fixed bug in flatten code refactor, expanded tests to catch

AmandaBirmingham · May 25, 2024 · 460893f · 460893f
1 parent 277fffc
commit 460893f
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Showing 2 changed files with 139 additions and 2 deletions.
diff --git a/qiimp/src/metadata_configurator.py b/qiimp/src/metadata_configurator.py
@@ -59,9 +59,11 @@ def flatten_nested_stds_dict(
                 curr_host_type_stds_nested_dict)
 
         # recurse into the next level--depth first search.
-        # is ok if this comes back as an empty dict; we are adding to it below.
-        wip_host_types_dict = flatten_nested_stds_dict(
+        # if this comes back empty, we ignore it.
+        curr_host_type_sub_host_dict = flatten_nested_stds_dict(
             curr_host_type_stds_nested_dict, curr_host_type_wip_flat_dict)
+        if curr_host_type_sub_host_dict:
+            wip_host_types_dict.update(curr_host_type_sub_host_dict)
 
         # assign the flattened wip dict for the current host type to the result
         # (which now contains flat records for the hosts lower down than

diff --git a/qiimp/tests/test_metadata_configurator.py b/qiimp/tests/test_metadata_configurator.py
@@ -166,6 +166,22 @@ class TestMetadataExtender(TestCase):
                                     }
                                 }
                             }
+                        },
+                        "control": {
+                            "metadata_fields": {
+                                # overrides stds parent host
+                                "description": {
+                                    "allowed": ["control"],
+                                    "default": "control",
+                                    "type": "string"
+                                },
+                                # overrides stds parent host
+                                "host_type": {
+                                    "allowed": ["control"],
+                                    "default": "control",
+                                    "type": "string"
+                                }
+                            }
                         }
                     }
                 }
@@ -412,6 +428,22 @@ class TestMetadataExtender(TestCase):
                                     }
                                 }
                             }
+                        },
+                        "control": {
+                            "metadata_fields": {
+                                # overrides stds parent host
+                                "description": {
+                                    "allowed": ["control"],
+                                    "default": "control",
+                                    "type": "string"
+                                },
+                                # overrides stds parent host
+                                "host_type": {
+                                    "allowed": ["control"],
+                                    "default": "control",
+                                    "type": "string"
+                                }
+                            }
                         }
                     }
                 }
@@ -522,6 +554,109 @@ class TestMetadataExtender(TestCase):
                     }
                 }
             },
+            "control": {
+                "default": "not provided",
+                "metadata_fields": {
+                    # from stds same level host
+                    "country": {
+                        "allowed": ["USA"],
+                        "default": "USA",
+                        "empty": False,
+                        "is_phi": False,
+                        "required": True,
+                        "type": "string"
+                    },
+                    # from stds same level host
+                    "description": {
+                        "allowed": ["control"],
+                        "default": "control",
+                        "empty": False,
+                        "is_phi": False,
+                        "required": True,
+                        "type": "string"
+                    },
+                    # from stds same level host
+                    "dna_extracted": {
+                        "allowed": ["true", "false"],
+                        "default": "true",
+                        "empty": False,
+                        "is_phi": False,
+                        "required": True,
+                        "type": "string"
+                    },
+                    # from stds same level host
+                    "elevation": {
+                        "anyof": [
+                            {
+                                "allowed": [
+                                    "not collected",
+                                    "not provided",
+                                    "restricted access"],
+                                "type": "string"
+                            },
+                            {
+                                "min": -413.0,
+                                "type": "number"
+                            }],
+                        "empty": False,
+                        "is_phi": False,
+                        "required": True
+                    },
+                    # from stds same level host
+                    "geo_loc_name": {
+                        "allowed": ["USA:CA:San Diego"],
+                        "default": "USA:CA:San Diego",
+                        "empty": False,
+                        "is_phi": False,
+                        "required": True,
+                        "type": "string"
+                    },
+                    # overridden in stds lower host
+                    "host_type": {
+                        "allowed": ["control"],
+                        "default": "control",
+                        "empty": False,
+                        "is_phi": False,
+                        "required": True,
+                        "type": "string"
+                    }
+                },
+                "sample_type_specific_metadata": {
+                    "fe": {
+                        "alias": "stool"
+                    },
+                    "stool": {
+                        "metadata_fields": {
+                            # from stds same level host + sample type
+                            "description": {
+                                "allowed": ["host associated stool"],
+                                "default": "host associated stool",
+                                "type": "string"
+                            },
+                            # from stds same level host + sample type
+                            # (NB: comes from study)
+                            "physical_specimen_location": {
+                                "allowed": ["UCSDST"],
+                                "default": "UCSDST",
+                                "empty": False,
+                                "is_phi": False,
+                                "required": True,
+                                "type": "string"
+                            },
+                            # from stds same level host + sample type
+                            # (NB: comes from study)
+                            "physical_specimen_remaining": {
+                                "allowed": ["true", "false"],
+                                "default": "true",
+                                "empty": False,
+                                "is_phi": False,
+                                "required": True,
+                                "type": "string"
+                            }
+                        }
+                    }
+                }
+            },
             "human": {
                 "default": "not collected",
                 "metadata_fields": {