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refactor: InvestigationFileWriter write method is now aware of inheri…
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…ted classes of Investigation model
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@oyurekten
oyurekten committed Sep 18, 2024
1 parent ebf17b4 commit 1928d04
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Showing 4 changed files with 140 additions and 25 deletions.
155 changes: 131 additions & 24 deletions metabolights_utils/isatab/default/investigation_file.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -129,10 +129,12 @@ def write(
values_in_quotation_mark: bool = True,
verify_file_after_update: bool = True,
skip_parser_info_messages: bool = True,
investigation_module_name: Union[None, str] = None,
) -> InvestigationFileReaderResult:
content = InvestigationFileSerializer.to_isa_file_string(
investigation=investigation,
values_in_quotation_mark=values_in_quotation_mark,
investigation_module_name=investigation_module_name,
)
file_path = None
try:
Expand Down Expand Up @@ -183,10 +185,19 @@ def write(
class InvestigationFileSerializer(object):
@classmethod
def to_isa_file_lines(
cls, investigation: Investigation, values_in_quotation_mark: bool = False
cls,
investigation: Investigation,
values_in_quotation_mark: bool = False,
investigation_module_name: Union[None, str] = None,
):
module_name = (
investigation_module_name if investigation_module_name else inv_module_name
)
file_lines = []
for row in cls.to_isa_file_line_list(investigation):
for row in cls.to_isa_file_line_list(
investigation,
investigation_module_name=module_name,
):
for i in range(len(row)):
item = row[i].strip('"')
row[i] = f'"{item}"' if i > 0 and values_in_quotation_mark else item
Expand All @@ -196,59 +207,102 @@ def to_isa_file_lines(

@classmethod
def to_isa_file_string(
cls, investigation: Investigation, values_in_quotation_mark: bool = False
cls,
investigation: Investigation,
values_in_quotation_mark: bool = False,
investigation_module_name: Union[None, str] = None,
):
file_lines = cls.to_isa_file_lines(investigation, values_in_quotation_mark)
file_lines = cls.to_isa_file_lines(
investigation,
values_in_quotation_mark,
investigation_module_name=investigation_module_name,
)

return "\n".join(file_lines) + "\n"

@classmethod
def to_isa_file_line_list(cls, investigation: Investigation):
def to_isa_file_line_list(
cls,
investigation: Investigation,
investigation_module_name: Union[None, str] = None,
):
rows: List[List[str]] = []
rows.extend(cls.add_sub_section("", investigation.ontology_source_references))
rows.extend(cls.add_sub_section("", investigation))
rows.extend(
cls.add_sub_section(
"",
investigation.ontology_source_references,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
"",
investigation,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
investigation.isatab_config.section_prefix,
investigation.investigation_publications,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
investigation.isatab_config.section_prefix,
investigation.investigation_contacts,
investigation_module_name=investigation_module_name,
)
)
for study in investigation.studies:
rows.extend(cls.add_sub_section("", study))
rows.extend(
cls.add_sub_section(
study.isatab_config.section_prefix, study.study_design_descriptors
"",
study,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
study.isatab_config.section_prefix, study.study_publications
study.isatab_config.section_prefix,
study.study_design_descriptors,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
study.isatab_config.section_prefix, study.study_factors
study.isatab_config.section_prefix,
study.study_publications,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
study.isatab_config.section_prefix, study.study_assays
study.isatab_config.section_prefix,
study.study_factors,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
study.isatab_config.section_prefix, study.study_protocols
study.isatab_config.section_prefix,
study.study_assays,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
study.isatab_config.section_prefix, study.study_contacts
study.isatab_config.section_prefix,
study.study_protocols,
investigation_module_name=investigation_module_name,
)
)
rows.extend(
cls.add_sub_section(
study.isatab_config.section_prefix,
study.study_contacts,
investigation_module_name=investigation_module_name,
)
)
return rows
Expand All @@ -259,7 +313,15 @@ def get_attribute(model, field_name):
return getattr(model, model_field_name)

@classmethod
def add_sub_section(cls, prefix, model: BaseSection):
def add_sub_section(
cls,
prefix,
model: BaseSection,
investigation_module_name: Union[None, str] = None,
):
module_name = (
investigation_module_name if investigation_module_name else inv_module_name
)
rows: List[List[str]] = [[model.isatab_config.section_header]]
header = []
if prefix:
Expand All @@ -285,13 +347,29 @@ def add_sub_section(cls, prefix, model: BaseSection):
default_object_name = item_ref.replace(
"#/definitions/", ""
).replace("#/$defs/", "")
obj: BaseModel = getattr(
sys.modules[inv_module_name], default_object_name
)
props = obj.model_json_schema()["properties"]
obj = None
if module_name != inv_module_name:
try:
obj: BaseModel = getattr(
sys.modules[module_name],
default_object_name,
)
except:
pass
# not set a value try to find on default module
if not obj:
obj: BaseModel = getattr(
sys.modules[inv_module_name],
default_object_name,
)
props_base = obj.model_json_schema(by_alias=False)["properties"]
props = {to_camel(x): props_base[x] for x in props_base}
header.append(data_schema["properties"][field_key]["header_name"])
sub_model_rows = cls.add_model_content(
" ".join(header).strip(), value, props
" ".join(header).strip(),
value,
props,
investigation_module_name=module_name,
)
if sub_model_rows:
rows.extend(sub_model_rows)
Expand Down Expand Up @@ -323,7 +401,16 @@ def add_comments(cls, model: BaseSection, rows: List[List[str]]):
comment_line.append(value)

@classmethod
def add_model_content(cls, prefix, items: List[IsaAbstractModel], properties):
def add_model_content(
cls,
prefix,
items: List[IsaAbstractModel],
properties,
investigation_module_name: Union[None, str] = None,
):
module_name = (
investigation_module_name if investigation_module_name else inv_module_name
)
rows = []
row_map = {}
fields = properties["isatabConfig"]["default"]["fieldOrder"]
Expand All @@ -346,14 +433,34 @@ def add_model_content(cls, prefix, items: List[IsaAbstractModel], properties):
class_name = item_ref.replace("#/definitions/", "").replace(
"#/$defs/", ""
)
obj: BaseModel = getattr(sys.modules[inv_module_name], class_name)
props = obj.model_json_schema()["properties"]
obj = None
if module_name != inv_module_name:
try:
obj: BaseModel = getattr(
sys.modules[module_name],
class_name,
)
except:
pass
# not set a value try to find on default module
if not obj:
obj: BaseModel = getattr(
sys.modules[inv_module_name],
class_name,
)
props_base = obj.model_json_schema(by_alias=False)["properties"]
props = {to_camel(x): props_base[x] for x in props_base}
input_items = (
[cls.get_attribute(item, field_key) for item in items]
if items
else [obj()]
)
item_values = cls.add_model_content(header_name, input_items, props)
item_values = cls.add_model_content(
header_name,
input_items,
props,
investigation_module_name=module_name,
)
rows.extend(item_values)
elif "type" in properties[field_key]:
cls.assign_type(
Expand Down
3 changes: 3 additions & 0 deletions metabolights_utils/isatab/writer.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ def write(
values_in_quotation_mark: bool = True,
verify_file_after_update: bool = True,
skip_parser_info_messages: bool = True,
investigation_module_name: Union[None, str] = None,
) -> InvestigationFileReaderResult:
"""Converts investigation file model to isatab inverstigation format and writes to file buffer.
If file buffer is not defined, it creates/updates a file on file_path.
Expand All @@ -31,6 +32,8 @@ def write(
values_in_quotation_mark (bool, optional): add values in quatation_mark. Defaults to True.
verify_file_after_update (bool, optional): Reads investigation file if it is True. Defaults to True.
skip_parser_info_messages (bool, optional): clear INFO messages from parser messages. Defaults to True.
investigation_module_name: Union[None, str] = investigation file module name to find domain classes referenced in json schema.
e.g. 'metabolights_utils.models.isa.investigation_file'
Returns:
InvestigationFileReaderResult: Returns updated investigation model and parser messages if verify_file_after_update is True.
If verify_file_after_update is False, return input investigation and empty parser message report
Expand Down
5 changes: 5 additions & 0 deletions metabolights_utils/models/isa/common.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -378,6 +378,11 @@ class IsaTableColumn(IsaAbstractModel):
str, Field(description="Column prefix if header has a value between [].")
] = ""

default_value: Annotated[
str,
Field(description="Default value", exclude=True),
] = ""

column_search_pattern: Annotated[
str,
Field(
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ default = "semantic-release <semantic-release>"
[tool.semantic_release.commit_parser_options]
allowed_tags = ["build", "chore", "ci", "docs", "feat", "fix", "perf", "style", "refactor", "test", "CLI", "API"]
minor_tags = ["feat", "API", "CLI"]
patch_tags = ["fix", "perf"]
patch_tags = ["fix", "perf", "refactor"]
default_bump_level = 0

[tool.semantic_release.remote]
Expand Down

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