replace contained with located in the python script

lmb-embrapa · Oct 13, 2023 · b6213c9 · b6213c9
1 parent 855b427
commit b6213c9
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Showing 19 changed files with 29 additions and 29 deletions.
diff --git a/machado/loaders/analysis.py b/machado/loaders/analysis.py
@@ -27,7 +27,7 @@ class AnalysisLoader(object):
     def __init__(self) -> None:
         """Execute the init function."""
         self.cvterm_contained_in = Cvterm.objects.get(
-            name="contained in", cv__name="relationship"
+            name="located in", cv__name="relationship"
         )
 
     def store_analysis(

diff --git a/machado/loaders/assay.py b/machado/loaders/assay.py
@@ -47,7 +47,7 @@ def __init__(self) -> None:
             name="Null",
         )
         self.cvterm_contained_in = Cvterm.objects.get(
-            name="contained in", cv__name="relationship"
+            name="located in", cv__name="relationship"
         )
 
     def store_assay(

diff --git a/machado/loaders/biomaterial.py b/machado/loaders/biomaterial.py
@@ -24,7 +24,7 @@ class BiomaterialLoader(object):
     def __init__(self) -> None:
         """Execute the init function."""
         self.cvterm_contained_in = Cvterm.objects.get(
-            name="contained in", cv__name="relationship"
+            name="located in", cv__name="relationship"
         )
 
     def store_biomaterial(

diff --git a/machado/loaders/feature.py b/machado/loaders/feature.py
@@ -64,7 +64,7 @@ def __init__(self, source: str, filename: str, doi: str = None) -> None:
         )
 
         self.cvterm_contained_in = Cvterm.objects.get(
-            name="contained in", cv__name="relationship"
+            name="located in", cv__name="relationship"
         )
         self.aa_cvterm = Cvterm.objects.get(name="polypeptide", cv__name="sequence")
         self.so_term_protein_match = Cvterm.objects.get(

diff --git a/machado/loaders/project.py b/machado/loaders/project.py
@@ -20,7 +20,7 @@ class ProjectLoader(object):
     def __init__(self) -> None:
         """Execute the init function."""
         self.cvterm_contained_in = Cvterm.objects.get(
-            name="contained in", cv__name="relationship"
+            name="located in", cv__name="relationship"
         )
 
     def store_project(self, name: str, filename: str) -> Project:

diff --git a/machado/loaders/sequence.py b/machado/loaders/sequence.py
@@ -40,7 +40,7 @@ def __init__(
 
         # Retrieve sequence ontology object
         self.cvterm_contained_in = Cvterm.objects.get(
-            name="contained in", cv__name="relationship"
+            name="located in", cv__name="relationship"
         )
 
         # Retrieve DOI's Dbxref

diff --git a/machado/loaders/similarity.py b/machado/loaders/similarity.py
@@ -61,7 +61,7 @@ def __init__(
                 name="in similarity relationship with", cv__name="relationship"
             )
             self.cvterm_contained_in = Cvterm.objects.get(
-                name="contained in", cv__name="relationship"
+                name="located in", cv__name="relationship"
             )
             self.analysis_loader = AnalysisLoader()
             self.analysis = self.analysis_loader.store_analysis(

diff --git a/machado/management/commands/remove_analysis.py b/machado/management/commands/remove_analysis.py
@@ -40,7 +40,7 @@ def handle(self, name: str, verbosity: int = 1, **options):
             )
 
         cvterm_contained_in = Cvterm.objects.get(
-            name="contained in", cv__name="relationship"
+            name="located in", cv__name="relationship"
         )
         analysisprop_list = Analysisprop.objects.filter(
             value=name, type_id=cvterm_contained_in.cvterm_id

diff --git a/machado/management/commands/remove_relationship.py b/machado/management/commands/remove_relationship.py
@@ -29,9 +29,9 @@ def add_arguments(self, parser):
 
     def handle(self, file: str, verbosity: int = 0, **options):
         """Execute the main function."""
-        # get cvterm for contained in
+        # get cvterm for located in
         try:
-            cvterm = Cvterm.objects.get(name="contained in", cv__name="relationship")
+            cvterm = Cvterm.objects.get(name="located in", cv__name="relationship")
         except IntegrityError as e:
             raise ImportingError(e)
         filename = os.path.basename(file)

diff --git a/machado/tests/test_loaders_analysis.py b/machado/tests/test_loaders_analysis.py
@@ -55,7 +55,7 @@ def test_store_analysis(self):
             is_relationshiptype=0,
         )
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv2,
             dbxref=test_dbxref2,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_assay.py b/machado/tests/test_loaders_assay.py
@@ -25,7 +25,7 @@ def test_store_assay(self):
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_biomaterial.py b/machado/tests/test_loaders_biomaterial.py
@@ -24,7 +24,7 @@ def test_store_biomaterial(self):
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_coexpression.py b/machado/tests/test_loaders_coexpression.py
@@ -62,7 +62,7 @@ def test_load_coexpression_pairs(self):
         #    is_obsolete=0, is_relationshiptype=0)
         # register features.
         cvterm_contained_in = Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv2,
             dbxref=test_dbxref2,
             is_obsolete=0,
@@ -232,7 +232,7 @@ def test_load_coexpression_clusters(self):
         #    is_obsolete=0, is_relationshiptype=0)
         # register features.
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv2,
             dbxref=test_dbxref2,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_feature.py b/machado/tests/test_loaders_feature.py
@@ -89,12 +89,12 @@ def test_store_tabix_GFF_feature(self):
             is_obsolete=0,
             is_relationshiptype=0,
         )
-        # create RO term: contained in
+        # create RO term: located in
         test_db = Db.objects.create(name="RO")
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,
@@ -282,12 +282,12 @@ def test_store_tabix_VCF_feature(self):
             is_relationshiptype=0,
         )
 
-        # create RO term: contained in
+        # create RO term: located in
         test_db = Db.objects.create(name="RO")
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,
@@ -399,12 +399,12 @@ class TabixFeature(object):
 
     def test_store_bio_searchio_hit(self):
         """Tests - store bio searchio hit."""
-        # create RO term: contained in
+        # create RO term: located in
         test_db = Db.objects.create(name="RO")
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,
@@ -493,7 +493,7 @@ def test_store_feature_annotation(self):
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,
@@ -606,7 +606,7 @@ def test_store_feature_publication(self):
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,
@@ -697,7 +697,7 @@ def test_store_feature_dbxref(self):
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_featureattributes.py b/machado/tests/test_loaders_featureattributes.py
@@ -94,7 +94,7 @@ def test_process_attributes(self):
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_orthology.py b/machado/tests/test_loaders_orthology.py
@@ -35,7 +35,7 @@ def test_orthology(self):
         ro_dbxref = Dbxref.objects.create(accession="658", db=ro_db)
         # creating test SO term
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=ro_cv,
             dbxref=ro_dbxref,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_project.py b/machado/tests/test_loaders_project.py
@@ -24,7 +24,7 @@ def test_store_project(self):
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_sequence.py b/machado/tests/test_loaders_sequence.py
@@ -40,7 +40,7 @@ def setUp(self):
         test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
         test_cv = Cv.objects.create(name="relationship")
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv,
             dbxref=test_dbxref,
             is_obsolete=0,

diff --git a/machado/tests/test_loaders_similarity.py b/machado/tests/test_loaders_similarity.py
@@ -79,7 +79,7 @@ def test_store_bio_searchio_blast_record(self):
         )
         test_dbxref4 = Dbxref.objects.create(accession="12345678", db=test_db2)
         Cvterm.objects.create(
-            name="contained in",
+            name="located in",
             cv=test_cv2,
             dbxref=test_dbxref4,
             is_obsolete=0,