Updated more inserts data files from fourfront-data to ease importing…

… of data for local dev.
4dn-dcic · Nov 21, 2024 · 543b178 · 543b178
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Showing 15 changed files with 55 additions and 47 deletions.
diff --git 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": "[email protected]",
         "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": "[email protected]",
         "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": "[email protected]",
         "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": "[email protected]",
         "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": "[email protected]",
         "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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -12,12 +12,13 @@
         "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, 
         "recognition_sequence": "GATC", 
         "site_length": 4, 
         "schema_version": "1"
     }
-]
+]
diff --git 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
@@ -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
@@ -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"
     }
-]
+]
diff --git 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": "[email protected]",
         "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
@@ -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
@@ -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
@@ -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",