From ea3bdd20414d7494fe49749ef4d8bdfb5ea1d37f Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 14:49:53 -0600 Subject: [PATCH 01/36] Some optimizations --- src/sssom/util.py | 34 ++++++++++++++++++---------------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index 1f094906..87ba8807 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -148,25 +148,27 @@ def from_mapping_set_document(cls, doc: MappingSetDocument) -> "MappingSetDataFr """Instantiate from a mapping set document.""" if doc.mapping_set.mappings is None: return cls(df=pd.DataFrame(), converter=doc.converter) - + df = pd.DataFrame(get_dict_from_mapping(mapping) for mapping in doc.mapping_set.mappings) meta = _extract_global_metadata(doc) - + # remove columns where all values are blank. df.replace("", np.nan, inplace=True) df.dropna(axis=1, how="all", inplace=True) # remove columns with all row = 'None'-s. - + + slots = _get_sssom_schema_object().dict["slots"] slots_with_double_as_range = { slot - for slot, slot_metadata in _get_sssom_schema_object().dict["slots"].items() + for slot, slot_metadata in slots.items() if slot_metadata["range"] == "double" } non_double_cols = df.loc[:, ~df.columns.isin(slots_with_double_as_range)] non_double_cols = non_double_cols.replace(np.nan, "") df[non_double_cols.columns] = non_double_cols - + df = sort_df_rows_columns(df) return cls.with_converter(df=df, converter=doc.converter, metadata=meta) + def to_mapping_set_document(self) -> "MappingSetDocument": """Get a mapping set document.""" @@ -1050,21 +1052,23 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> :return: Dictionary """ map_dict = {} + sssom_schema_object = _get_sssom_schema_object().dict + slots = sssom_schema_object["slots"] + enums_keys = sssom_schema_object["enums"].keys() + slots_with_double_as_range = [ s - for s in _get_sssom_schema_object().dict["slots"].keys() - if _get_sssom_schema_object().dict["slots"][s]["range"] == "double" + for s in slots.keys() + if slots[s]["range"] == "double" ] + for property in map_obj: if map_obj[property] is not None: if isinstance(map_obj[property], list): # IF object is an enum - if ( - _get_sssom_schema_object().dict["slots"][property]["range"] - in _get_sssom_schema_object().dict["enums"].keys() - ): + if slots[property]["range"] in enums_keys: # IF object is a multivalued enum - if _get_sssom_schema_object().dict["slots"][property]["multivalued"]: + if slots[property]["multivalued"]: map_dict[property] = "|".join( enum_value.code.text for enum_value in map_obj[property] ) @@ -1077,10 +1081,7 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> # IF object NOT a list else: # IF object is an enum - if ( - _get_sssom_schema_object().dict["slots"][property]["range"] - in _get_sssom_schema_object().dict["enums"].keys() - ): + if slots[property]["range"] in enums_keys: map_dict[property] = map_obj[property].code.text else: map_dict[property] = map_obj[property] @@ -1094,6 +1095,7 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> return map_dict + CURIE_PATTERN = r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]" CURIE_RE = re.compile(CURIE_PATTERN) From d47bf81e5762b05eb6c9675e644a24ce767f33c7 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 14:49:58 -0600 Subject: [PATCH 02/36] poetry update --- poetry.lock | 536 ++++++++++++++++++++-------------------------------- 1 file changed, 209 insertions(+), 327 deletions(-) diff --git a/poetry.lock b/poetry.lock index bceafd81..9bf5ccbf 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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"""Instantiate from a mapping set document.""" if doc.mapping_set.mappings is None: return cls(df=pd.DataFrame(), converter=doc.converter) - + df = pd.DataFrame(get_dict_from_mapping(mapping) for mapping in doc.mapping_set.mappings) meta = _extract_global_metadata(doc) - + # remove columns where all values are blank. df.replace("", np.nan, inplace=True) df.dropna(axis=1, how="all", inplace=True) # remove columns with all row = 'None'-s. - + slots = _get_sssom_schema_object().dict["slots"] slots_with_double_as_range = { - slot - for slot, slot_metadata in slots.items() - if slot_metadata["range"] == "double" + slot for slot, slot_metadata in slots.items() if slot_metadata["range"] == "double" } non_double_cols = df.loc[:, ~df.columns.isin(slots_with_double_as_range)] non_double_cols = non_double_cols.replace(np.nan, "") df[non_double_cols.columns] = non_double_cols - + df = sort_df_rows_columns(df) return cls.with_converter(df=df, converter=doc.converter, metadata=meta) - def to_mapping_set_document(self) -> "MappingSetDocument": """Get a mapping set document.""" @@ -1056,11 +1053,7 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> slots = sssom_schema_object["slots"] enums_keys = sssom_schema_object["enums"].keys() - slots_with_double_as_range = [ - s - for s in slots.keys() - if slots[s]["range"] == "double" - ] + slots_with_double_as_range = [s for s in slots.keys() if slots[s]["range"] == "double"] for property in map_obj: if map_obj[property] is not None: @@ -1095,7 +1088,6 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> return map_dict - CURIE_PATTERN = r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]" CURIE_RE = re.compile(CURIE_PATTERN) From 0a32cf8e5d056de55f0a3cb44c462bc63a4e743a Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 17:46:43 -0600 Subject: [PATCH 04/36] cleaned list comprehension --- src/sssom/util.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index 5f671a27..d0627596 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1053,7 +1053,7 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> slots = sssom_schema_object["slots"] enums_keys = sssom_schema_object["enums"].keys() - slots_with_double_as_range = [s for s in slots.keys() if slots[s]["range"] == "double"] + slots_with_double_as_range = [k for k, v in slots.items() if v["range"] == "double"] for property in map_obj: if map_obj[property] is not None: From 8a8c0fe68ca6fe04cfe5002e78350e8839e77264 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 18:08:05 -0600 Subject: [PATCH 05/36] pandas apply() over iterrows() --- src/sssom/parsers.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index cda463ce..7ddb1e27 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -795,11 +795,17 @@ def to_mapping_set_document(msdf: MappingSetDataFrame) -> MappingSetDocument: def _get_mapping_set_from_df(df: pd.DataFrame, meta: Optional[MetadataType] = None) -> MappingSet: mapping_set = _init_mapping_set(meta) bad_attrs: Counter = Counter() - for _, row in df.iterrows(): - mapping_dict = _get_mapping_dict(row, bad_attrs) - _add_valid_mapping_to_list(mapping_dict, mapping_set.mappings) + + df.apply( + lambda row: _add_valid_mapping_to_list( + _get_mapping_dict(row, bad_attrs), mapping_set.mappings + ), + axis=1, + ) + for k, v in bad_attrs.items(): logging.warning(f"No attr for {k} [{v} instances]") + return mapping_set From 62f76911bd519b34d019ee628e7e809847e6b00d Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 18:11:34 -0600 Subject: [PATCH 06/36] filter notnull() rows out before entering the for loop --- src/sssom/parsers.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index 7ddb1e27..b2517806 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -332,17 +332,19 @@ def _init_mapping_set(meta: Optional[MetadataType]) -> MappingSet: def _get_mapping_dict(row: pd.Series, bad_attrs: Counter) -> Dict[str, Any]: mdict = {} sssom_schema_object = _get_sssom_schema_object() - for k, v in row.items(): - if not v or pd.isna(v): - continue + mapping_slots = set(sssom_schema_object.mapping_slots) + + # Use items() with notnull() to iterate over non-null values only + for k, v in row[row.notnull()].items(): k = cast(str, k) - if k in sssom_schema_object.mapping_slots: + if k in mapping_slots: mdict[k] = _address_multivalued_slot(k, v) else: # There's the possibility that the key is in # sssom_schema_object.mapping_set_slots, but # this is skipped for now bad_attrs[k] += 1 + return mdict From 48225df70ff5edd496f30b61c0917b97ed3d1b2e Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 18:17:15 -0600 Subject: [PATCH 07/36] rollback prev commit --- src/sssom/parsers.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index b2517806..7ddb1e27 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -332,19 +332,17 @@ def _init_mapping_set(meta: Optional[MetadataType]) -> MappingSet: def _get_mapping_dict(row: pd.Series, bad_attrs: Counter) -> Dict[str, Any]: mdict = {} sssom_schema_object = _get_sssom_schema_object() - mapping_slots = set(sssom_schema_object.mapping_slots) - - # Use items() with notnull() to iterate over non-null values only - for k, v in row[row.notnull()].items(): + for k, v in row.items(): + if not v or pd.isna(v): + continue k = cast(str, k) - if k in mapping_slots: + if k in sssom_schema_object.mapping_slots: mdict[k] = _address_multivalued_slot(k, v) else: # There's the possibility that the key is in # sssom_schema_object.mapping_set_slots, but # this is skipped for now bad_attrs[k] += 1 - return mdict From e2e7288c83df9677873593988f29b8adf63b586d Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 18:19:55 -0600 Subject: [PATCH 08/36] check value first and then check if k is multivalued --- src/sssom/parsers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index 7ddb1e27..e2be7e97 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -313,7 +313,7 @@ def _get_prefix_map_and_metadata( def _address_multivalued_slot(k: str, v: Any) -> Union[str, List[str]]: - if is_multivalued_slot(k) and v is not None and isinstance(v, str): + if isinstance(v, str) and is_multivalued_slot(k): # IF k is multivalued, then v = List[values] return [s.strip() for s in v.split("|")] else: From 4c738f54a167499b0826026f586340711bdd7071 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 18:26:43 -0600 Subject: [PATCH 09/36] switched to dict comprehension from for loop --- src/sssom/parsers.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index e2be7e97..48c1ba3a 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -332,17 +332,17 @@ def _init_mapping_set(meta: Optional[MetadataType]) -> MappingSet: def _get_mapping_dict(row: pd.Series, bad_attrs: Counter) -> Dict[str, Any]: mdict = {} sssom_schema_object = _get_sssom_schema_object() - for k, v in row.items(): - if not v or pd.isna(v): - continue - k = cast(str, k) - if k in sssom_schema_object.mapping_slots: - mdict[k] = _address_multivalued_slot(k, v) - else: - # There's the possibility that the key is in - # sssom_schema_object.mapping_set_slots, but - # this is skipped for now - bad_attrs[k] += 1 + + mdict = { + k: _address_multivalued_slot(k, v) + for k, v in row.items() + if v and not pd.isna(v) and k in sssom_schema_object.mapping_slots + } + + # Update bad_attrs for keys not in mapping_slots + bad_keys = set(row.keys()) - set(sssom_schema_object.mapping_slots) + for k in bad_keys: + bad_attrs[k] += 1 return mdict From 4ab2660d1a45210a3d6d846a7f4028add0eabfc5 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 21:44:18 -0600 Subject: [PATCH 10/36] dict comprehension instead of for loop --- src/sssom/util.py | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index d0627596..ccaa644f 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1139,18 +1139,21 @@ def get_prefixes_used_in_table(df: pd.DataFrame, converter: Converter) -> Set[st prefixes = set(SSSOM_BUILT_IN_PREFIXES) if df.empty: return prefixes - for col in _get_sssom_schema_object().entity_reference_slots: - if col not in df.columns: - continue - prefixes.update( - converter.parse_curie(row).prefix - for row in df[col] - # we don't use the converter here since get_prefixes_used_in_table - # is often used to identify prefixes that are not properly registered - # in the converter - if not _is_iri(row) and _is_curie(row) - ) - return set(prefixes) + sssom_schema_object = _get_sssom_schema_object() + entity_reference_slots = set(sssom_schema_object.entity_reference_slots) & set(df.columns) + new_prefixes = { + converter.parse_curie(row).prefix + for col in entity_reference_slots + for row in df[col] + if not _is_iri(row) and _is_curie(row) + # we don't use the converter here since get_prefixes_used_in_table + # is often used to identify prefixes that are not properly registered + # in the converter + } + + prefixes.update(new_prefixes) + + return prefixes def get_prefixes_used_in_metadata(meta: MetadataType) -> Set[str]: From 1618b52164a7c743a00d55a0f3ae45345cbd4f39 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 22:33:30 -0600 Subject: [PATCH 11/36] Use sets instead of lists --- src/sssom/util.py | 37 ++++++++++++++++++------------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index ccaa644f..1fbd9cf2 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1051,43 +1051,42 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> map_dict = {} sssom_schema_object = _get_sssom_schema_object().dict slots = sssom_schema_object["slots"] - enums_keys = sssom_schema_object["enums"].keys() + enums_keys = set(sssom_schema_object["enums"].keys()) - slots_with_double_as_range = [k for k, v in slots.items() if v["range"] == "double"] + slots_with_double_as_range = {s for s in slots.keys() if slots[s]["range"] == "double"} - for property in map_obj: - if map_obj[property] is not None: - if isinstance(map_obj[property], list): + for property, value in map_obj.items(): + if value is not None: + slot = slots[property] + is_enum = slot["range"] in enums_keys + + if isinstance(value, list): # IF object is an enum - if slots[property]["range"] in enums_keys: + if is_enum: # IF object is a multivalued enum - if slots[property]["multivalued"]: - map_dict[property] = "|".join( - enum_value.code.text for enum_value in map_obj[property] - ) + if slot["multivalued"]: + map_dict[property] = "|".join(enum_value.code.text for enum_value in value) # If object is NOT multivalued BUT an enum. else: - map_dict[property] = map_obj[property].code.text + map_dict[property] = value.code.text # IF object is NOT an enum but a list else: - map_dict[property] = "|".join(enum_value for enum_value in map_obj[property]) + map_dict[property] = "|".join(enum_value for enum_value in value) # IF object NOT a list else: # IF object is an enum - if slots[property]["range"] in enums_keys: - map_dict[property] = map_obj[property].code.text + if is_enum: + map_dict[property] = value.code.text else: - map_dict[property] = map_obj[property] + map_dict[property] = value else: # IF map_obj[property] is None: - if property in slots_with_double_as_range: - map_dict[property] = np.nan - else: - map_dict[property] = "" + map_dict[property] = np.nan if property in slots_with_double_as_range else "" return map_dict + CURIE_PATTERN = r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]" CURIE_RE = re.compile(CURIE_PATTERN) From 77e02ab8b99b2a53122aedf772f60c13d7091df1 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 23:00:04 -0600 Subject: [PATCH 12/36] corrected previous commit --- src/sssom/util.py | 57 ++++++++++++++++++++++++----------------------- 1 file changed, 29 insertions(+), 28 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index 1fbd9cf2..0f8fe201 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1053,40 +1053,41 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> slots = sssom_schema_object["slots"] enums_keys = set(sssom_schema_object["enums"].keys()) - slots_with_double_as_range = {s for s in slots.keys() if slots[s]["range"] == "double"} - - for property, value in map_obj.items(): - if value is not None: - slot = slots[property] - is_enum = slot["range"] in enums_keys - - if isinstance(value, list): - # IF object is an enum - if is_enum: - # IF object is a multivalued enum - if slot["multivalued"]: - map_dict[property] = "|".join(enum_value.code.text for enum_value in value) - # If object is NOT multivalued BUT an enum. - else: - map_dict[property] = value.code.text - # IF object is NOT an enum but a list - else: - map_dict[property] = "|".join(enum_value for enum_value in value) - # IF object NOT a list + slots_with_double_as_range = {k for k, v in slots.items() if v["range"] == "double"} + + for property in map_obj: + mapping_property = map_obj[property] + if mapping_property is None: + map_dict[property] = np.nan if property in slots_with_double_as_range else "" + continue + + slot_of_interest = slots[property] + is_enum = slot_of_interest["range"] in enums_keys + + # Check if the mapping_property is a list + if isinstance(mapping_property, list): + # If the property is an enumeration and it allows multiple values + if is_enum and slot_of_interest["multivalued"]: + # Join all the enum values into a string separated by '|' + map_dict[property] = "|".join( + enum_value.code.text for enum_value in mapping_property + ) else: - # IF object is an enum - if is_enum: - map_dict[property] = value.code.text - else: - map_dict[property] = value + # If the property is not an enumeration or doesn't allow multiple values, + # join all the values into a string separated by '|' + map_dict[property] = "|".join(enum_value for enum_value in mapping_property) + # If the mapping_property is not a list but an enumeration + elif is_enum: + # Assign the text of the enumeration code to the property in the dictionary + map_dict[property] = mapping_property.code.text else: - # IF map_obj[property] is None: - map_dict[property] = np.nan if property in slots_with_double_as_range else "" + # If the mapping_property is neither a list nor an enumeration, + # assign the value directly to the property in the dictionary + map_dict[property] = mapping_property return map_dict - CURIE_PATTERN = r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]" CURIE_RE = re.compile(CURIE_PATTERN) From 14b0475c352f372a0ab600296f154af7fcac2001 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 13 Nov 2023 23:18:54 -0600 Subject: [PATCH 13/36] Use sets instead of lists --- src/sssom/constants.py | 10 +++++----- src/sssom/util.py | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/sssom/constants.py b/src/sssom/constants.py index 84ecd18b..eb080f33 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -4,7 +4,7 @@ import uuid from enum import Enum from functools import lru_cache -from typing import Any, Dict, List, Literal +from typing import Any, Dict, List, Literal, Set import pkg_resources import yaml @@ -247,14 +247,14 @@ def mapping_set_slots(self) -> List[str]: return self.view.get_class("mapping set").slots @property - def multivalued_slots(self) -> List[str]: + def multivalued_slots(self) -> Set[str]: """Return list of multivalued slots.""" - return [c for c in self.view.all_slots() if self.view.get_slot(c).multivalued] + return {c for c in self.view.all_slots() if self.view.get_slot(c).multivalued} @property - def entity_reference_slots(self) -> List[str]: + def entity_reference_slots(self) -> Set[str]: """Return list of entity reference slots.""" - return [c for c in self.view.all_slots() if self.view.get_slot(c).range == ENTITY_REFERENCE] + return {c for c in self.view.all_slots() if self.view.get_slot(c).range == ENTITY_REFERENCE} @lru_cache(1) diff --git a/src/sssom/util.py b/src/sssom/util.py index 0f8fe201..9c67331a 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1140,7 +1140,7 @@ def get_prefixes_used_in_table(df: pd.DataFrame, converter: Converter) -> Set[st if df.empty: return prefixes sssom_schema_object = _get_sssom_schema_object() - entity_reference_slots = set(sssom_schema_object.entity_reference_slots) & set(df.columns) + entity_reference_slots = sssom_schema_object.entity_reference_slots & set(df.columns) new_prefixes = { converter.parse_curie(row).prefix for col in entity_reference_slots From d74e72a037b2ba070eaf354c745f0bf92868ee24 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 14 Nov 2023 09:56:58 -0600 Subject: [PATCH 14/36] Improved SchemaView instantiation and persistence --- src/sssom/constants.py | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/src/sssom/constants.py b/src/sssom/constants.py index eb080f33..f411942e 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -215,12 +215,16 @@ class SSSOMSchemaView(object): _view = None _dict = None + _mapping_slots = None + _mapping_set_slots = None + _multivalued_slots = None + _entity_reference_slots = None def __new__(cls): """Create a instance of the SSSOM schema view if non-existent.""" if not hasattr(cls, "instance"): cls.instance = super(SSSOMSchemaView, cls).__new__(cls) - return cls.instance + return cls.instance @property def view(self) -> SchemaView: @@ -239,22 +243,34 @@ def dict(self) -> dict: @property def mapping_slots(self) -> List[str]: """Return list of mapping slots.""" - return self.view.get_class("mapping").slots + if self._mapping_slots is None: + self._mapping_slots = self.view.get_class("mapping").slots + return self._mapping_slots @property def mapping_set_slots(self) -> List[str]: """Return list of mapping set slots.""" - return self.view.get_class("mapping set").slots + if self._mapping_set_slots is None: + self._mapping_set_slots = self.view.get_class("mapping set").slots + return self._mapping_set_slots @property def multivalued_slots(self) -> Set[str]: """Return list of multivalued slots.""" - return {c for c in self.view.all_slots() if self.view.get_slot(c).multivalued} + if self._multivalued_slots is None: + self._multivalued_slots = { + c for c in self.view.all_slots() if self.view.get_slot(c).multivalued + } + return self._multivalued_slots @property def entity_reference_slots(self) -> Set[str]: """Return list of entity reference slots.""" - return {c for c in self.view.all_slots() if self.view.get_slot(c).range == ENTITY_REFERENCE} + if self._entity_reference_slots is None: + self._entity_reference_slots = { + c for c in self.view.all_slots() if self.view.get_slot(c).range == ENTITY_REFERENCE + } + return self._entity_reference_slots @lru_cache(1) From 52b2e1232b7f8ddae305beea498c8d5b276f367e Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 14 Nov 2023 09:57:18 -0600 Subject: [PATCH 15/36] log warnings only if bad_attrs exists --- src/sssom/parsers.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index 48c1ba3a..de53ba9e 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -803,8 +803,9 @@ def _get_mapping_set_from_df(df: pd.DataFrame, meta: Optional[MetadataType] = No axis=1, ) - for k, v in bad_attrs.items(): - logging.warning(f"No attr for {k} [{v} instances]") + if bad_attrs: + for k, v in bad_attrs.items(): + logging.warning(f"No attr for {k} [{v} instances]") return mapping_set From f2fb5b579dcf0dfbbdb8ffb64dd5b6300c2259ae Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 14 Nov 2023 09:57:41 -0600 Subject: [PATCH 16/36] avoid unnecessary variable assignments --- src/sssom/util.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index 9c67331a..3f8488ab 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -161,8 +161,8 @@ def from_mapping_set_document(cls, doc: MappingSetDocument) -> "MappingSetDataFr slot for slot, slot_metadata in slots.items() if slot_metadata["range"] == "double" } non_double_cols = df.loc[:, ~df.columns.isin(slots_with_double_as_range)] - non_double_cols = non_double_cols.replace(np.nan, "") - df[non_double_cols.columns] = non_double_cols + non_double_cols.replace(np.nan, "", inplace=True) + df.update(non_double_cols) df = sort_df_rows_columns(df) return cls.with_converter(df=df, converter=doc.converter, metadata=meta) From c12dc618b66dd2f3166dd56e62d8c232420eda08 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 14 Nov 2023 10:35:12 -0600 Subject: [PATCH 17/36] move line into try except --- src/sssom/parsers.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index de53ba9e..3bf637e9 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -882,9 +882,8 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]): :param mdict: A dictionary containing the mapping metadata. :return: A valid Mapping object, or None. """ - mdict.setdefault(MAPPING_JUSTIFICATION, MAPPING_JUSTIFICATION_UNSPECIFIED) - try: + mdict.setdefault(MAPPING_JUSTIFICATION, MAPPING_JUSTIFICATION_UNSPECIFIED) m = Mapping(**mdict) except ValueError as e: logging.warning( From c24e0a84f7b9917f1d7f5dc347c6b83fca9c6e29 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 14 Nov 2023 10:58:30 -0600 Subject: [PATCH 18/36] updated lock file --- poetry.lock | 349 ++++++++++++++++++++++++++++++++++------------------ 1 file changed, 228 insertions(+), 121 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9bf5ccbf..f32a7321 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. [[package]] name = "alabaster" @@ -11,6 +11,20 @@ files = [ {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, ] +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, +] + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} + [[package]] name = "attrs" version = "23.1.0" @@ -224,13 +238,13 @@ files = [ [[package]] name = "curies" -version = "0.7.2" +version = "0.7.4" description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." optional = false python-versions = 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platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\""} +greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""} typing-extensions = ">=4.2.0" [package.extras] From 5d2f327bed03a96f492ab6174d3557900476d5ee Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 14 Nov 2023 11:08:52 -0600 Subject: [PATCH 19/36] use of @ cached_property --- src/sssom/constants.py | 49 +++++++++++------------------------------- 1 file changed, 13 insertions(+), 36 deletions(-) diff --git a/src/sssom/constants.py b/src/sssom/constants.py index f411942e..906f1189 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -3,7 +3,7 @@ import pathlib import uuid from enum import Enum -from functools import lru_cache +from functools import cached_property, lru_cache from typing import Any, Dict, List, Literal, Set import pkg_resources @@ -213,64 +213,41 @@ class SSSOMSchemaView(object): Implemented via PR: https://github.com/mapping-commons/sssom-py/pull/323 """ - _view = None - _dict = None - _mapping_slots = None - _mapping_set_slots = None - _multivalued_slots = None - _entity_reference_slots = None - def __new__(cls): """Create a instance of the SSSOM schema view if non-existent.""" if not hasattr(cls, "instance"): cls.instance = super(SSSOMSchemaView, cls).__new__(cls) return cls.instance - @property + @cached_property def view(self) -> SchemaView: """Return SchemaView object.""" - if self._view is None: - self._view = SchemaView(SCHEMA_YAML) - return self._view + return SchemaView(SCHEMA_YAML) - @property + @cached_property def dict(self) -> dict: """Return SchemaView as a dictionary.""" - if self._dict is None: - self._dict = schema_as_dict(self.view.schema) - return self._dict + return schema_as_dict(self.view.schema) - @property + @cached_property def mapping_slots(self) -> List[str]: """Return list of mapping slots.""" - if self._mapping_slots is None: - self._mapping_slots = self.view.get_class("mapping").slots - return self._mapping_slots + return self.view.get_class("mapping").slots - @property + @cached_property def mapping_set_slots(self) -> List[str]: """Return list of mapping set slots.""" - if self._mapping_set_slots is None: - self._mapping_set_slots = self.view.get_class("mapping set").slots - return self._mapping_set_slots + return self.view.get_class("mapping set").slots - @property + @cached_property def multivalued_slots(self) -> Set[str]: """Return list of multivalued slots.""" - if self._multivalued_slots is None: - self._multivalued_slots = { - c for c in self.view.all_slots() if self.view.get_slot(c).multivalued - } - return self._multivalued_slots + return {c for c in self.view.all_slots() if self.view.get_slot(c).multivalued} - @property + @cached_property def entity_reference_slots(self) -> Set[str]: """Return list of entity reference slots.""" - if self._entity_reference_slots is None: - self._entity_reference_slots = { - c for c in self.view.all_slots() if self.view.get_slot(c).range == ENTITY_REFERENCE - } - return self._entity_reference_slots + return {c for c in self.view.all_slots() if self.view.get_slot(c).range == ENTITY_REFERENCE} @lru_cache(1) From 964f032a3a962ed5f28a2b2d9183090c75ea8cf1 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 14 Nov 2023 11:10:40 -0600 Subject: [PATCH 20/36] shortened code --- src/sssom/util.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index 7208cbd8..a3bd7680 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -164,8 +164,8 @@ def from_mapping_set_document(cls, doc: MappingSetDocument) -> "MappingSetDataFr non_double_cols.replace(np.nan, "", inplace=True) df.update(non_double_cols) - df = sort_df_rows_columns(df) - return cls.with_converter(df=df, converter=doc.converter, metadata=meta) + return cls.with_converter(df=sort_df_rows_columns(df), converter=doc.converter, metadata=meta) + def to_mapping_set_document(self) -> "MappingSetDocument": """Get a mapping set document.""" From d5390fbbd7ff605dc69d17f6b3ee1b83a9840320 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 14 Nov 2023 11:15:37 -0600 Subject: [PATCH 21/36] formatted --- src/sssom/util.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index a3bd7680..0495778f 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -164,8 +164,9 @@ def from_mapping_set_document(cls, doc: MappingSetDocument) -> "MappingSetDataFr non_double_cols.replace(np.nan, "", inplace=True) df.update(non_double_cols) - return cls.with_converter(df=sort_df_rows_columns(df), converter=doc.converter, metadata=meta) - + return cls.with_converter( + df=sort_df_rows_columns(df), converter=doc.converter, metadata=meta + ) def to_mapping_set_document(self) -> "MappingSetDocument": """Get a mapping set document.""" From c8e4ea5a0b7a5be55fde119a9ce3c8efa656eba4 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 15 Nov 2023 16:22:17 -0600 Subject: [PATCH 22/36] Added test for get_dict_from_mapping() --- tests/test_utils.py | 105 +++++++++++++++++++++++++++++++++++++++----- 1 file changed, 95 insertions(+), 10 deletions(-) diff --git a/tests/test_utils.py b/tests/test_utils.py index 4e414d0a..aa3e355b 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -2,11 +2,21 @@ import unittest +import numpy as np import pandas as pd import yaml from curies import Converter, Record - -from sssom.constants import OBJECT_ID, SUBJECT_ID +from sssom_schema import Mapping as SSSOM_Mapping + +from sssom.constants import ( + CREATOR_ID, + OBJECT_ID, + OBJECT_LABEL, + PREDICATE_ID, + SEMAPV, + SUBJECT_ID, + SUBJECT_LABEL, +) from sssom.context import SSSOM_BUILT_IN_PREFIXES, ensure_converter from sssom.io import extract_iris from sssom.parsers import parse_sssom_table @@ -14,6 +24,7 @@ MappingSetDataFrame, filter_out_prefixes, filter_prefixes, + get_dict_from_mapping, get_prefixes_used_in_table, inject_metadata_into_df, invert_mappings, @@ -30,6 +41,7 @@ def setUp(self) -> None: self.msdf = parse_sssom_table(f"{data_dir}/basic.tsv") self.msdf2 = parse_sssom_table(f"{data_dir}/basic7.tsv") self.features = [SUBJECT_ID, OBJECT_ID] + self.mapping_justification = SEMAPV.ManualMappingCuration.value def test_broken_predicate_list(self): """Test merging of multiple msdfs.""" @@ -314,18 +326,18 @@ def test_msdf_from_mappings(self): "skos:exactMatch", "UMLS:C1863204", "ADULT SYNDROME", - "semapv:ManualMappingCuration", + SEMAPV.ManualMappingCuration.value, "orcid:0000-0003-4423-4370", ) ] columns = [ - "subject_id", - "subject_label", - "predicate_id", - "object_id", - "object_label", - "mapping_justification", - "creator_id", + SUBJECT_ID, + SUBJECT_LABEL, + PREDICATE_ID, + OBJECT_ID, + OBJECT_LABEL, + SEMAPV.ManualMappingCuration.value, + CREATOR_ID, ] df = pd.DataFrame(rows, columns=columns) msdf = MappingSetDataFrame(df=df, converter=ensure_converter()) @@ -345,3 +357,76 @@ def test_msdf_from_mappings(self): self.assertEqual(1, len(new_msdf.df.index)) self.assertEqual(rows[0], tuple(msdf.df.iloc[0])) self.assertEqual(new_msdf.metadata, msdf.metadata) + + def test_get_dict_from_mapping(self): + """Test getting dict from a SSSOM mapping object or a dictionary.""" + mapping_obj = SSSOM_Mapping( + subject_id="DOID:0050601", + predicate_id="skos:exactMatch", + object_id="UMLS:C1863204", + mapping_justification=SEMAPV.ManualMappingCuration.value, + author_id=["orcid:xxxxxxxx", "orcid:yyyyyyyy"], + confidence=0.5, + ) + mapping_dict = mapping_obj.__dict__ + + expected_result = { + "subject_id": "DOID:0050601", + "predicate_id": "skos:exactMatch", + "object_id": "UMLS:C1863204", + "mapping_justification": "semapv:ManualMappingCuration", + "subject_label": "", + "subject_category": "", + "predicate_label": "", + "predicate_modifier": "", + "object_label": "", + "object_category": "", + "author_id": "orcid:xxxxxxxx|orcid:yyyyyyyy", + "author_label": "", + "reviewer_id": "", + "reviewer_label": "", + "creator_id": "", + "creator_label": "", + "license": "", + "subject_type": "", + "subject_source": "", + "subject_source_version": "", + "object_type": "", + "object_source": "", + "object_source_version": "", + "mapping_provider": "", + "mapping_source": "", + "mapping_cardinality": "", + "mapping_tool": "", + "mapping_tool_version": "", + "mapping_date": "", + "publication_date": "", + "confidence": 0.5, + "curation_rule": "", + "curation_rule_text": "", + "subject_match_field": "", + "object_match_field": "", + "match_string": "", + "subject_preprocessing": "", + "object_preprocessing": "", + "semantic_similarity_score": np.nan, + "semantic_similarity_measure": "", + "see_also": "", + "issue_tracker_item": "", + "other": "", + "comment": "", + } + + result_with_mapping_object = get_dict_from_mapping(mapping_obj) + result_with_dict = get_dict_from_mapping(mapping_dict) + self.assertEqual(result_with_mapping_object, result_with_dict) + + # Assert that every attribute value in expected_result + # equals the corresponding key in result_with_mapping_object (except lists) + for key, value in expected_result.items(): + if value is None or value == [] or value is np.nan: + self.assertTrue(result_with_mapping_object[key] in [np.nan, ""]) + self.assertTrue(result_with_dict[key] in [np.nan, ""]) + else: + self.assertEqual(value, result_with_mapping_object[key]) + self.assertEqual(value, result_with_dict[key]) From a666ea1d1373fb15e61ebcf0191eeacdca7de01c Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 15 Nov 2023 16:22:33 -0600 Subject: [PATCH 23/36] Added extra comments --- src/sssom/parsers.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index 3bf637e9..8f000abf 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -330,13 +330,22 @@ def _init_mapping_set(meta: Optional[MetadataType]) -> MappingSet: def _get_mapping_dict(row: pd.Series, bad_attrs: Counter) -> Dict[str, Any]: + """ + Generate a mapping dictionary from a given row of data. + + It also updates the 'bad_attrs' counter for keys that are not present + in the sssom_schema_object's mapping_slots. + """ mdict = {} sssom_schema_object = _get_sssom_schema_object() + # Populate the mapping dictionary with key-value pairs from the row, + # only if the value exists, is not NaN, and the key is in the schema's mapping slots. + # The value could be a string or a list and is handled accordingly via _address_multivalued_slot(). mdict = { k: _address_multivalued_slot(k, v) for k, v in row.items() - if v and not pd.isna(v) and k in sssom_schema_object.mapping_slots + if v and pd.notna(v) and k in sssom_schema_object.mapping_slots } # Update bad_attrs for keys not in mapping_slots @@ -803,9 +812,8 @@ def _get_mapping_set_from_df(df: pd.DataFrame, meta: Optional[MetadataType] = No axis=1, ) - if bad_attrs: - for k, v in bad_attrs.items(): - logging.warning(f"No attr for {k} [{v} instances]") + for k, v in bad_attrs.items(): + logging.warning(f"No attr for {k} [{v} instances]") return mapping_set From 788cc7e1747dbfcee249391b3baeb65f6ffec49a Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 16 Nov 2023 13:45:45 -0600 Subject: [PATCH 24/36] extended prefix map change effect --- tests/test_parsers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_parsers.py b/tests/test_parsers.py index 335ae68b..52bc123b 100644 --- a/tests/test_parsers.py +++ b/tests/test_parsers.py @@ -127,7 +127,7 @@ def test_parse_obographs(self): self.assertEqual( # this number went up from 8099 when the curies.Converter was introduced # since it was able to handle CURIE prefix and URI prefix synonyms - 8488, + 8489, len(msdf.df), f"{self.obographs_file} has the wrong number of mappings.", ) From f3d16aee2f306568fa6a1a72bf163da1a134ce64 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 20 Nov 2023 12:02:58 +0100 Subject: [PATCH 25/36] Revert inclusion in try/except --- src/sssom/parsers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index 8f000abf..756f3468 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -890,8 +890,8 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]): :param mdict: A dictionary containing the mapping metadata. :return: A valid Mapping object, or None. """ + mdict.setdefault(MAPPING_JUSTIFICATION, MAPPING_JUSTIFICATION_UNSPECIFIED) try: - mdict.setdefault(MAPPING_JUSTIFICATION, MAPPING_JUSTIFICATION_UNSPECIFIED) m = Mapping(**mdict) except ValueError as e: logging.warning( From 4ec556ed93d07234395f597aac68e54c1a7dd570 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 20 Nov 2023 12:04:48 +0100 Subject: [PATCH 26/36] Revert style change --- src/sssom/util.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index 0495778f..7208cbd8 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -164,9 +164,8 @@ def from_mapping_set_document(cls, doc: MappingSetDocument) -> "MappingSetDataFr non_double_cols.replace(np.nan, "", inplace=True) df.update(non_double_cols) - return cls.with_converter( - df=sort_df_rows_columns(df), converter=doc.converter, metadata=meta - ) + df = sort_df_rows_columns(df) + return cls.with_converter(df=df, converter=doc.converter, metadata=meta) def to_mapping_set_document(self) -> "MappingSetDocument": """Get a mapping set document.""" From 8681b812e5beb2be080f2abf5875266fb3ab87da Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 20 Nov 2023 12:17:34 +0100 Subject: [PATCH 27/36] Cache reused constants --- src/sssom/constants.py | 4 ++-- src/sssom/parsers.py | 17 ++++++++--------- src/sssom/util.py | 17 ++++++++--------- 3 files changed, 18 insertions(+), 20 deletions(-) diff --git a/src/sssom/constants.py b/src/sssom/constants.py index 906f1189..168cc5ef 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -230,9 +230,9 @@ def dict(self) -> dict: return schema_as_dict(self.view.schema) @cached_property - def mapping_slots(self) -> List[str]: + def mapping_slots(self) -> Set[str]: """Return list of mapping slots.""" - return self.view.get_class("mapping").slots + return set(self.view.get_class("mapping").slots) @cached_property def mapping_set_slots(self) -> List[str]: diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index 756f3468..195035e3 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -329,29 +329,28 @@ def _init_mapping_set(meta: Optional[MetadataType]) -> MappingSet: return mapping_set +MAPPING_SLOTS = _get_sssom_schema_object().mapping_slots + + def _get_mapping_dict(row: pd.Series, bad_attrs: Counter) -> Dict[str, Any]: - """ - Generate a mapping dictionary from a given row of data. + """Generate a mapping dictionary from a given row of data. It also updates the 'bad_attrs' counter for keys that are not present in the sssom_schema_object's mapping_slots. """ - mdict = {} - sssom_schema_object = _get_sssom_schema_object() - # Populate the mapping dictionary with key-value pairs from the row, # only if the value exists, is not NaN, and the key is in the schema's mapping slots. # The value could be a string or a list and is handled accordingly via _address_multivalued_slot(). mdict = { k: _address_multivalued_slot(k, v) for k, v in row.items() - if v and pd.notna(v) and k in sssom_schema_object.mapping_slots + if v and pd.notna(v) and k in MAPPING_SLOTS } # Update bad_attrs for keys not in mapping_slots - bad_keys = set(row.keys()) - set(sssom_schema_object.mapping_slots) - for k in bad_keys: - bad_attrs[k] += 1 + bad_keys = set(row.keys()) - MAPPING_SLOTS + for bad_key in bad_keys: + bad_attrs[bad_key] += 1 return mdict diff --git a/src/sssom/util.py b/src/sssom/util.py index 7208cbd8..495be934 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1035,6 +1035,11 @@ def to_mapping_set_dataframe(doc: MappingSetDocument) -> MappingSetDataFrame: return MappingSetDataFrame.from_mapping_set_document(doc) +DICT_FROM_MAPPING_ENUM_KEYS = set(_get_sssom_schema_object().dict["enums"].keys()) +SLOTS = _get_sssom_schema_object().dict["slots"] +DOUBLE_SLOTS = {k for k, v in SLOTS.items() if v["range"] == "double"} + + def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> dict: """ Get information for linkml objects (MatchTypeEnum, PredicateModifierEnum) from the Mapping object and return the dictionary form of the object. @@ -1043,20 +1048,14 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> :return: Dictionary """ map_dict = {} - sssom_schema_object = _get_sssom_schema_object().dict - slots = sssom_schema_object["slots"] - enums_keys = set(sssom_schema_object["enums"].keys()) - - slots_with_double_as_range = {k for k, v in slots.items() if v["range"] == "double"} - for property in map_obj: mapping_property = map_obj[property] if mapping_property is None: - map_dict[property] = np.nan if property in slots_with_double_as_range else "" + map_dict[property] = np.nan if property in DOUBLE_SLOTS else "" continue - slot_of_interest = slots[property] - is_enum = slot_of_interest["range"] in enums_keys + slot_of_interest = SLOTS[property] + is_enum = slot_of_interest["range"] in DICT_FROM_MAPPING_ENUM_KEYS # Check if the mapping_property is a list if isinstance(mapping_property, list): From 92e8158507583ea28242e509faaeb38a4402bcc0 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 20 Nov 2023 12:17:39 +0100 Subject: [PATCH 28/36] Add TODOs --- src/sssom/util.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index 495be934..f6e6d86b 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1061,6 +1061,7 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> if isinstance(mapping_property, list): # If the property is an enumeration and it allows multiple values if is_enum and slot_of_interest["multivalued"]: + # FIXME needs test # Join all the enum values into a string separated by '|' map_dict[property] = "|".join( enum_value.code.text for enum_value in mapping_property @@ -1069,8 +1070,8 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> # If the property is not an enumeration or doesn't allow multiple values, # join all the values into a string separated by '|' map_dict[property] = "|".join(enum_value for enum_value in mapping_property) - # If the mapping_property is not a list but an enumeration elif is_enum: + # FIXME needs test # Assign the text of the enumeration code to the property in the dictionary map_dict[property] = mapping_property.code.text else: From 558ca15a301293be561803719d971fb4f6c67450 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 20 Nov 2023 12:18:28 +0100 Subject: [PATCH 29/36] Reduce diff --- src/sssom/parsers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index 195035e3..96e7fc4e 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -813,7 +813,6 @@ def _get_mapping_set_from_df(df: pd.DataFrame, meta: Optional[MetadataType] = No for k, v in bad_attrs.items(): logging.warning(f"No attr for {k} [{v} instances]") - return mapping_set @@ -890,6 +889,7 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]): :return: A valid Mapping object, or None. """ mdict.setdefault(MAPPING_JUSTIFICATION, MAPPING_JUSTIFICATION_UNSPECIFIED) + try: m = Mapping(**mdict) except ValueError as e: From 2b2be7ba31daba3b4f8549867773608034cd9b61 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 20 Nov 2023 12:21:08 +0100 Subject: [PATCH 30/36] Fix list --- src/sssom/constants.py | 4 ++-- src/sssom/parsers.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/sssom/constants.py b/src/sssom/constants.py index 168cc5ef..906f1189 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -230,9 +230,9 @@ def dict(self) -> dict: return schema_as_dict(self.view.schema) @cached_property - def mapping_slots(self) -> Set[str]: + def mapping_slots(self) -> List[str]: """Return list of mapping slots.""" - return set(self.view.get_class("mapping").slots) + return self.view.get_class("mapping").slots @cached_property def mapping_set_slots(self) -> List[str]: diff --git a/src/sssom/parsers.py b/src/sssom/parsers.py index 96e7fc4e..87ad603d 100644 --- a/src/sssom/parsers.py +++ b/src/sssom/parsers.py @@ -329,7 +329,7 @@ def _init_mapping_set(meta: Optional[MetadataType]) -> MappingSet: return mapping_set -MAPPING_SLOTS = _get_sssom_schema_object().mapping_slots +MAPPING_SLOTS = set(_get_sssom_schema_object().mapping_slots) def _get_mapping_dict(row: pd.Series, bad_attrs: Counter) -> Dict[str, Any]: From aa8a45c782e15abf4dbff0d6f35bbddcc9234b47 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 20 Nov 2023 08:05:21 -0600 Subject: [PATCH 31/36] changed assertion test --- tests/test_utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_utils.py b/tests/test_utils.py index aa3e355b..ae16b97f 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -425,8 +425,8 @@ def test_get_dict_from_mapping(self): # equals the corresponding key in result_with_mapping_object (except lists) for key, value in expected_result.items(): if value is None or value == [] or value is np.nan: - self.assertTrue(result_with_mapping_object[key] in [np.nan, ""]) - self.assertTrue(result_with_dict[key] in [np.nan, ""]) + self.assertIn(result_with_mapping_object[key], [np.nan, ""]) + self.assertIn(result_with_dict[key], [np.nan, ""]) else: self.assertEqual(value, result_with_mapping_object[key]) self.assertEqual(value, result_with_dict[key]) From 964aac81636eb55e552c2f4881ef8c24949ddc53 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 20 Nov 2023 08:08:05 -0600 Subject: [PATCH 32/36] added real orcids --- tests/test_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_utils.py b/tests/test_utils.py index ae16b97f..89cf8bd6 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -365,7 +365,7 @@ def test_get_dict_from_mapping(self): predicate_id="skos:exactMatch", object_id="UMLS:C1863204", mapping_justification=SEMAPV.ManualMappingCuration.value, - author_id=["orcid:xxxxxxxx", "orcid:yyyyyyyy"], + author_id=["orcid:0000-0002-2411-565X", "orcid:0000-0002-7356-1779"], confidence=0.5, ) mapping_dict = mapping_obj.__dict__ From 036f66e03c8b81b527a299e0da53a9862481fbc9 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 20 Nov 2023 08:21:39 -0600 Subject: [PATCH 33/36] orcid updated --- tests/test_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_utils.py b/tests/test_utils.py index 89cf8bd6..fb943115 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -381,7 +381,7 @@ def test_get_dict_from_mapping(self): "predicate_modifier": "", "object_label": "", "object_category": "", - "author_id": "orcid:xxxxxxxx|orcid:yyyyyyyy", + "author_id": "orcid:0000-0002-2411-565X|orcid:0000-0002-7356-1779", "author_label": "", "reviewer_id": "", "reviewer_label": "", From d2338f04d6a443328b798ba1cead69aa9f049c26 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 20 Nov 2023 08:52:21 -0600 Subject: [PATCH 34/36] removed comments --- src/sssom/util.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/sssom/util.py b/src/sssom/util.py index f6e6d86b..813ffedf 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1061,7 +1061,6 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> if isinstance(mapping_property, list): # If the property is an enumeration and it allows multiple values if is_enum and slot_of_interest["multivalued"]: - # FIXME needs test # Join all the enum values into a string separated by '|' map_dict[property] = "|".join( enum_value.code.text for enum_value in mapping_property @@ -1071,7 +1070,6 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> # join all the values into a string separated by '|' map_dict[property] = "|".join(enum_value for enum_value in mapping_property) elif is_enum: - # FIXME needs test # Assign the text of the enumeration code to the property in the dictionary map_dict[property] = mapping_property.code.text else: From 7cae890ba81293c1031393469f5f16aea2b08dd4 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 20 Nov 2023 09:05:25 -0600 Subject: [PATCH 35/36] moved constants to the SSSOMSchemaView class as attributes --- src/sssom/constants.py | 19 +++++++++++++++++-- src/sssom/util.py | 12 ++++-------- 2 files changed, 21 insertions(+), 10 deletions(-) diff --git a/src/sssom/constants.py b/src/sssom/constants.py index 906f1189..f33f90f3 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -241,14 +241,29 @@ def mapping_set_slots(self) -> List[str]: @cached_property def multivalued_slots(self) -> Set[str]: - """Return list of multivalued slots.""" + """Return set of multivalued slots.""" return {c for c in self.view.all_slots() if self.view.get_slot(c).multivalued} @cached_property def entity_reference_slots(self) -> Set[str]: - """Return list of entity reference slots.""" + """Return set of entity reference slots.""" return {c for c in self.view.all_slots() if self.view.get_slot(c).range == ENTITY_REFERENCE} + @cached_property + def mapping_enum_keys(self) -> Set[str]: + """Return a set of mapping enum keys.""" + return set(_get_sssom_schema_object().dict["enums"].keys()) + + @cached_property + def slots(self) -> Dict[str, str]: + """Return the slot names for SSSOMSchemaView object as a set.""" + return self.dict["slots"] + + @cached_property + def double_slots(self) -> Set[str]: + """Return the slot names for SSSOMSchemaView object.""" + return {k for k, v in self.dict["slots"].items() if v["range"] == "double"} + @lru_cache(1) def _get_sssom_schema_object() -> SSSOMSchemaView: diff --git a/src/sssom/util.py b/src/sssom/util.py index 813ffedf..e45592a6 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1035,11 +1035,6 @@ def to_mapping_set_dataframe(doc: MappingSetDocument) -> MappingSetDataFrame: return MappingSetDataFrame.from_mapping_set_document(doc) -DICT_FROM_MAPPING_ENUM_KEYS = set(_get_sssom_schema_object().dict["enums"].keys()) -SLOTS = _get_sssom_schema_object().dict["slots"] -DOUBLE_SLOTS = {k for k, v in SLOTS.items() if v["range"] == "double"} - - def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> dict: """ Get information for linkml objects (MatchTypeEnum, PredicateModifierEnum) from the Mapping object and return the dictionary form of the object. @@ -1048,14 +1043,15 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> :return: Dictionary """ map_dict = {} + sssom_schema_object = _get_sssom_schema_object() for property in map_obj: mapping_property = map_obj[property] if mapping_property is None: - map_dict[property] = np.nan if property in DOUBLE_SLOTS else "" + map_dict[property] = np.nan if property in sssom_schema_object.double_slots else "" continue - slot_of_interest = SLOTS[property] - is_enum = slot_of_interest["range"] in DICT_FROM_MAPPING_ENUM_KEYS + slot_of_interest = sssom_schema_object.slots[property] + is_enum = slot_of_interest["range"] in sssom_schema_object.mapping_enum_keys # Check if the mapping_property is a list if isinstance(mapping_property, list): From fbeeb88f25a7db04d276a91e7b7d52005df0505d Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Mon, 20 Nov 2023 09:13:58 -0600 Subject: [PATCH 36/36] docstring update and mypy check fix --- src/sssom/constants.py | 2 +- src/sssom/util.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/sssom/constants.py b/src/sssom/constants.py index f33f90f3..9f8a09c0 100644 --- a/src/sssom/constants.py +++ b/src/sssom/constants.py @@ -256,7 +256,7 @@ def mapping_enum_keys(self) -> Set[str]: @cached_property def slots(self) -> Dict[str, str]: - """Return the slot names for SSSOMSchemaView object as a set.""" + """Return the slots for SSSOMSchemaView object.""" return self.dict["slots"] @cached_property diff --git a/src/sssom/util.py b/src/sssom/util.py index e45592a6..64db60ed 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -1051,12 +1051,12 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> continue slot_of_interest = sssom_schema_object.slots[property] - is_enum = slot_of_interest["range"] in sssom_schema_object.mapping_enum_keys + is_enum = slot_of_interest["range"] in sssom_schema_object.mapping_enum_keys # type:ignore # Check if the mapping_property is a list if isinstance(mapping_property, list): # If the property is an enumeration and it allows multiple values - if is_enum and slot_of_interest["multivalued"]: + if is_enum and slot_of_interest["multivalued"]: # type:ignore # Join all the enum values into a string separated by '|' map_dict[property] = "|".join( enum_value.code.text for enum_value in mapping_property