Merge pull request #495 from pepkit/dev

Release 0.40.7

Author: khoroshevskyi

peppy/_version.py

@@ -1 +1 @@
-__version__ = "0.40.6"
+__version__ = "0.40.7"

peppy/project.py

@@ -809,7 +809,7 @@ def attr_merge(self):
                 if len(this_sample_rows) == 0:
                     _LOGGER.debug(
                         "No merge rows for sample '%s', skipping",
-                        sample[SAMPLE_NAME_ATTR],
+                        sample[self.st_index],
                     )
                     continue
                 _LOGGER.debug("%d rows to merge", len(this_sample_rows))

tests/data/example_peps-master/example_multiple_subsamples/project_config.yaml

@@ -0,0 +1,21 @@
+pep_version: "2.1.0"
+sample_table: sample_table.csv
+subsample_table:
+  - subsample_table1.csv
+  - subsample_table2.csv
+
+sample_table_index: sample_id
+
+sample_modifiers:
+  append:
+    local_files: LOCAL
+    genome: "fg"
+  derive:
+    attributes: [local_files]
+    sources:
+      LOCAL: "../data/{file_path}"
+  imply:
+    - if:
+        identifier: "frog1"
+      then:
+        genome: "frog_frog"

tests/data/example_peps-master/example_multiple_subsamples/sample_table.csv

@@ -0,0 +1,5 @@
+sample_id,protocol,identifier
+frog_1,anySampleType,frog1
+frog_2,anySampleType,frog2
+frog_3,anySampleType,frog3
+frog_4,anySampleType,frog4

tests/data/example_peps-master/example_multiple_subsamples/subsample_table1.csv

@@ -0,0 +1,6 @@
+sample_id,file_path,subsample_name
+frog_1,file/a.txt,a
+frog_1,file/b.txt,b
+frog_1,file/c.txt,c
+frog_2,file/a.txt,a
+frog_2,file/b.txt,b

tests/data/example_peps-master/example_multiple_subsamples/subsample_table2.csv

@@ -0,0 +1,6 @@
+sample_id,random_string,subsample_name
+frog_1,x_x,x
+frog_1,y_y,y
+frog_1,z_z,z
+frog_2,xy_yx,xy
+frog_2,xx_xx,xx

tests/test_Project.py

@@ -226,8 +226,10 @@ def test_subsample_table_works_when_no_sample_mods(self, example_pep_cfg_path):
         p = Project(cfg=example_pep_cfg_path)
         assert any([s["file"] != "multi" for s in p.samples])
 
-    @pytest.mark.parametrize("example_pep_cfg_path", ["custom_index"], indirect=True)
-    def test_cutsom_sample_table_index_config(self, example_pep_cfg_path):
+    @pytest.mark.parametrize(
+        "example_pep_cfg_path", ["custom_index", "multiple_subsamples"], indirect=True
+    )
+    def test_custom_sample_table_index_config(self, example_pep_cfg_path):
         """
         Verify that custom sample table index is sourced from the config
         """
@@ -599,7 +601,7 @@ def test_unequality(self, example_pep_cfg_path, example_pep_csv_path):
 
     @pytest.mark.parametrize(
         "example_pep_cfg_path",
-        ["append", "custom_index", "imply", "subtables"],
+        ["append", "custom_index", "imply", "subtables", "multiple_subsamples"],
         indirect=True,
     )
     @pytest.mark.parametrize("orient", ["dict", "records"])