Repository: DataBiosphere/newt-transformer

Issue:
Add `program` metadata
The Gen3 data model provides a `program` object, in addition to `project` and `study`.
Currently the `newt` output includes `project` and `study` yet not `program`.
The `program` object should be included in the `newt` output for indexing/display purposes.

┆Issue is synchronized with this [JIRA Task](https://ucsc-cgl.atlassian.net/browse/NEWT-23)
┆Project Name: CGP-Newt
┆Issue Number: NEWT-23


Comments:

Patch:
diff --git a/newt/main.py b/newt/main.py
index f44243e..3910850 100644
--- a/newt/main.py
+++ b/newt/main.py
@@ -16,9 +16,9 @@ def open_json_file(json_path):
         return json.load(fp)
 
 
-def write_output(bundles: typing.Iterator[Bundle], out_file):
+def write_output(bundles: typing.Iterator[Bundle], out_file, pretty_print):
     with open(out_file, 'w') as fp:
-        json.dump(list(bundles), fp)
+        json.dump(list(bundles), fp, indent=2 if pretty_print else None)
 
 
 def add_parser_to_subparser(sub_parser, parse_name, parse_help):
@@ -29,6 +29,8 @@ def add_parser_to_subparser(sub_parser, parse_name, parse_help):
     parser.add_argument('--output-json', dest='output_json',
                         help='where to write transformed output.', required=False,
                         default='out.json')
+    parser.add_argument('--pp', action='store_true', default=False,
+                        help='pretty print output json.')
 
 
 def main(argv=None):
@@ -61,4 +63,4 @@ def main(argv=None):
         raise ValueError(f'Invalid metadata source format {options.transform_source}')
 
     bundle_iterator = transformer.transform()
-    write_output(bundle_iterator, options.output_json)
+    write_output(bundle_iterator, options.output_json, options.pp)
diff --git a/newt/transform/gen3standard.py b/newt/transform/gen3standard.py
index c68389d..4c48f91 100644
--- a/newt/transform/gen3standard.py
+++ b/newt/transform/gen3standard.py
@@ -51,7 +51,10 @@ class Bundle(dict):
         :param linked_field_name: the metadata field that is linked to
         :param link_name: the actual name of the link in the source_field. Usually there is some subtle variation
         """
-        if source_field_name in self.metadata.keys():
+        if linked_field_name == 'program':
+            # Since gen3 export exports a single program, we just grab the only value
+            self.metadata[linked_field_name] = list(metadata_source[linked_field_name].values())[0]
+        elif source_field_name in self.metadata.keys():
             # Get the id of the specific item we want to add
             linked_field_key = self.metadata[source_field_name]['link_fields'][link_name]
             # Get the dictionary that goes with that specific item
@@ -130,7 +133,8 @@ class Gen3Transformer(AbstractTransformer):
                                 MetadataLink('sample', 'case', 'cases.id'),
                                 MetadataLink('case', 'study', 'studies.id#1'),
                                 MetadataLink('demographic', 'case', 'cases.id'),
-                                MetadataLink('study', 'project', 'projects.id')
+                                MetadataLink('study', 'project', 'projects.id'),
+                                MetadataLink('project', 'program', 'id')
                                 ]
 
     def _build_bundle(self, metadata_dict: dict):
diff --git a/scripts/data_bleach.py b/scripts/data_bleach.py
index 8a9be24..c2f17e2 100644
--- a/scripts/data_bleach.py
+++ b/scripts/data_bleach.py
@@ -26,8 +26,9 @@ PUBLIC_FIELDS = [x.split('.') for x in [
     "aliquot.analyte_isolation_method",
     "sample.biospecimen_anatomic_site_detail",
     "sample.biospecimen_anatomic_site",
-    "project.code",
-    "project.name"]]
+    "project.name",
+    "program.code",
+    "project.dbgap_accession_number"]]
 
 
 def error(*args, **kwargs):


Test patch:
diff --git a/tests/schemas.py b/tests/schemas.py
index 1acc954..8ac2944 100644
--- a/tests/schemas.py
+++ b/tests/schemas.py
@@ -124,7 +124,7 @@ data_object_schema = {
 data_bundle = {
     "type": "object",
     # TODO: required, but we don't have checksums for bundles
-    'required': ['data_object_ids', 'created', 'updated', 'version'],  # , 'checksums'],
+    'required': ['data_object_ids', 'created', 'updated', 'version', 'user_metadata'],  # , 'checksums'],
     "properties": {
         "id": {
             "type": "string",
@@ -211,8 +211,14 @@ data_bundle = {
         "user_metadata": {
             "type": "object",
             "additionalProperties": True,
-            "description": "OPTIONAL\n"
-                           "A set of key-value pairs that represent metadata provided by the uploader."
+            "description": "REQUIRED\n"
+                           "A set of key-value pairs that represent metadata provided by the uploader.",
+            'required': ['project', 'program'],
+            "properties": {
+                "project": {"type": "object"},
+                "program": {"type": "object"}
+
+            }
         }
     }
 }
diff --git a/tests/test_all.py b/tests/test_all.py
index 03f3f9b..501d145 100644
--- a/tests/test_all.py
+++ b/tests/test_all.py
@@ -83,7 +83,7 @@ class TestSheepdogGen3TransformingStandard(AbstractTransformerTest, unittest.Tes
 
     def test_sheepdog_gen3_transforming(self):
         message('Run the transformer on sheepdog\'s output')
-        argv = ['new', str(self.test_file), '--output-json', str(self.out_file)]
+        argv = ['new', str(self.test_file), '--output-json', str(self.out_file), '--pp']
         message(f'Passing args: {" ".join(argv)}')
         main(argv)
 
diff --git a/tests/test_data/topmed-public.json b/tests/test_data/topmed-public.json
index 61fce82..d0a64e6 100644
--- a/tests/test_data/topmed-public.json
+++ b/tests/test_data/topmed-public.json
@@ -1,1 +1,1 @@
-{"metadata": {"medication": [], "electrocardiogram_test": [], "aggregated_snp_array": [], "medical_history": [], "sample": [{"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01110_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "57a5282b-8a48-4b30-afe7-63e19bd3aaca", "cases.submitter_id": "HG01110"}, "method_of_sample_procurement": "", "node_id": "d5f553d2-7af5-47eb-be1a-4fa742fd812d", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - blood derived", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}, {"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "NA19238_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "31f6dc4c-a8e7-402e-a292-f6de85287a58", "cases.submitter_id": "NA19238"}, "method_of_sample_procurement": "", "node_id": "e450679d-0c17-467c-8fd5-dba1510f041b", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - other", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}, {"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01111_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "6d13d82a-aa6c-4a3c-8f3d-528899391043", "cases.submitter_id": "HG01111"}, "method_of_sample_procurement": "", "node_id": "f2555751-d329-4b81-a0e9-7989562c860d", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - blood", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}, {"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01249_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "04733067-8a9a-4088-b623-b11debb5caf6", "cases.submitter_id": "HG01249"}, "method_of_sample_procurement": "", "node_id": "4ba2771a-57d9-477f-b0c9-306fceb0a29b", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - blood derived", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}, {"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "NA12878_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "a2630bd9-7849-45fa-b5a0-27aff866bef6", "cases.submitter_id": "NA12878"}, "method_of_sample_procurement": "", "node_id": "eadf3fbd-69dd-4adb-822b-382a9296860a", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - solid tissue", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}], "psychosocial_questionnaire": [], "death_record": [], "simple_germline_variation": [], "core_metadata_collection": [{"publisher": "DCP Data Commons", "rights": "open access", "description": "TopMED Open Access Aligned Reads", "data_type": "WGS", "link_fields": {"projects.id": "09c26ed7-ed2f-52b1-a366-d7dede15cc32", "projects.code": "public"}, "language": "en-US", "format": "CRAM/CRAI", "creator": "Francisco Ortuno", "label": "core_metadata_collection", "submitter_id": "topmed_1000g_collection", "date": "04/13/18", "node_id": "365738d7-487f-48ea-a250-ec3a9124acbd", "relation": "Uchicago", "source": "1000 Genomes", "coverage": "US", "contributor": "DCP", "title": "TopMED 1000G Public Collection", "project_id": "topmed-public", "subject": "sequencing"}, {"publisher": "DCP Data Commons", "rights": "open access", "description": "TopMED Open Access Aligned Reads", "data_type": "WGS", "link_fields": {"projects.id": "09c26ed7-ed2f-52b1-a366-d7dede15cc32", "projects.code": "public"}, "language": "en-US", "format": "CRAM/CRAI", "creator": "Francisco Ortuno", "label": "core_metadata_collection", "submitter_id": "topmed_hapmap_collection", "date": "04/13/18", "node_id": "0a83ffaa-1f90-4bad-9491-ec691e0836b6", "relation": "Uchicago", "source": "HapMap", "coverage": "US", "contributor": "DCP", "title": "TopMED HapMap Public Collection", "project_id": "topmed-public", "subject": "sequencing"}], "primary_history": [], "read_group_qc": [], "publication": [], "cardiac_ct_scan": [], "demographic": [{"age_range": "", "weight": "", "bmi_category": "", "submitter_id": "HG01110-demo", "ethnicity": "hispanic or latino", "girth_protocol_modification": "", "label": "demographic", "height_protocol_modification": "", "hip_circumference": "", "project_id": "topmed-public", "weight_protocol_modification": "", "link_fields": {"cases.id": "57a5282b-8a48-4b30-afe7-63e19bd3aaca", "cases.submitter_id": "HG01110"}, "bmi": "", "year_of_birth": "", "node_id": "91826df5-8b13-4678-b992-aa2cf8231d9b", "height": "", "bsa": "", "waist": "", "gender": "male", "race": "Unknown", "age_at_index": "", "year_of_death": ""}, {"age_range": "", "weight": "", "bmi_category": "", "submitter_id": "NA12878-demo", "ethnicity": "not hispanic or latino", "girth_protocol_modification": "", "label": "demographic", "height_protocol_modification": "", "hip_circumference": "", "project_id": "topmed-public", "weight_protocol_modification": "", "link_fields": {"cases.id": "a2630bd9-7849-45fa-b5a0-27aff866bef6", "cases.submitter_id": "NA12878"}, "bmi": "", "year_of_birth": "", "node_id": "63821bc1-1a22-4dc5-9452-12461cd19ae7", "height": "", "bsa": "", "waist": "", "gender": "female", "race": "white", "age_at_index": "", "year_of_death": ""}, {"age_range": "", "weight": "", "bmi_category": "", "submitter_id": "NA19238-demo", "ethnicity": "not hispanic or latino", "girth_protocol_modification": "", "label": "demographic", "height_protocol_modification": "", "hip_circumference": "", "project_id": "topmed-public", "weight_protocol_modification": "", "link_fields": {"cases.id": "31f6dc4c-a8e7-402e-a292-f6de85287a58", "cases.submitter_id": "NA19238"}, "bmi": "", "year_of_birth": "", "node_id": "2b96e812-4d8f-4cc9-882d-17c3f935b26e", "height": "", "bsa": "", "waist": "", "gender": "female", "race": "black or african american", "age_at_index": "", "year_of_death": ""}, {"age_range": "", "weight": "", "bmi_category": "", "submitter_id": "HG01111-demo", "ethnicity": "hispanic or latino", "girth_protocol_modification": "", "label": "demographic", "height_protocol_modification": "", "hip_circumference": "", "project_id": "topmed-public", "weight_protocol_modification": "", "link_fields": {"cases.id": "6d13d82a-aa6c-4a3c-8f3d-528899391043", "cases.submitter_id": "HG01111"}, "bmi": "", "year_of_birth": "", "node_id": "8d62d054-382d-40f4-8011-cf485545cd90", "height": "", "bsa": "", "waist": "", "gender": "female", "race": "Unknown", "age_at_index": "", "year_of_death": ""}, {"age_range": "", "weight": "", "bmi_category": "", "submitter_id": "HG01249-demo", "ethnicity": "hispanic or latino", "girth_protocol_modification": "", "label": "demographic", "height_protocol_modification": "", "hip_circumference": "", "project_id": "topmed-public", "weight_protocol_modification": "", "link_fields": {"cases.id": "04733067-8a9a-4088-b623-b11debb5caf6", "cases.submitter_id": "HG01249"}, "bmi": "", "year_of_birth": "", "node_id": "94d6c5f2-3733-493e-9f45-4d75d5b7f385", "height": "", "bsa": "", "waist": "", "gender": "female", "race": "Unknown", "age_at_index": "", "year_of_death": ""}], "copy_number_workflow": [], "lab_result": [], "program": [{"dbgap_accession_number": "topmed", "id": "45b91a48-1961-5b9f-9b0f-766bd30665d8", "name": "topmed"}], "phenotype": [], "data_release": {}, "germline_variation_index": [], "allele_expression": [], "reference_file": [], "treatment": [], "alignment_cocleaning_workflow": [], "snp_array_variation": [], "aliquot": [{"aliquot_quantity": "", "aliquot_volume": "", "link_fields": {"samples.submitter_id#1": "NA19238_sample", "samples.id#1": "e450679d-0c17-467c-8fd5-dba1510f041b"}, "analyte_isolation_batch_id": "", "experimental_strategy": "", "experiment_date": "", "analyte_isolation_date": "", "label": "aliquot", "submitter_id": "NWD967078", "amount": "", "node_id": "ad3cf609-1ebf-44bc-bb51-2a72482cf37b", "analyte_isolation_method": "", "analyte_type": "DNA", "exclude": "", "concentration": "", "project_id": "topmed-public", "exclusion_criteria": "", "experiment_batch_id": ""}, {"aliquot_quantity": "", "aliquot_volume": "", "link_fields": {"samples.submitter_id#1": "HG01110_sample", "samples.id#1": "d5f553d2-7af5-47eb-be1a-4fa742fd812d"}, "analyte_isolation_batch_id": "", "experimental_strategy": "", "experiment_date": "", "analyte_isolation_date": "", "label": "aliquot", "submitter_id": "NWD968809", "amount": "", "node_id": "579f0534-7113-42e3-bce8-93067119a19d", "analyte_isolation_method": "", "analyte_type": "DNA", "exclude": "", "concentration": "", "project_id": "topmed-public", "exclusion_criteria": "", "experiment_batch_id": ""}, {"aliquot_quantity": "", "aliquot_volume": "", "link_fields": {"samples.submitter_id#1": "NA12878_sample", "samples.id#1": "eadf3fbd-69dd-4adb-822b-382a9296860a"}, "analyte_isolation_batch_id": "", "experimental_strategy": "", "experiment_date": "", "analyte_isolation_date": "", "label": "aliquot", "submitter_id": "NWD991001", "amount": "", "node_id": "b56735ae-561d-487b-9363-ae8841396b14", "analyte_isolation_method": "", "analyte_type": "DNA", "exclude": "", "concentration": "", "project_id": "topmed-public", "exclusion_criteria": "", "experiment_batch_id": ""}, {"aliquot_quantity": "", "aliquot_volume": "", "link_fields": {"samples.submitter_id#1": "HG01110_sample", "samples.id#1": "d5f553d2-7af5-47eb-be1a-4fa742fd812d"}, "analyte_isolation_batch_id": "", "experimental_strategy": "", "experiment_date": "", "analyte_isolation_date": "", "label": "aliquot", "submitter_id": "NWD100953", "amount": "", "node_id": "eb74367b-cd71-4874-a85d-3c3eb54d74da", "analyte_isolation_method": "", "analyte_type": "DNA", "exclude": "", "concentration": "", "project_id": "topmed-public", "exclusion_criteria": "", "experiment_batch_id": ""}, {"aliquot_quantity": "", "aliquot_volume": "", "link_fields": {"samples.submitter_id#1": "NA12878_sample", "samples.id#1": "eadf3fbd-69dd-4adb-822b-382a9296860a"}, "analyte_isolation_batch_id": "", "experimental_strategy": "", "experiment_date": "", "analyte_isolation_date": "", "label": "aliquot", "submitter_id": "NWD119844", "amount": "", "node_id": "2b231f96-d9ba-4f85-9e7f-fdd3f3b8e615", "analyte_isolation_method": "", "analyte_type": "DNA", "exclude": "", "concentration": "", "project_id": "topmed-public", "exclusion_criteria": "", "experiment_batch_id": ""}, {"aliquot_quantity": "", "aliquot_volume": "", "link_fields": {"samples.submitter_id#1": "NA19238_sample", "samples.id#1": "e450679d-0c17-467c-8fd5-dba1510f041b"}, "analyte_isolation_batch_id": "", "experimental_strategy": "", "experiment_date": "", "analyte_isolation_date": "", "label": "aliquot", "submitter_id": "NWD146103", "amount": "", "node_id": "24d99a44-db65-4cf4-a8fd-254405909820", "analyte_isolation_method": "", "analyte_type": "DNA", "exclude": "", "concentration": "", "project_id": "topmed-public", "exclusion_criteria": "", 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diff --git a/tests/test_data/transformer_sample_output.json b/tests/test_data/transformer_sample_output.json
index 08e583c..118af04 100644
--- a/tests/test_data/transformer_sample_output.json
+++ b/tests/test_data/transformer_sample_output.json
@@ -1,1 +1,1 @@
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