Merge pull request #73 from pepkit/dev_schema_revisions

refactor files and required_files to sizing and tangible keys respect…

eido/const.py

@@ -14,8 +14,9 @@
     CONVERT_CMD: "Convert PEP format using filters",
 }
 PROP_KEY = "properties"
-REQUIRED_FILES_KEY = "required_files"
-FILES_KEY = "files"
+
+TANGIBLE_KEY = "tangible"
+SIZING_KEY = "sizing"
 
 # sample schema input validation key names, these values are required by looper
 # to refer to the dict values
@@ -34,7 +35,9 @@
     "FILTERS_CMD",
     "SUBPARSER_MSGS",
 ]
-SCHEMA_SECTIONS = ["PROP_KEY", "REQUIRED_FILES_KEY", "FILES_KEY"]
+
+SCHEMA_SECTIONS = ["PROP_KEY", "TANGIBLE_KEY", "SIZING_KEY"]
+
 SCHEMA_VALIDAION_KEYS = [
     "MISSING_KEY",
     "REQUIRED_INPUTS_KEY",

eido/inspection.py

@@ -7,12 +7,12 @@
 
 from .const import (
     ALL_INPUTS_KEY,
-    FILES_KEY,
     INPUT_FILE_SIZE_KEY,
     MISSING_KEY,
     PROP_KEY,
-    REQUIRED_FILES_KEY,
     REQUIRED_INPUTS_KEY,
+    SIZING_KEY,
+    TANGIBLE_KEY,
 )
 from .schema import read_schema
 from .validation import _validate_sample_object, _get_attr_values
@@ -68,11 +68,11 @@ def get_input_files_size(sample, schema):
     required_inputs = set()
     schema = schema[-1]  # use only first schema, in case there are imports
     sample_schema_dict = schema["properties"]["_samples"]["items"]
-    if FILES_KEY in sample_schema_dict:
-        all_inputs.update(_get_attr_values(sample, sample_schema_dict[FILES_KEY]))
-    if REQUIRED_FILES_KEY in sample_schema_dict:
+    if SIZING_KEY in sample_schema_dict:
+        all_inputs.update(_get_attr_values(sample, sample_schema_dict[SIZING_KEY]))
+    if TANGIBLE_KEY in sample_schema_dict:
         required_inputs = set(
-            _get_attr_values(sample, sample_schema_dict[REQUIRED_FILES_KEY])
+            _get_attr_values(sample, sample_schema_dict[TANGIBLE_KEY])
         )
         all_inputs.update(required_inputs)
     with catch_warnings(record=True) as w:

eido/validation.py

@@ -13,9 +13,9 @@
 import peppy
 
 from .const import (
-    FILES_KEY,
     PROP_KEY,
-    REQUIRED_FILES_KEY,
+    SIZING_KEY,
+    TANGIBLE_KEY,
 )
 from .exceptions import PathAttrNotFoundError
 from .schema import preprocess_schema, read_schema
@@ -212,11 +212,11 @@ def validate_input_files(
         required_inputs = set()
         schema = schemas[-1]  # use only first schema, in case there are imports
         sample_schema_dict = schema["properties"]["_samples"]["items"]
-        if FILES_KEY in sample_schema_dict:
-            all_inputs.update(_get_attr_values(sample, sample_schema_dict[FILES_KEY]))
-        if REQUIRED_FILES_KEY in sample_schema_dict:
+        if SIZING_KEY in sample_schema_dict:
+            all_inputs.update(_get_attr_values(sample, sample_schema_dict[SIZING_KEY]))
+        if TANGIBLE_KEY in sample_schema_dict:
             required_inputs = set(
-                _get_attr_values(sample, sample_schema_dict[REQUIRED_FILES_KEY])
+                _get_attr_values(sample, sample_schema_dict[TANGIBLE_KEY])
             )
             all_inputs.update(required_inputs)
 

tests/data/schemas/schema_test_file_exist.yaml

@@ -21,10 +21,10 @@ properties:
             - type: array
               items:
                 type: string
-      files:
+      sizing:
         - local_files
 
-      required_files:
+      tangible:
         - local_files
 
       required: