Merge pull request #24 from databio/pipestat_060_update

adjust get_orm to get_model, update version number

bbconf/_version.py

@@ -1 +1 @@
-__version__ = "0.4.0a2"
+__version__ = "0.4.0a3"

bbconf/bbconf.py

@@ -50,6 +50,7 @@
 
 _LOGGER = getLogger(PKG_NAME)
 
+
 class BedBaseConf:
     """
     This class standardizes reporting of bedstat and bedbuncher results.
@@ -399,14 +400,14 @@ def BedfileORM(self) -> SQLModel:
         """
         return: ORM of bedfile table (SQLModelMetaclass)
         """
-        return self.bed.backend.get_orm("bedfile__sample")
+        return self.bed.backend.get_model("bedfile__sample")
 
     @property
     def BedsetORM(self) -> SQLModel:
         """
         return: ORM of bedset table (SQLModelMetaclass)
         """
-        return self.bedset.backend.get_orm("bedsets__sample")
+        return self.bedset.backend.get_model("bedsets__sample")
 
     @property
     def t2bsi(self) -> text2bednn.Text2BEDSearchInterface:

bbconf/schemas/bedfiles_schema.yaml

@@ -83,7 +83,7 @@ samples:
     type: image
     label: GC_content
     description: GC content plot
-  paritions:
+  partitions:
     type: image
     label: Regions_dist_partitions
     description: Regions distribution over genomic partitions plot

requirements/requirements-all.txt

@@ -1,5 +1,6 @@
 logmuse
 yacman>=0.9.1
-pipestat>=0.4.0
+pipestat>=0.6.0a1
 sqlalchemy<2.0.0
+qdrant_client
 # geniml

requirements/requirements-dev.txt

@@ -1 +1 @@
-pipestat>=0.4.0
+

tests/test_bbconf.py

@@ -50,31 +50,31 @@ def test_data_insert(self, cfg_pth, test_data_bed, test_data_bedset):
             bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth))
             # bedfiles table
             ori_cnt = bbc.bed.record_count
-            bbc.bed.report(sample_name="bed1", values=test_data_bed)
+            bbc.bed.report(record_identifier="bed1", values=test_data_bed)
             assert ori_cnt + 1 == bbc.bed.record_count
             # bedsets table
             ori_cnt = bbc.bedset.record_count
-            bbc.bedset.report(sample_name="bedset1", values=test_data_bedset)
+            bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset)
             assert ori_cnt + 1 == bbc.bedset.record_count
 
     def test_nonunique_digest_insert_error(
         self, cfg_pth, test_data_bed, test_data_bedset
     ):
         with ContextManagerDBTesting(DB_URL):
             bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth))
-            bbc.bed.report(sample_name="bed1", values=test_data_bed)
-            assert not bbc.bed.report(sample_name="bed1", values=test_data_bed)
-            bbc.bedset.report(sample_name="bedset1", values=test_data_bedset)
-            assert not bbc.bedset.report(sample_name="bedset1", values=test_data_bedset)
+            bbc.bed.report(record_identifier="bed1", values=test_data_bed)
+            assert not bbc.bed.report(record_identifier="bed1", values=test_data_bed)
+            bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset)
+            assert not bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset)
 
     def test_reporting_relationships(self, cfg_pth, test_data_bed, test_data_bedset):
         with ContextManagerDBTesting(DB_URL):
             bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth))
-            bbc.bed.report(sample_name="bed1", values=test_data_bed)
-            bed_id = bbc.bed.retrieve(sample_name="bed1", result_identifier="id")
-            bbc.bedset.report(sample_name="bedset1", values=test_data_bedset)
+            bbc.bed.report(record_identifier="bed1", values=test_data_bed)
+            bed_id = bbc.bed.retrieve(record_identifier="bed1", result_identifier="id")
+            bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset)
             bedset_id = bbc.bedset.retrieve(
-                sample_name="bedset1", result_identifier="id"
+                record_identifier="bedset1", result_identifier="id"
             )
             bbc.report_relationship(bedfile_id=bed_id, bedset_id=bedset_id)
             print("a")
@@ -84,52 +84,52 @@ def test_cant_remove_record_if_in_reltable(
     ):
         with ContextManagerDBTesting(DB_URL):
             bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth))
-            bbc.bed.report(sample_name="bed1", values=test_data_bed)
-            bed_id = bbc.bed.retrieve(sample_name="bed1", result_identifier="id")
-            bbc.bedset.report(sample_name="bedset1", values=test_data_bedset)
+            bbc.bed.report(record_identifier="bed1", values=test_data_bed)
+            bed_id = bbc.bed.retrieve(record_identifier="bed1", result_identifier="id")
+            bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset)
             bedset_id = bbc.bedset.retrieve(
-                sample_name="bedset1", result_identifier="id"
+                record_identifier="bedset1", result_identifier="id"
             )
             bbc.report_relationship(bedfile_id=bed_id, bedset_id=bedset_id)
             with pytest.raises(IntegrityError):
-                bbc.bed.remove(sample_name="bed1")
+                bbc.bed.remove(record_identifier="bed1")
             with pytest.raises(IntegrityError):
-                bbc.bedset.remove(sample_name="bedset1")
+                bbc.bedset.remove(record_identifier="bedset1")
 
     def test_select(self, cfg_pth, test_data_bed, test_data_bedset):
         with ContextManagerDBTesting(DB_URL):
             bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth))
-            bbc.bed.report(sample_name="bed1", values=test_data_bed)
-            bbc.bedset.report(sample_name="bedset1", values=test_data_bedset)
+            bbc.bed.report(record_identifier="bed1", values=test_data_bed)
+            bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset)
             bedset_id = bbc.bedset.retrieve(
-                sample_name="bedset1", result_identifier="id"
+                record_identifier="bedset1", result_identifier="id"
             )
-            bed_id = bbc.bed.retrieve(sample_name="bed1", result_identifier="id")
+            bed_id = bbc.bed.retrieve(record_identifier="bed1", result_identifier="id")
             bbc.report_relationship(bedfile_id=bed_id, bedset_id=bedset_id)
 
             unique_bedfiles = bbc.select_unique(table_name="bedfile__sample")
-            assert unique_bedfiles[0].sample_name == "bed1"
+            assert unique_bedfiles[0].record_identifier == "bed1"
             unique_bedsets = bbc.select_unique(table_name="bedsets__sample")
-            assert unique_bedsets[0].sample_name == "bedset1"
+            assert unique_bedsets[0].record_identifier == "bedset1"
             results = bbc.select_bedfiles_for_bedset()
             assert results is not None
 
     def test_removal(self, cfg_pth, test_data_bed, test_data_bedset):
         with ContextManagerDBTesting(DB_URL):
             bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth))
-            bbc.bed.report(sample_name="bed1", values=test_data_bed)
-            bbc.bedset.report(sample_name="bedset1", values=test_data_bedset)
+            bbc.bed.report(record_identifier="bed1", values=test_data_bed)
+            bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset)
             bedset_id = bbc.bedset.retrieve(
-                sample_name="bedset1", result_identifier="id"
+                record_identifier="bedset1", result_identifier="id"
             )
-            bed_id = bbc.bed.retrieve(sample_name="bed1", result_identifier="id")
+            bed_id = bbc.bed.retrieve(record_identifier="bed1", result_identifier="id")
             bbc.report_relationship(bedfile_id=bed_id, bedset_id=bedset_id)
             bbc.remove_relationship(bedset_id=bedset_id, bedfile_ids=[bed_id])
             ori_cnt = bbc.bed.record_count
-            bbc.bed.remove(sample_name="bed1")
+            bbc.bed.remove(record_identifier="bed1")
             assert ori_cnt - 1 == bbc.bed.record_count
             ori_cnt = bbc.bedset.record_count
-            bbc.bedset.remove(sample_name="bedset1")
+            bbc.bedset.remove(record_identifier="bedset1")
             assert ori_cnt - 1 == bbc.bedset.record_count
 
     def test_config_variables_are_set(self, cfg_pth, test_data_bed, test_data_bedset):