Merge pull request #119 from c3g/fix-allele-descriptions

Add allele descriptions

chord_metadata_service/experiments/descriptions.py

@@ -1,22 +1,29 @@
 from chord_metadata_service.restapi.description_utils import EXTRA_PROPERTIES
 
+
 EXPERIMENT = {
-    "description": "A subject of a phenopacket, representing either a human (typically) or another organism.",
+    "description": "Experiment related metadata.",
     "properties": {
         "id": "An arbitrary identifier for the experiment.",
 
-        "reference_registry_id": "The IHEC EpiRR ID for this dataset, only for IHEC Reference Epigenome datasets. Otherwise leave empty.",
+        "reference_registry_id": "The IHEC EpiRR ID for this dataset, only for IHEC Reference Epigenome datasets. "
+                                 "Otherwise leave empty.",
         "qc_flags": "Any quanlity control observations can be noted here. This field can be omitted if empty",
-        "experiment_type": "(Controlled Vocabulary) The assay target (e.g. ‘DNA Methylation’, ‘mRNA-Seq’, ‘smRNA-Seq’, 'Histone H3K4me1').",
+        "experiment_type": "(Controlled Vocabulary) The assay target (e.g. ‘DNA Methylation’, ‘mRNA-Seq’, ‘smRNA-Seq’, "
+                           "'Histone H3K4me1').",
         "experiment_ontology": "(Ontology: OBI) links to experiment ontology information.",
         "molecule_ontology": "(Ontology: SO) links to molecule ontology information.",
-        "molecule": "(Controlled Vocabulary) The type of molecule that was extracted from the biological material. Include one of the following: total RNA, polyA RNA, cytoplasmic RNA, nuclear RNA, small RNA, genomic DNA, protein, or other.",
-        "library_strategy": "(Controlled Vocabulary) The assay used. These are defined within the SRA metadata specifications with a controlled vocabulary (e.g. ‘Bisulfite-Seq’, ‘RNA-Seq’, ‘ChIP-Seq’). For a complete list, see https://www.ebi.ac.uk/ena/submit/reads-library-strategy.",
+        "molecule": "(Controlled Vocabulary) The type of molecule that was extracted from the biological material."
+                    "Include one of the following: total RNA, polyA RNA, cytoplasmic RNA, nuclear RNA, small RNA, "
+                    "genomic DNA, protein, or other.",
+        "library_strategy": "(Controlled Vocabulary) The assay used. These are defined within the SRA metadata "
+                            "specifications with a controlled vocabulary (e.g. ‘Bisulfite-Seq’, ‘RNA-Seq’, ‘ChIP-Seq’)."
+                            " For a complete list, see https://www.ebi.ac.uk/ena/submit/reads-library-strategy.",
 
-        "other_fields": "The other fields for the experiment",
+        "other_fields": "The other fields for the experiment.",
 
-        "biosample": "Biosample on which this experiment was done",
-        "individual": "Donor on which this experiment was done",
+        "biosample": "Biosample on which this experiment was done.",
+        "individual": "Donor on which this experiment was done.",
 
         **EXTRA_PROPERTIES
     }

chord_metadata_service/experiments/migrations/0006_auto_20200514_1541.py

@@ -0,0 +1,46 @@
+# Generated by Django 2.2.12 on 2020-05-14 19:41
+
+import chord_metadata_service.restapi.validators
+import django.contrib.postgres.fields.jsonb
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0005_auto_20200513_1401'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='experiment',
+            name='biosample',
+            field=models.ForeignKey(blank=True, help_text='Biosample on which this experiment was done.', null=True, on_delete=django.db.models.deletion.SET_NULL, to='phenopackets.Biosample'),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='experiment_ontology',
+            field=django.contrib.postgres.fields.jsonb.JSONField(blank=True, help_text='(Ontology: OBI) links to experiment ontology information.', null=True, validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'chord_metadata_service:ontology_class_list_schema', '$schema': 'http://json-schema.org/draft-07/schema#', 'description': 'Ontology class list', 'items': {'$id': 'chord_metadata_service:ontology_class_schema', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'Schema to describe terms from ontologies.', 'properties': {'id': {'description': 'CURIE style identifier.', 'type': 'string'}, 'label': {'description': 'Human-readable class name.', 'type': 'string'}}, 'required': ['id', 'label'], 'title': 'Ontology class schema', 'type': 'object'}, 'title': 'Ontology class list', 'type': 'array'}, formats=None)]),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='individual',
+            field=models.ForeignKey(blank=True, help_text='Donor on which this experiment was done.', null=True, on_delete=django.db.models.deletion.SET_NULL, to='patients.Individual'),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='molecule',
+            field=models.CharField(blank=True, choices=[('total RNA', 'total RNA'), ('polyA RNA', 'polyA RNA'), ('cytoplasmic RNA', 'cytoplasmic RNA'), ('nuclear RNA', 'nuclear RNA'), ('small RNA', 'small RNA'), ('genomic DNA', 'genomic DNA'), ('protein', 'protein'), ('other', 'other')], help_text='(Controlled Vocabulary) The type of molecule that was extracted from the biological material.Include one of the following: total RNA, polyA RNA, cytoplasmic RNA, nuclear RNA, small RNA, genomic DNA, protein, or other.', max_length=20, null=True),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='molecule_ontology',
+            field=django.contrib.postgres.fields.jsonb.JSONField(blank=True, help_text='(Ontology: SO) links to molecule ontology information.', null=True, validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'chord_metadata_service:ontology_class_list_schema', '$schema': 'http://json-schema.org/draft-07/schema#', 'description': 'Ontology class list', 'items': {'$id': 'chord_metadata_service:ontology_class_schema', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'Schema to describe terms from ontologies.', 'properties': {'id': {'description': 'CURIE style identifier.', 'type': 'string'}, 'label': {'description': 'Human-readable class name.', 'type': 'string'}}, 'required': ['id', 'label'], 'title': 'Ontology class schema', 'type': 'object'}, 'title': 'Ontology class list', 'type': 'array'}, formats=None)]),
+        ),
+        migrations.AlterField(
+            model_name='experiment',
+            name='other_fields',
+            field=django.contrib.postgres.fields.jsonb.JSONField(blank=True, help_text='The other fields for the experiment.', null=True, validators=[chord_metadata_service.restapi.validators.JsonSchemaValidator({'$id': 'chord_metadata_service:key_value_object_schema', '$schema': 'http://json-schema.org/draft-07/schema#', 'additionalProperties': False, 'description': 'The schema represents a key-value object.', 'patternProperties': {'^.*$': {'type': 'string'}}, 'title': 'Key-value object', 'type': 'object'}, formats=None)]),
+        ),
+    ]