json @@ -2,7 +2,7 @@ { "start_date": "2015-09-07", "schema_version": "1", - "title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER", + "title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators with a strong track record in analysis of chromatin interaction data, image processing and three-dimensional data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and flexible cloud technologies. In Aim 1, we will develop efficient submission pipelines for data and metadata from 4DN data production groups. We will define data/metadata requirements and quality metrics in conjunction with the production groups and ensure that high-quality, well- annotated data become available to the wider scientific community in a timely manner. In Aim 2, we will develop a user-friendly data portal for the broad scientific community. This portal will provide an easy-to-navigate interface for accessing raw and intermediate data files, allow for programmatic access via APIs, and will incorporate novel analysis and visualization tools developed by DCIC as well as other Network members. For computing and storage scalability and cost-effectiveness, significant efforts will be devoted to development and deployment of cloud-based technology. We will conduct tutorials and workshops to facilitate the use of 4DN data and tools by external investigators. In Aim 3, we will coordinate and assist in conducting integrative analysis of the multiple data types. These efforts will examine key questions in higher-order chromatin organization using both sequence and image data, and the tools and algorithms developed here will be incorporated into the data portal for use by other investigators. These three aims will ensure that the data generated in 4DN will have maximal impact for the scientific community.", "url": "https://projectreporter.nih.gov/project_info_description.cfm?aid=8987140&icde=30570219", diff --git a/src/encoded/tests/data/master-inserts/experiment_type.json b/src/encoded/tests/data/master-inserts/experiment_type.json index e2ce6fe0ee..3b35781637 100644 --- a/src/encoded/tests/data/master-inserts/experiment_type.json +++ b/src/encoded/tests/data/master-inserts/experiment_type.json @@ -185,7 +185,7 @@ "lab": "4dn-dcic-lab", "award": "1U01CA200059-01", "status": "released", - "uuid": "e27b17cd-544a-3a3b-abc3-17a544544b3c", + "uuid": "47a593da-c458-422a-a974-82b3302e89cb", "valid_item_types": ["ExperimentSeq"] }, { diff --git a/src/encoded/tests/data/master-inserts/ontology.json b/src/encoded/tests/data/master-inserts/ontology.json index f240636dc9..dc69fd2b60 100644 --- a/src/encoded/tests/data/master-inserts/ontology.json +++ b/src/encoded/tests/data/master-inserts/ontology.json @@ -14,7 +14,7 @@ { "uuid": "530016bc-8535-4448-903e-854af460b254", "ontology_name": "Uberon", - "ontology_url": "http://uberon.github.io/", + "ontology_url": "http://obophenotype.github.io/uberon/", "download_url": "http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl", "namespace_url": "http://purl.obolibrary.org/obo/", "ontology_prefix": "UBERON", @@ -25,7 +25,7 @@ { "uuid": "530026bc-8535-4448-903e-854af460b254", "ontology_name": "Ontology for Biomedical Investigations", - "ontology_url": "https://obi-ontology.org/", + "ontology_url": "http://obi-ontology.org", "download_url": "http://purl.obolibrary.org/obo/obi.owl", "namespace_url": "http://purl.obolibrary.org/obo/", "ontology_prefix": "OBI", From dbcbab799b3ee42cbbd345a0e5ea11387992ca2b Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 19 Nov 2024 08:51:31 -0500 Subject: [PATCH 02/10] fixed up some inserts data to match 4dn/data/staging --- src/encoded/tests/data/inserts/biosource.json | 14 +++++++------- src/encoded/tests/data/inserts/enzyme.json | 4 ++-- src/encoded/tests/data/inserts/vendor.json | 4 ++-- src/encoded/tests/data/perf-testing/vendor.json | 5 +++-- 4 files changed, 14 insertions(+), 13 deletions(-) diff --git a/src/encoded/tests/data/inserts/biosource.json b/src/encoded/tests/data/inserts/biosource.json index 705246b2be..5246fdd61d 100644 --- a/src/encoded/tests/data/inserts/biosource.json +++ b/src/encoded/tests/data/inserts/biosource.json @@ -9,7 +9,7 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "status": "in review by lab", - "biosource_vendor": "b31106bc-8535-4448-903e-854af460b21e" + "biosource_vendor": "11f94a17-51ed-4a0f-93b1-1cac2fd2844f" }, { "uuid": "331111bc-8535-4448-903e-854af460a254", @@ -21,7 +21,7 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "status": "in review by lab", - "biosource_vendor": "b31106bc-8535-4448-903e-854af460b21e" + "biosource_vendor": "11f94a17-51ed-4a0f-93b1-1cac2fd2844f" }, { "uuid": "331111bc-8535-4448-903e-854ab460b254", @@ -32,7 +32,7 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "status": "in review by lab", - "biosource_vendor": "b31106bc-8535-4448-903e-854af460b21e" + "biosource_vendor": "11f94a17-51ed-4a0f-93b1-1cac2fd2844f" }, { "uuid": "331111bc-8535-2248-903e-854af460b254", @@ -43,7 +43,7 @@ "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", - "biosource_vendor": "b31106bc-8535-4448-903e-854af460b21e", + "biosource_vendor": "11f94a17-51ed-4a0f-93b1-1cac2fd2844f", "status": "in review by lab", "modifications": ["431106bc-8535-4448-903e-854af460b265"] }, @@ -56,7 +56,7 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "status": "in review by lab", - "biosource_vendor": "b31106bc-8535-4448-903e-854af460b21e" + "biosource_vendor": "11f94a17-51ed-4a0f-93b1-1cac2fd2844f" }, { "uuid": "111116bc-8535-4448-903e-854af460b254", @@ -76,7 +76,7 @@ "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", - "biosource_vendor": "b31106bc-8535-4448-903e-854af460b21e" + "biosource_vendor": "11f94a17-51ed-4a0f-93b1-1cac2fd2844f" }, { "uuid": "0f011b1e-b772-4f2a-8c24-cc55de28a994", @@ -86,7 +86,7 @@ "award": "1U01CA200059-01", "lab": "dcic-testing-lab", "submitted_by": "wrangler@wrangler.com", - "biosource_vendor": "b31106bc-8535-4448-903e-854af460b21e" + "biosource_vendor": "11f94a17-51ed-4a0f-93b1-1cac2fd2844f" }, { "uuid": "c9165aa4-2ab5-428d-b5a7-db86dbb2d815", diff --git a/src/encoded/tests/data/inserts/enzyme.json b/src/encoded/tests/data/inserts/enzyme.json index 26561b640f..db9a595c4a 100644 --- a/src/encoded/tests/data/inserts/enzyme.json +++ b/src/encoded/tests/data/inserts/enzyme.json @@ -53,7 +53,7 @@ }, { "name": "DpnII", - "aliases":["dcic:dpnII_neb"], + "aliases":["4dn-dcic-lab:dpnII_neb", "dcic:dpnII_neb"], "enzyme_source": "new-england-biolabs", "catalog_number":"R0543", "recognition_sequence": "GATC", @@ -63,7 +63,7 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "url": "https://www.neb.com/products/r0543-dpnii", - "uuid": "557d7469-d1f6-4200-8ed4-c40374383dd3" + "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5" }, { "name": "NcoI_MspI_BspHI", diff --git a/src/encoded/tests/data/inserts/vendor.json b/src/encoded/tests/data/inserts/vendor.json index cad22bc21a..e0629faa14 100644 --- a/src/encoded/tests/data/inserts/vendor.json +++ b/src/encoded/tests/data/inserts/vendor.json @@ -13,13 +13,13 @@ { "title": "New England Biolabs", "name": "new-england-biolabs", - "aliases":["dcic:neb"], + "aliases":["dcic:neb", "4dn-dcic-lab:neb"], "description": "", "url": "https://www.neb.com", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", - "uuid": "b31106bc-8535-4448-903e-854af460b21e" + "uuid": "11f94a17-51ed-4a0f-93b1-1cac2fd2844f" }, { "title": "ThermoFisher Scientific", diff --git a/src/encoded/tests/data/perf-testing/vendor.json b/src/encoded/tests/data/perf-testing/vendor.json index 6c1916d911..d48869ef9c 100644 --- a/src/encoded/tests/data/perf-testing/vendor.json +++ b/src/encoded/tests/data/perf-testing/vendor.json @@ -44,8 +44,9 @@ "public_release": "2017-04-10", "date_created": "2017-04-09T17:24:14.968417+00:00", "aliases": [ - "dcic:neb" + "dcic:neb", + "4dn-dcic-lab:neb" ], "schema_version": "1" } -] \ No newline at end of file +] From 7d84730cfab2587c20ab5ae4fb7567ae74e522af Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 19 Nov 2024 11:33:24 -0500 Subject: [PATCH 03/10] update dcicutils to 8.16.4 --- CHANGELOG.rst | 1 + poetry.lock | 8 ++++---- pyproject.toml | 2 +- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index f17b5b9ddf..20e35f99b1 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -11,6 +11,7 @@ Change Log ===== * 2024-11-18/dmichaels * Fixed up some inserts data to match 4dn/data/staging. +* Updated dcicutils to latest version (8.16.4). 8.4.4 diff --git a/poetry.lock b/poetry.lock index 7ae146daf4..27c2c799d3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1173,13 +1173,13 @@ xlrd = ">=1.0.0,<2.0.0" [[package]] name = "dcicutils" -version = "8.16.3" +version = "8.16.4" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" optional = false python-versions = "<3.13,>=3.8.1" files = [ - {file = "dcicutils-8.16.3-py3-none-any.whl", hash = "sha256:94c80322a2eb3e77220e7eb32017bc2a138cd1bc772be38a8ddc16876fc374a9"}, - {file = "dcicutils-8.16.3.tar.gz", hash = "sha256:1241682a4fceca8e17d2ea5d336937afa9ba1e1ca09ed0ec44618e5d873d6f9a"}, + {file = "dcicutils-8.16.4-py3-none-any.whl", hash = "sha256:963df9f21c7721b70096632bcab9297cdc8a7abc7e8098a2aee17d4a2ff8fbb0"}, + {file = "dcicutils-8.16.4.tar.gz", hash = "sha256:a22bf915a7d8ce103c593568fcf5f33aa080a826928e50e2c883999302b9520c"}, ] [package.dependencies] @@ -4482,4 +4482,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "609b63a076ea13ec3032ff4d0a59aba39e685105d6587664d896317e93027b9b" +content-hash = "a701e72e86c4b23f45b2cb2281b255ab12bb796c66a622afddab5a86dfd62afd" diff --git a/pyproject.toml b/pyproject.toml index dbf59fac33..a90b5625a2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,7 +50,7 @@ colorama = "0.3.3" # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. # cryptography = "39.0.2" dcicsnovault = "^11.22.0" -dcicutils = "^8.16.3" +dcicutils = "^8.16.4" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses execnet = "1.4.1" From da201da2616548191407bdb6d3974b11f1b4fc48 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 19 Nov 2024 11:38:35 -0500 Subject: [PATCH 04/10] update dcicsnovault version 11.23.0 --- CHANGELOG.rst | 1 + poetry.lock | 8 ++++---- pyproject.toml | 2 +- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 20e35f99b1..b51109dca0 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -12,6 +12,7 @@ Change Log * 2024-11-18/dmichaels * Fixed up some inserts data to match 4dn/data/staging. * Updated dcicutils to latest version (8.16.4). +* Updated dcicsnovault to latest version (11.23.0). 8.4.4 diff --git a/poetry.lock b/poetry.lock index 27c2c799d3..9e9f997995 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1115,13 +1115,13 @@ files = [ [[package]] name = "dcicsnovault" -version = "11.22.0" +version = "11.23.0" description = "Storage support for 4DN Data Portals." optional = false python-versions = "<3.13,>=3.9" files = [ - {file = "dcicsnovault-11.22.0-py3-none-any.whl", hash = "sha256:8b6b585188d23f43b3778779b67327deb71365e94894d08b3a309d6b8b17a4b0"}, - {file = "dcicsnovault-11.22.0.tar.gz", hash = "sha256:fe307cc988b07431a0fb11b20723c7b0d769c0adf690960605d57b17cd16cf81"}, + {file = "dcicsnovault-11.23.0-py3-none-any.whl", hash = "sha256:5ab18fa0c5427fdeb83d3944cc11ee49234e986c8836845c54b79493a6077b65"}, + {file = "dcicsnovault-11.23.0.tar.gz", hash = "sha256:44f1169d2d59b1b0015cbde116b9b21e98ba4cca42f905b9ced3a544d10ba423"}, ] [package.dependencies] @@ -4482,4 +4482,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "a701e72e86c4b23f45b2cb2281b255ab12bb796c66a622afddab5a86dfd62afd" +content-hash = "a9aac3acd26636b75567df929a241d44ee05f0085c0b1e0a9fa57fd1650243e4" diff --git a/pyproject.toml b/pyproject.toml index a90b5625a2..223fc7c592 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. # cryptography = "39.0.2" -dcicsnovault = "^11.22.0" +dcicsnovault = "^11.23.0" dcicutils = "^8.16.4" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses From 543b1782c6d44f8ebdb016686440f2ab5227236d Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 21 Nov 2024 18:13:00 -0500 Subject: [PATCH 05/10] Updated more inserts data files from fourfront-data to ease importing of data for local dev. --- src/encoded/tests/data/inserts/enzyme.json | 23 +++++++++++-------- .../tests/data/inserts/experiment_hi_c.json | 16 ++++++------- .../data/master-inserts/experiment_type.json | 4 ++-- .../data/master-inserts/ontology_term.json | 2 +- .../tests/data/master-inserts/page.json | 5 ++-- .../data/master-inserts/static_section.json | 6 ++--- .../tests/data/perf-testing/enzyme.json | 5 ++-- .../data/perf-testing/experiment_hi_c.json | 16 ++++++------- .../data/perf-testing/experiment_type.json | 2 +- src/encoded/tests/data/perf-testing/lab.json | 4 ++-- .../tests/data/workbook-inserts/enzyme.json | 7 ++++-- .../workbook-inserts/experiment_hi_c.json | 6 ++--- .../workbook-inserts/experiment_type.json | 2 +- .../tests/data/workbook-inserts/lab.json | 2 +- src/encoded/visualization.py | 2 ++ 15 files changed, 55 insertions(+), 47 deletions(-) diff --git a/src/encoded/tests/data/inserts/enzyme.json b/src/encoded/tests/data/inserts/enzyme.json index db9a595c4a..d413a7c08b 100644 --- a/src/encoded/tests/data/inserts/enzyme.json +++ b/src/encoded/tests/data/inserts/enzyme.json @@ -1,7 +1,7 @@ [ { "name": "HindIII", - "aliases": ["dcic:hindIII_neb"], + "aliases": ["4dn-dcic-lab:hindIII_neb", "dcic:hindIII_neb"], "enzyme_source": "new-england-biolabs", "catalog_number":"R0104", "recognition_sequence": "AAGCTT", @@ -11,7 +11,7 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "url": "https://www.neb.com/products/r0104-hindiii", - "uuid": "4d44d12c-b37c-478b-9bc7-d843cba4bb91" + "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e" }, { "name": "DNaseI", @@ -27,7 +27,10 @@ }, { "name": "MboI", - "aliases":["dcic:mboI_neb"], + "aliases": [ + "dcic:mboI_neb", + "4dn-dcic-lab:mboI_neb" + ], "enzyme_source": "new-england-biolabs", "catalog_number":"R0147", "recognition_sequence": "GATC", @@ -37,7 +40,7 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "url": "https://www.neb.com/products/r0147-mboi", - "uuid": "37750c1c-fce5-4ec5-baa7-ce7858f898ae" + "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03" }, { "name": "MNase", @@ -67,17 +70,17 @@ }, { "name": "NcoI_MspI_BspHI", - "aliases":["dcic:3nzNMB_neb"], + "aliases":["dcic:3nzNMB_neb", "4dn-dcic-lab:3nzNMB_neb"], "enzyme_source": "new-england-biolabs", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "description": "Mixed Enzymes", - "uuid": "6b88eb35-92e7-46fd-87b8-a779cec40c31" + "uuid": "f57bbab4-acb9-4951-9099-a57b015b80c6" }, { "name": "NcoI", - "aliases":["dcic:ncoI_neb"], + "aliases":["dcic:ncoI_neb", "4dn-dcic-lab:ncoI_neb"], "enzyme_source": "new-england-biolabs", "catalog_number":"R0193", "recognition_sequence": "CCATGG", @@ -87,11 +90,11 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "url": "https://www.neb.com/products/r0193-ncoi", - "uuid": "aa5ecd3d-69bf-478c-acbc-82f88b785f7c" + "uuid": "9ff58460-3e4c-4bb1-820d-81bc1127ac53" }, { "name": "MspI", - "aliases":["dcic:mspI_neb"], + "aliases":["dcic:mspI_neb", "4dn-dcic-lab:mspI_neb"], "enzyme_source": "new-england-biolabs", "catalog_number":"R0106", "recognition_sequence": "CCGG", @@ -101,7 +104,7 @@ "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "url": "https://www.neb.com/products/r0106-mspi", - "uuid": "1ff66969-52bc-4226-a056-53b9b0541fe2" + "uuid": "bd56fbbe-9124-4431-8529-2918dc487385" }, { "name": "Tn5 Transposase", diff --git a/src/encoded/tests/data/inserts/experiment_hi_c.json b/src/encoded/tests/data/inserts/experiment_hi_c.json index 54f0f9e584..2592d4e9d9 100644 --- a/src/encoded/tests/data/inserts/experiment_hi_c.json +++ b/src/encoded/tests/data/inserts/experiment_hi_c.json @@ -3,7 +3,7 @@ "accession":"4DNEXO67APU1", "biosample":"231111bc-8535-4448-903e-854af460b254", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, @@ -44,7 +44,7 @@ "accession":"4DNEXO67APT1", "biosample":"231111bc-8535-4448-903e-854af460b254", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, @@ -82,7 +82,7 @@ "accession":"4DNEXO67APV1", "biosample": "231111bc-8535-4448-903e-854af460b242", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "digestion_enzyme": "DNaseI", "digestion_time": 30, "digestion_temperature": 37, @@ -108,7 +108,7 @@ "accession":"4DNEXO67APY1", "biosample":"231111bc-8535-4448-903e-854af460ba4d", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, @@ -138,7 +138,7 @@ "accession":"4DNEXO67APZ1", "biosample":"231111bc-8535-4448-903e-854af460b254", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, @@ -168,7 +168,7 @@ "accession":"4DNEXO67APZ7", "biosample":"111111bc-1111-4448-903e-854af460b123", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, @@ -193,7 +193,7 @@ "accession":"4DNEXO67APZ8", "biosample":"111112bc-1111-4448-903e-854af460b123", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, @@ -218,7 +218,7 @@ "accession":"4DNEXO67APZ9", "biosample":"111112bc-1111-4448-903e-854af460b123", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, diff --git a/src/encoded/tests/data/master-inserts/experiment_type.json b/src/encoded/tests/data/master-inserts/experiment_type.json index 3b35781637..79182d7966 100644 --- a/src/encoded/tests/data/master-inserts/experiment_type.json +++ b/src/encoded/tests/data/master-inserts/experiment_type.json @@ -6,7 +6,7 @@ "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_subclass_short": "Hi-C", "raw_file_types": "Reads (fastq) provided by lab", - "uuid": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "lab": "4dn-dcic-lab", "award": "1U01CA200059-01", "status": "released", @@ -22,7 +22,7 @@ "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_subclass_short": "Hi-C", "raw_file_types": "Reads (fastq) provided by lab", - "uuid": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "lab": "4dn-dcic-lab", "award": "1U01CA200059-01", "status": "released", diff --git a/src/encoded/tests/data/master-inserts/ontology_term.json b/src/encoded/tests/data/master-inserts/ontology_term.json index 461f25d639..30b3c27d8b 100644 --- a/src/encoded/tests/data/master-inserts/ontology_term.json +++ b/src/encoded/tests/data/master-inserts/ontology_term.json @@ -187,7 +187,7 @@ }, { "uuid": "111136bc-8535-4448-903e-854af460a233", - "preferred_name": "CNS", + "preferred_name": "central nervous system", "term_name": "central nervous system", "term_id": "UBERON:0001017", "source_ontologies": ["530016bc-8535-4448-903e-854af460b254"], diff --git a/src/encoded/tests/data/master-inserts/page.json b/src/encoded/tests/data/master-inserts/page.json index 1f030aac64..71121a72eb 100644 --- a/src/encoded/tests/data/master-inserts/page.json +++ b/src/encoded/tests/data/master-inserts/page.json @@ -40,9 +40,8 @@ "description": "Documentation and information about file transformation and analysis pipelines.", "content": [ "reusable-dummy-sections.lorem-ipsum-overview", - "resources.analysis.hi-c-pipeline.alignment", - "resources.analysis.hi-c-pipeline.step-ii", - "resources.analysis.hi-c-pipeline.step-iii-options" + "resources.data-analysis.hi_c-processing-pipeline.alignment", + "resources.data-analysis.hi_c-processing-pipeline.matrix-aggregation" ], "table-of-contents": { "enabled": true, diff --git a/src/encoded/tests/data/master-inserts/static_section.json b/src/encoded/tests/data/master-inserts/static_section.json index 5e88ed60f6..bb139c312f 100644 --- a/src/encoded/tests/data/master-inserts/static_section.json +++ b/src/encoded/tests/data/master-inserts/static_section.json @@ -310,7 +310,7 @@ { - "name" : "resources.analysis.hi-c-pipeline.alignment", + "name" : "resources.data-analysis.hi_c-processing-pipeline.alignment", "uuid" : "10000000-0000-0000-0000-ffff00001000", "title" : "Alignment", "body" : "Lorem ipsum dolor amet offal plaid readymade unicorn kombucha skateboard. Direct trade pop-up salvia organic. Truffaut lomo food truck man bun gastropub hella portland seitan post-ironic quinoa swag. Franzen flexitarian pour-over fam ennui. Freegan fanny pack tumeric vaporware tacos gluten-free quinoa +1 activated charcoal portland pok pok chartreuse actually. Church-key unicorn brooklyn migas paleo wolf.\n\n### A Header\n\nTaxidermy celiac scenester sustainable disrupt vaporware. Authentic chicharrones direct trade narwhal VHS iceland. Messenger bag intelligentsia seitan quinoa, hashtag YOLO cornhole VHS bitters. Gochujang sriracha messenger bag, mlkshk lyft authentic sartorial vinyl flexitarian godard green juice vice fam roof party jianbing.", @@ -321,7 +321,7 @@ "award": "b0b9c607-f8b4-4f02-93f4-9895b461334b" }, { - "name" : "resources.analysis.hi-c-pipeline.step-ii", + "name" : "resources.data-analysis.hi_c-processing-pipeline.filtering", "uuid" : "10000000-0000-0000-0000-ffff00001001", "title" : "Step II", "body" : "Lorem ipsum dolor amet offal plaid readymade unicorn kombucha skateboard. Direct trade pop-up salvia organic. Truffaut lomo food truck man bun gastropub hella portland seitan post-ironic quinoa swag. Franzen flexitarian pour-over fam ennui. Freegan fanny pack tumeric vaporware tacos gluten-free quinoa +1 activated charcoal portland pok pok chartreuse actually. Church-key unicorn brooklyn migas paleo wolf.\n\n### Header 4\n\nTaxidermy celiac scenester sustainable disrupt vaporware. Authentic chicharrones direct trade narwhal VHS iceland. Messenger bag intelligentsia seitan quinoa, hashtag YOLO cornhole VHS bitters. Gochujang sriracha messenger bag, mlkshk lyft authentic sartorial vinyl flexitarian godard green juice vice fam roof party jianbing.", @@ -332,7 +332,7 @@ "award": "b0b9c607-f8b4-4f02-93f4-9895b461334b" }, { - "name" : "resources.analysis.hi-c-pipeline.step-iii-options", + "name" : "resources.data-analysis.hi_c-processing-pipeline.matrix-aggregation", "uuid" : "10000000-0000-0000-0000-ffff00001002", "title" : "Step III Options", "body" : "Lorem ipsum dolor amet offal plaid readymade unicorn kombucha skateboard. Direct trade pop-up salvia organic. Truffaut lomo food truck man bun gastropub hella portland seitan post-ironic quinoa swag. Franzen flexitarian pour-over fam ennui. Freegan fanny pack tumeric vaporware tacos gluten-free quinoa +1 activated charcoal portland pok pok chartreuse actually. Church-key unicorn brooklyn migas paleo wolf.\n\n### Header Five Maybe\n\nTaxidermy celiac scenester sustainable disrupt vaporware. Authentic chicharrones direct trade narwhal VHS iceland. Messenger bag intelligentsia seitan quinoa, hashtag YOLO cornhole VHS bitters. Gochujang sriracha messenger bag, mlkshk lyft authentic sartorial vinyl flexitarian godard green juice vice fam roof party jianbing.", diff --git a/src/encoded/tests/data/perf-testing/enzyme.json b/src/encoded/tests/data/perf-testing/enzyme.json index 87b79a5e7d..a47a6d4481 100644 --- a/src/encoded/tests/data/perf-testing/enzyme.json +++ b/src/encoded/tests/data/perf-testing/enzyme.json @@ -12,7 +12,8 @@ "award": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "public_release": "2017-04-10", "aliases": [ - "dcic:mboI_neb" + "dcic:mboI_neb", + "4dn-dcic-lab:mboI_neb" ], "date_created": "2017-04-09T17:24:16.590926+00:00", "cut_position": 0, @@ -20,4 +21,4 @@ "site_length": 4, "schema_version": "1" } -] \ No newline at end of file +] diff --git a/src/encoded/tests/data/perf-testing/experiment_hi_c.json b/src/encoded/tests/data/perf-testing/experiment_hi_c.json index e0ad493bff..e30d44acf2 100644 --- a/src/encoded/tests/data/perf-testing/experiment_hi_c.json +++ b/src/encoded/tests/data/perf-testing/experiment_hi_c.json @@ -39,7 +39,7 @@ "ligation_time": 240.0, "digestion_enzyme": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "fragment_size_selection_method": "SPRI beads", - "experiment_type": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "tagging_method": "bio-dATP" }, { @@ -82,7 +82,7 @@ "ligation_time": 240.0, "digestion_enzyme": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "fragment_size_selection_method": "SPRI beads", - "experiment_type": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "tagging_method": "bio-dATP" }, { @@ -125,7 +125,7 @@ "ligation_time": 240.0, "digestion_enzyme": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "fragment_size_selection_method": "SPRI beads", - "experiment_type": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "date_created": "2018-05-27T04:58:03.564710+00:00" }, { @@ -168,7 +168,7 @@ "ligation_time": 240.0, "digestion_enzyme": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "fragment_size_selection_method": "SPRI beads", - "experiment_type": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "date_created": "2018-05-27T04:58:07.673563+00:00" }, { @@ -211,7 +211,7 @@ "ligation_time": 240.0, "digestion_enzyme": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "fragment_size_selection_method": "SPRI beads", - "experiment_type": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "date_created": "2018-05-27T04:58:04.606757+00:00" }, { @@ -254,7 +254,7 @@ "ligation_time": 240.0, "digestion_enzyme": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "fragment_size_selection_method": "SPRI beads", - "experiment_type": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "date_created": "2018-05-27T04:58:08.674387+00:00" }, { @@ -297,7 +297,7 @@ "ligation_time": 240.0, "digestion_enzyme": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "fragment_size_selection_method": "SPRI beads", - "experiment_type": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "date_created": "2018-05-27T04:58:05.618160+00:00" }, { @@ -340,7 +340,7 @@ "ligation_time": 240.0, "digestion_enzyme": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "fragment_size_selection_method": "SPRI beads", - "experiment_type": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "date_created": "2018-05-27T04:58:09.669947+00:00" } ] diff --git a/src/encoded/tests/data/perf-testing/experiment_type.json b/src/encoded/tests/data/perf-testing/experiment_type.json index 10ebb009d4..cdfe1bfbe0 100644 --- a/src/encoded/tests/data/perf-testing/experiment_type.json +++ b/src/encoded/tests/data/perf-testing/experiment_type.json @@ -6,7 +6,7 @@ "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_subclass_short": "Hi-C", "raw_file_types": "Reads (fastq) provided by lab", - "uuid": "a17b17cd-544a-3a3b-abc3-17a544544b3c", + "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "lab": "4dn-dcic-lab", "award": "1U01CA200059-01", "other_tags": ["DNA-DNA"], diff --git a/src/encoded/tests/data/perf-testing/lab.json b/src/encoded/tests/data/perf-testing/lab.json index 0052bc52f3..15a3cc1f62 100644 --- a/src/encoded/tests/data/perf-testing/lab.json +++ b/src/encoded/tests/data/perf-testing/lab.json @@ -17,7 +17,7 @@ "awards": [ "b0b9c607-f8b4-4f02-93f4-9895b461334b" ], - "title": "4DN DCIC Lab, HMS", + "title": "4DN DCIC, HMS", "institute_label": "HMS", "date_created": "2017-04-07T19:56:09.652127+00:00", "pi": "986b362f-4eb6-4a9c-8173-3ab267307e3a", @@ -47,4 +47,4 @@ "institute_label": "UCSD", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf" } -] \ No newline at end of file +] diff --git a/src/encoded/tests/data/workbook-inserts/enzyme.json b/src/encoded/tests/data/workbook-inserts/enzyme.json index 2f63b0a379..6950e37019 100644 --- a/src/encoded/tests/data/workbook-inserts/enzyme.json +++ b/src/encoded/tests/data/workbook-inserts/enzyme.json @@ -13,7 +13,10 @@ }, { "name": "MboI", - "aliases": ["dcic:mboI_neb"], + "aliases": [ + "dcic:mboI_neb", + "4dn-dcic-lab:mboI_neb" + ], "enzyme_source": "thermofisher-scientific", "catalog_number": "R0147", "recognition_sequence": "GATC", @@ -23,6 +26,6 @@ "lab": "test-4dn-lab", "submitted_by": "wrangler@wrangler.com", "url": "https://www.neb.com/products/r0147-mboi", - "uuid": "37750c1c-fce5-4ec5-baa7-ce7858f898ae" + "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03" } ] diff --git a/src/encoded/tests/data/workbook-inserts/experiment_hi_c.json b/src/encoded/tests/data/workbook-inserts/experiment_hi_c.json index 918c6ee5a3..5b70c0a683 100644 --- a/src/encoded/tests/data/workbook-inserts/experiment_hi_c.json +++ b/src/encoded/tests/data/workbook-inserts/experiment_hi_c.json @@ -3,7 +3,7 @@ "accession": "4DNEXO67APU1", "biosample": "231111bc-8535-4448-903e-854af460b254", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, @@ -35,7 +35,7 @@ "accession": "4DNEXO67APT1", "biosample": "231111bc-8535-4448-903e-854af460b254", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "enzyme_lot_number": "123456", "average_fragment_size": 100, "digestion_time": 30, @@ -63,7 +63,7 @@ "accession": "4DNEXO67APV1", "biosample": "231111bc-8535-4448-903e-854af460b242", "fragmentation_method": "chemical", - "experiment_type": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "digestion_enzyme": "DNaseI", "digestion_time": 30, "digestion_temperature": 37, diff --git a/src/encoded/tests/data/workbook-inserts/experiment_type.json b/src/encoded/tests/data/workbook-inserts/experiment_type.json index fcab8fea5f..5e0dea4f85 100644 --- a/src/encoded/tests/data/workbook-inserts/experiment_type.json +++ b/src/encoded/tests/data/workbook-inserts/experiment_type.json @@ -6,7 +6,7 @@ "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_subclass_short": "Hi-C", "raw_file_types": "Reads (fastq) provided by lab", - "uuid": "b17b17cd-544a-3a3b-abc3-17a544544b3c", + "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "lab": "test-4dn-lab", "award": "1U01CA200059-02", "other_tags": ["DNA-DNA"], diff --git a/src/encoded/tests/data/workbook-inserts/lab.json b/src/encoded/tests/data/workbook-inserts/lab.json index eb3b298385..dbc2d26010 100644 --- a/src/encoded/tests/data/workbook-inserts/lab.json +++ b/src/encoded/tests/data/workbook-inserts/lab.json @@ -2,7 +2,7 @@ { "awards": ["Test-4DN"], "name": "test-4dn-lab", - "title": "4DN Testing Lab", + "title": "4DN DCIC, HMS", "address2": "10 Schattuck Street", "address1": "Biomedical Bioinfomatics", "city": "Boston", diff --git a/src/encoded/visualization.py b/src/encoded/visualization.py index eaee9dccb1..0f2322b30f 100644 --- a/src/encoded/visualization.py +++ b/src/encoded/visualization.py @@ -292,6 +292,8 @@ def bar_plot_chart(context, request): search_param_lists['limit'] = search_param_lists['from'] = [0] subreq = make_search_subreq(request, '{}?{}'.format('/browse/', urlencode(search_param_lists, True)) ) + # TODO/FYI/20241120: Set breakpoint here and observe ES query WRT smaht-portal work for C4-1192, i.e. + # recently released files grouped by month, and cell-line/donor, and then file type/sequencer/assay. search_result = perform_search_request(None, subreq, custom_aggregations=primary_agg) for field_to_delete in ['@context', '@id', '@type', '@graph', 'title', 'filters', 'facets', 'sort', 'clear_filters', 'actions', 'columns']: From 084b0ce808fadc8a04174b12705b0ef7c8ca8ca6 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 21 Nov 2024 21:52:53 -0500 Subject: [PATCH 06/10] backed out inserts data update to static_section.json and page.json - not needed --- src/encoded/tests/data/master-inserts/page.json | 5 +++-- src/encoded/tests/data/master-inserts/static_section.json | 6 +++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/encoded/tests/data/master-inserts/page.json b/src/encoded/tests/data/master-inserts/page.json index 71121a72eb..1f030aac64 100644 --- a/src/encoded/tests/data/master-inserts/page.json +++ b/src/encoded/tests/data/master-inserts/page.json @@ -40,8 +40,9 @@ "description": "Documentation and information about file transformation and analysis pipelines.", "content": [ "reusable-dummy-sections.lorem-ipsum-overview", - "resources.data-analysis.hi_c-processing-pipeline.alignment", - "resources.data-analysis.hi_c-processing-pipeline.matrix-aggregation" + "resources.analysis.hi-c-pipeline.alignment", + "resources.analysis.hi-c-pipeline.step-ii", + "resources.analysis.hi-c-pipeline.step-iii-options" ], "table-of-contents": { "enabled": true, diff --git a/src/encoded/tests/data/master-inserts/static_section.json b/src/encoded/tests/data/master-inserts/static_section.json index bb139c312f..5e88ed60f6 100644 --- a/src/encoded/tests/data/master-inserts/static_section.json +++ b/src/encoded/tests/data/master-inserts/static_section.json @@ -310,7 +310,7 @@ { - "name" : "resources.data-analysis.hi_c-processing-pipeline.alignment", + "name" : "resources.analysis.hi-c-pipeline.alignment", "uuid" : "10000000-0000-0000-0000-ffff00001000", "title" : "Alignment", "body" : "Lorem ipsum dolor amet offal plaid readymade unicorn kombucha skateboard. Direct trade pop-up salvia organic. Truffaut lomo food truck man bun gastropub hella portland seitan post-ironic quinoa swag. Franzen flexitarian pour-over fam ennui. Freegan fanny pack tumeric vaporware tacos gluten-free quinoa +1 activated charcoal portland pok pok chartreuse actually. Church-key unicorn brooklyn migas paleo wolf.\n\n### A Header\n\nTaxidermy celiac scenester sustainable disrupt vaporware. Authentic chicharrones direct trade narwhal VHS iceland. Messenger bag intelligentsia seitan quinoa, hashtag YOLO cornhole VHS bitters. Gochujang sriracha messenger bag, mlkshk lyft authentic sartorial vinyl flexitarian godard green juice vice fam roof party jianbing.", @@ -321,7 +321,7 @@ "award": "b0b9c607-f8b4-4f02-93f4-9895b461334b" }, { - "name" : "resources.data-analysis.hi_c-processing-pipeline.filtering", + "name" : "resources.analysis.hi-c-pipeline.step-ii", "uuid" : "10000000-0000-0000-0000-ffff00001001", "title" : "Step II", "body" : "Lorem ipsum dolor amet offal plaid readymade unicorn kombucha skateboard. Direct trade pop-up salvia organic. Truffaut lomo food truck man bun gastropub hella portland seitan post-ironic quinoa swag. Franzen flexitarian pour-over fam ennui. Freegan fanny pack tumeric vaporware tacos gluten-free quinoa +1 activated charcoal portland pok pok chartreuse actually. Church-key unicorn brooklyn migas paleo wolf.\n\n### Header 4\n\nTaxidermy celiac scenester sustainable disrupt vaporware. Authentic chicharrones direct trade narwhal VHS iceland. Messenger bag intelligentsia seitan quinoa, hashtag YOLO cornhole VHS bitters. Gochujang sriracha messenger bag, mlkshk lyft authentic sartorial vinyl flexitarian godard green juice vice fam roof party jianbing.", @@ -332,7 +332,7 @@ "award": "b0b9c607-f8b4-4f02-93f4-9895b461334b" }, { - "name" : "resources.data-analysis.hi_c-processing-pipeline.matrix-aggregation", + "name" : "resources.analysis.hi-c-pipeline.step-iii-options", "uuid" : "10000000-0000-0000-0000-ffff00001002", "title" : "Step III Options", "body" : "Lorem ipsum dolor amet offal plaid readymade unicorn kombucha skateboard. Direct trade pop-up salvia organic. Truffaut lomo food truck man bun gastropub hella portland seitan post-ironic quinoa swag. Franzen flexitarian pour-over fam ennui. Freegan fanny pack tumeric vaporware tacos gluten-free quinoa +1 activated charcoal portland pok pok chartreuse actually. Church-key unicorn brooklyn migas paleo wolf.\n\n### Header Five Maybe\n\nTaxidermy celiac scenester sustainable disrupt vaporware. Authentic chicharrones direct trade narwhal VHS iceland. Messenger bag intelligentsia seitan quinoa, hashtag YOLO cornhole VHS bitters. Gochujang sriracha messenger bag, mlkshk lyft authentic sartorial vinyl flexitarian godard green juice vice fam roof party jianbing.", From 066c5016ba6f911ce1b86bf84ba17afba3bd61c1 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 21 Nov 2024 21:54:41 -0500 Subject: [PATCH 07/10] added comments to base.ini on how to run mitmproxy to observe elasticsearch traffic easily when running locally for dev --- base.ini | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/base.ini b/base.ini index dbdffccfcd..749907fb2e 100644 --- a/base.ini +++ b/base.ini @@ -9,6 +9,14 @@ file_wfout_bucket = encoded-4dn-files # this really shouldn't be used with development, only uncomment if your sure system_bucket = elasticbeanstalk-encoded-4dn-system elasticsearch.server = 127.0.0.1:9200 +# The elasticsearch.server.actual_port property is useful (only) for running a localhost ElasticSearch +# proxy in order to observe traffic (requests/responses) between portal and ElasticSearch with a tool like +# mitmweb; e.g. setting elasticsearch.server.actual_port to 9201 and elasticsearch.server to localhost:9200 +# will case ElasticSearch to actually run on port 9201 but will cause portal to talk to it via port 9200, +# and then we can run mitmweb --mode reverse:http://localhost:9201 -p 9200 --web-port 8081 which will +# allow us to browse to http://localhost:8081 locally to observe all of the ElasticSearch traffic; +# and note to install mitmweb do: pip install mitmproxy +# elasticsearch.server.actual_port = 9201 ontology_path = %(here)s/ontology.json aws_ip_ranges_path = %(here)s/aws-ip-ranges.json #this is to reroute downloads to something other than aws s3 From 460000d5cede2b7cbd6483fd7e11ea4407c28e32 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 21 Nov 2024 21:55:55 -0500 Subject: [PATCH 08/10] updated changelog --- CHANGELOG.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index b51109dca0..9bb57bb07e 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -13,6 +13,8 @@ Change Log * Fixed up some inserts data to match 4dn/data/staging. * Updated dcicutils to latest version (8.16.4). * Updated dcicsnovault to latest version (11.23.0). +* Added comments to base.ini on how to use the open sourch mitmproxy utility to observe OpenSearch + traffic easily when running locally for development; via the elasticsearch.server.actual_port property. 8.4.4 From 6dd1dc3ed1433d8da3982e648c91d0c324995382 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Sat, 23 Nov 2024 10:24:41 -0500 Subject: [PATCH 09/10] more inserts data updates to consistentize with prod --- Makefile | 2 ++ src/encoded/tests/data/inserts/biosource.json | 1 + src/encoded/tests/data/inserts/enzyme.json | 7 +++++-- src/encoded/tests/data/inserts/experiment_atacseq.json | 2 +- src/encoded/tests/data/inserts/vendor.json | 4 ++-- src/encoded/tests/data/master-inserts/experiment_type.json | 4 ++-- src/encoded/tests/data/master-inserts/ontology_term.json | 2 ++ src/encoded/tests/data/master-inserts/organism.json | 2 +- src/encoded/tests/data/master-inserts/page.json | 4 ++-- src/encoded/tests/data/master-inserts/static_section.json | 6 ++++-- 10 files changed, 22 insertions(+), 12 deletions(-) diff --git a/Makefile b/Makefile index 1d7689490e..7e66912fa3 100644 --- a/Makefile +++ b/Makefile @@ -112,7 +112,9 @@ kibana-stop: kill: # kills back-end processes associated with the application. Use with care. pkill -f postgres & pkill -f elasticsearch & + -pkill -f opensearch & pkill -f moto_server & + -pkill -f nginx & clean-python: @echo -n "Are you sure? This will wipe all libraries installed on this virtualenv [y/N] " && read ans && [ $${ans:-N} = y ] diff --git a/src/encoded/tests/data/inserts/biosource.json b/src/encoded/tests/data/inserts/biosource.json index 5246fdd61d..fc557ec5fe 100644 --- a/src/encoded/tests/data/inserts/biosource.json +++ b/src/encoded/tests/data/inserts/biosource.json @@ -80,6 +80,7 @@ }, { "uuid": "0f011b1e-b772-4f2a-8c24-cc55de28a994", + "accession": "4DNSRVWZS4XO", "description": "Homo sapiens GM12878 immortalized cell line", "biosource_type": "immortalized cell line", "individual":"4DNINOOOAAQ1", diff --git a/src/encoded/tests/data/inserts/enzyme.json b/src/encoded/tests/data/inserts/enzyme.json index d413a7c08b..136ae93e08 100644 --- a/src/encoded/tests/data/inserts/enzyme.json +++ b/src/encoded/tests/data/inserts/enzyme.json @@ -108,11 +108,14 @@ }, { "name": "Tn5 Transposase", - "aliases":["dcic:tn5transposase"], + "aliases": [ + "dcic:transposase_illumina", + "4dn-dcic-lab:transposase_illumina" + ], "enzyme_source": "dcic:illumina", "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", - "uuid": "1ff66969-52bc-4226-a056-111110541fe2" + "uuid": "cac89b2d-6985-4b14-af7e-0808a5fd103b" } ] diff --git a/src/encoded/tests/data/inserts/experiment_atacseq.json b/src/encoded/tests/data/inserts/experiment_atacseq.json index 2854bed42a..bd81a4e18a 100644 --- a/src/encoded/tests/data/inserts/experiment_atacseq.json +++ b/src/encoded/tests/data/inserts/experiment_atacseq.json @@ -2,7 +2,7 @@ { "accession":"4DNEX167AAA1", "biosample":"a9163992-7486-4edd-b21d-f492884bff63", - "experiment_type": "c17b17cd-544a-3a3b-abc3-17a544544b3c", + "experiment_type": "5b35245d-5777-4983-b7e8-8dffd9ab83ab", "enzyme_lot_number": "123456", "enzyme_incubation_time": 30, "incubation_temperature": 55, diff --git a/src/encoded/tests/data/inserts/vendor.json b/src/encoded/tests/data/inserts/vendor.json index e0629faa14..6f23846bf2 100644 --- a/src/encoded/tests/data/inserts/vendor.json +++ b/src/encoded/tests/data/inserts/vendor.json @@ -35,11 +35,11 @@ { "title": "Illumina", "name": "illumina", - "aliases":["dcic:illumina"], + "aliases":["dcic:illumina", "4dn-dcic-lab:illumina"], "award": "1U01CA200059-01", "lab": "4dn-dcic-lab", "submitted_by": "wrangler@wrangler.com", "url": "https://www.illumina.com/", - "uuid": "b31106bc-8535-4448-903e-854af4611111" + "uuid": "23ce3be3-a8fa-47e7-b414-3ce673c08257" } ] diff --git a/src/encoded/tests/data/master-inserts/experiment_type.json b/src/encoded/tests/data/master-inserts/experiment_type.json index 79182d7966..f84db89330 100644 --- a/src/encoded/tests/data/master-inserts/experiment_type.json +++ b/src/encoded/tests/data/master-inserts/experiment_type.json @@ -67,7 +67,7 @@ "lab": "4dn-dcic-lab", "award": "1U01CA200059-01", "status": "released", - "uuid": "c17b17cd-544a-3a3b-abc3-17a544544b3c", + "uuid": "5b35245d-5777-4983-b7e8-8dffd9ab83ab", "valid_item_types": ["ExperimentAtacseq"] }, { @@ -268,7 +268,7 @@ "assay_subclassification": "Single Particle Tracking", "assay_subclass_short": "SPT", "raw_file_types": "Reads (fastq) provided by lab", - "uuid": "a98e17cd-544a-3a3b-fed3-17a658544f3c", + "uuid": "d654c884-fc4f-4d53-818c-fc06fc33dfb3", "lab": "4dn-dcic-lab", "award": "1U01CA200059-01", "status": "released", diff --git a/src/encoded/tests/data/master-inserts/ontology_term.json b/src/encoded/tests/data/master-inserts/ontology_term.json index 30b3c27d8b..b2771bbadd 100644 --- a/src/encoded/tests/data/master-inserts/ontology_term.json +++ b/src/encoded/tests/data/master-inserts/ontology_term.json @@ -695,6 +695,8 @@ "source_ontologies": ["530016bc-8535-4448-903e-854af460b254"], "term_id": "UBERON:0002097", "term_name": "skin of body", + "preferred_name": "skin", + "synonyms": ["skin organ", "entire skin"], "term_url": "http://purl.obolibrary.org/obo/UBERON_0002097", "uuid": "111188bc-8535-4448-903e-854af460a233" }, diff --git a/src/encoded/tests/data/master-inserts/organism.json b/src/encoded/tests/data/master-inserts/organism.json index d84bc9e030..a24efbef10 100644 --- a/src/encoded/tests/data/master-inserts/organism.json +++ b/src/encoded/tests/data/master-inserts/organism.json @@ -14,7 +14,7 @@ "uuid": "3413218c-3d86-498b-a0a2-9a406638e786" }, { - "name": "fly", + "name": "fruit fly", "scientific_name": "Drosophila melanogaster", "taxon_id": "7227", "genome_assembly": "dm6", diff --git a/src/encoded/tests/data/master-inserts/page.json b/src/encoded/tests/data/master-inserts/page.json index 1f030aac64..5633c3aed7 100644 --- a/src/encoded/tests/data/master-inserts/page.json +++ b/src/encoded/tests/data/master-inserts/page.json @@ -40,8 +40,8 @@ "description": "Documentation and information about file transformation and analysis pipelines.", "content": [ "reusable-dummy-sections.lorem-ipsum-overview", - "resources.analysis.hi-c-pipeline.alignment", - "resources.analysis.hi-c-pipeline.step-ii", + "resources.data-analysis.hi_c-processing-pipeline.alignment", + "resources.data-analysis.hi_c-processing-pipeline.filtering", "resources.analysis.hi-c-pipeline.step-iii-options" ], "table-of-contents": { diff --git a/src/encoded/tests/data/master-inserts/static_section.json b/src/encoded/tests/data/master-inserts/static_section.json index 5e88ed60f6..b31dfc49f2 100644 --- a/src/encoded/tests/data/master-inserts/static_section.json +++ b/src/encoded/tests/data/master-inserts/static_section.json @@ -310,7 +310,8 @@ { - "name" : "resources.analysis.hi-c-pipeline.alignment", + "name": "resources.data-analysis.hi_c-processing-pipeline.alignment", + "aliases": ["dcic:resources.data-analysis.hi_c-processing-pipeline.alignment"], "uuid" : "10000000-0000-0000-0000-ffff00001000", "title" : "Alignment", "body" : "Lorem ipsum dolor amet offal plaid readymade unicorn kombucha skateboard. Direct trade pop-up salvia organic. Truffaut lomo food truck man bun gastropub hella portland seitan post-ironic quinoa swag. Franzen flexitarian pour-over fam ennui. Freegan fanny pack tumeric vaporware tacos gluten-free quinoa +1 activated charcoal portland pok pok chartreuse actually. Church-key unicorn brooklyn migas paleo wolf.\n\n### A Header\n\nTaxidermy celiac scenester sustainable disrupt vaporware. Authentic chicharrones direct trade narwhal VHS iceland. Messenger bag intelligentsia seitan quinoa, hashtag YOLO cornhole VHS bitters. Gochujang sriracha messenger bag, mlkshk lyft authentic sartorial vinyl flexitarian godard green juice vice fam roof party jianbing.", @@ -321,7 +322,8 @@ "award": "b0b9c607-f8b4-4f02-93f4-9895b461334b" }, { - "name" : "resources.analysis.hi-c-pipeline.step-ii", + "name": "resources.data-analysis.hi_c-processing-pipeline.filtering", + "aliases": ["dcic:resources.data-analysis.hi_c-processing-pipeline.filtering"], "uuid" : "10000000-0000-0000-0000-ffff00001001", "title" : "Step II", "body" : "Lorem ipsum dolor amet offal plaid readymade unicorn kombucha skateboard. Direct trade pop-up salvia organic. Truffaut lomo food truck man bun gastropub hella portland seitan post-ironic quinoa swag. Franzen flexitarian pour-over fam ennui. Freegan fanny pack tumeric vaporware tacos gluten-free quinoa +1 activated charcoal portland pok pok chartreuse actually. Church-key unicorn brooklyn migas paleo wolf.\n\n### Header 4\n\nTaxidermy celiac scenester sustainable disrupt vaporware. Authentic chicharrones direct trade narwhal VHS iceland. Messenger bag intelligentsia seitan quinoa, hashtag YOLO cornhole VHS bitters. Gochujang sriracha messenger bag, mlkshk lyft authentic sartorial vinyl flexitarian godard green juice vice fam roof party jianbing.", From 4c6c0c69566b74ec4d5d632e857d62b5372cda7c Mon Sep 17 00:00:00 2001 From: David Michaels Date: Sat, 23 Nov 2024 21:44:07 -0500 Subject: [PATCH 10/10] more data file fixups --- src/encoded/tests/data/inserts/workflow.json | 4 ++-- src/encoded/tests/data/master-inserts/ontology_term.json | 1 + src/encoded/tests/data/perf-testing/ontology_term.json | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/src/encoded/tests/data/inserts/workflow.json b/src/encoded/tests/data/inserts/workflow.json index 403a93a347..9e4d2bf29d 100644 --- a/src/encoded/tests/data/inserts/workflow.json +++ b/src/encoded/tests/data/inserts/workflow.json @@ -11262,7 +11262,7 @@ "uuid": "6fb021e9-858c-4561-8ce1-e0adc673e0b5" }, { - "accession": "4DNWF2BBZ1E1", + "accession": "4DNWF2BBZ1EE", "app_name": "encode-atacseq-aln", "app_version": "1.1.1", "arguments": [ @@ -11658,7 +11658,7 @@ "uuid": "d497c075-ab57-4c5b-8c65-7bb8410f26fa" }, { - "accession": "4DNWF2VTG8I1", + "accession": "4DNWF2VTG8II", "app_name": "encode-atacseq-postaln", "app_version": "1.1.1", "arguments": [ diff --git a/src/encoded/tests/data/master-inserts/ontology_term.json b/src/encoded/tests/data/master-inserts/ontology_term.json index b2771bbadd..05cb815b46 100644 --- a/src/encoded/tests/data/master-inserts/ontology_term.json +++ b/src/encoded/tests/data/master-inserts/ontology_term.json @@ -705,6 +705,7 @@ "namespace": "http://www.ebi.ac.uk/efo", "term_id": "EFO:0000322", "term_name": "cell line", + "preferred_name": "cell line", "uuid": "111189bc-8535-4448-903e-854af460a233", "source_ontologies": ["530006bc-8535-4448-903e-854af460b254"], "term_url": "http://www.ebi.ac.uk/efo/EFO_0000322" diff --git a/src/encoded/tests/data/perf-testing/ontology_term.json b/src/encoded/tests/data/perf-testing/ontology_term.json index af43642db7..759e5a2678 100644 --- a/src/encoded/tests/data/perf-testing/ontology_term.json +++ b/src/encoded/tests/data/perf-testing/ontology_term.json @@ -18,6 +18,7 @@ "status": "released", "submitted_by": "986b362f-4eb6-4a9c-8173-3ab267307e3a", "term_name": "cell line", + "preferred_name": "cell line", "definition": "A cell line is a population of cells cultured in vitro that are descended through one or more generations (and possible sub-cultures) from a single primary culture which was originally derived from part of an organism.", "term_url": "http://www.ebi.ac.uk/efo/EFO_0000322", "term_id": "EFO:0000322", @@ -147,4 +148,4 @@ "date_created": "2017-04-26T07:22:23.265915+00:00", "uuid": "111114bc-8535-4448-903e-854af460a233" } -] \ No newline at end of file +]