tests

Author: abretaud

chakin/commands/expression/delete_biomaterials.py

@@ -7,15 +7,11 @@
 @click.option(
     "--names",
     help="JSON list of biomaterial names to delete.",
-    default="[]",
-    show_default=True,
     type=str
 )
 @click.option(
     "--ids",
     help="JSON list of biomaterial ids to delete.",
-    default="[]",
-    show_default=True,
     type=str
 )
 @click.option(
@@ -31,7 +27,7 @@
 @pass_context
 @custom_exception
 @str_output
-def cli(ctx, names="[]", ids="[]", organism_id="", analysis_id=""):
+def cli(ctx, names="", ids="", organism_id="", analysis_id=""):
     """Will delete biomaterials based on selector. Only one selector will be used.
 
 Output:

docs/commands/expression.rst

@@ -130,8 +130,8 @@ Will delete biomaterials based on selector. Only one selector will be used.
 **Options**::
 
 
-      --names TEXT        JSON list of biomaterial names to delete.  [default: []]
-      --ids TEXT          JSON list of biomaterial ids to delete.  [default: []]
+      --names TEXT        JSON list of biomaterial names to delete.
+      --ids TEXT          JSON list of biomaterial ids to delete.
       --organism_id TEXT  Delete all biomaterial associated with this organism id.
       --analysis_id TEXT  Delete all biomaterial associated with this analysis id.
       -h, --help          Show this message and exit.

test/expression_test.py

@@ -9,15 +9,51 @@ def test_add_biomaterial(self):
         biomaterial_name = "test_biomat"
         biomaterial_provider = "Helena Ventseslav"
         biomaterial_description = "This is a description"
+        biosample_accession = 'biosample-foobar'
+        sra_accession = "sra-bar"
+        bioproject_accession = 'bioproject-foo'
+        attrs = {
+            'foo': 'bar',
+            'oof': 'arb'
+        }
         org = self._create_fake_org()
 
-        biomat = self.ci.expression.add_biomaterial(biomaterial_name, org["organism_id"], description=biomaterial_description, biomaterial_provider=biomaterial_provider, bioproject_accession="something")
+        biomat_ret = self.ci.expression.add_biomaterial(biomaterial_name, org["organism_id"], description=biomaterial_description, biomaterial_provider=biomaterial_provider, biosample_accession=biosample_accession, sra_accession=sra_accession, bioproject_accession=bioproject_accession, attributes=attrs)
+
+        biomat = self.ci.expression.get_biomaterials(biomaterial_name=biomaterial_name)[0]
+
+        assert biomat_ret == biomat
 
         assert biomat, "Issue : Biomaterial not created"
         assert biomat["name"] == biomaterial_name, "Biomaterial name issue : " + biomat["name"]
         assert biomat["provider_id"], "Bioprovider not set! "
         assert biomat["description"] == biomaterial_description, "Description issue : " + biomat["description"]
 
+        res = self.ci.session.query(self.ci.model.biomaterialprop).filter_by(biomaterial_id=biomat['biomaterial_id'])
+
+        props = {prop.type_id: prop.value for prop in res}
+        for at in attrs:
+            type_id = self.ci.get_cvterm_id(at, 'biomaterial_property')
+            assert type_id in props
+
+            assert props[type_id] == attrs[at]
+
+        dbs = self.ci.session.query(self.ci.model.db.db_id, self.ci.model.db.name, self.ci.model.db.description) \
+            .filter((self.ci.model.db.name == 'NCBI SRA') | (self.ci.model.db.name == 'NCBI BioProject') | (self.ci.model.db.name == 'NCBI BioSample'))
+
+        dbs = {db.name: db.db_id for db in dbs}
+
+        biomat = self.ci.session.query(self.ci.model.biomaterial).filter_by(biomaterial_id=biomat['biomaterial_id']).one()
+
+        xrefs = {dbx.dbxref.db_id: dbx.dbxref.accession for dbx in biomat.biomaterial_dbxref_collection}
+
+        assert len(dbs) == 3
+        assert len(xrefs) == 3
+
+        assert xrefs[dbs['NCBI SRA']] == "sra-bar"
+        assert xrefs[dbs['NCBI BioProject']] == "bioproject-foo"
+        assert xrefs[dbs['NCBI BioSample']] == "biosample-foobar"
+
     def test_add_expression(self):
 
         # Setup testing data