Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

adding base_schema_path to the converter #139

Merged
merged 1 commit into from
Mar 25, 2024
Merged

adding base_schema_path to the converter #139

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 16 additions & 4 deletions schemasheets/schemamaker.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ class SchemaMaker:
unique_slots: bool = None
gsheet_id: str = None
table_config_path: str = None
base_schema_path: str = None

def create_schema(self, csv_files: Union[str, List[str]], **kwargs) -> SchemaDefinition:
"""
Expand All @@ -55,8 +56,13 @@ def create_schema(self, csv_files: Union[str, List[str]], **kwargs) -> SchemaDef
:param kwargs:
:return: generated schema
"""
n = self.default_name
if n is None:
self.base_view = SchemaView(self.base_schema_path) if self.base_schema_path else None

if self.default_name:
n = self.default_name
elif self.base_view and self.base_view.schema.name:
n = self.base_view.schema.name
else:
n = 'TEMP'
self.schema = SchemaDefinition(id=n, name=n, default_prefix=n, default_range='string')
if not isinstance(csv_files, list):
Expand All @@ -70,6 +76,9 @@ def create_schema(self, csv_files: Union[str, List[str]], **kwargs) -> SchemaDef
if prefix not in self.schema.prefixes:
logging.error(f'Prefix {prefix} not declared: using default')
self.schema.prefixes[prefix] = Prefix(prefix, f'https://example.org/{prefix}/')

if self.base_view:
SchemaView(self.schema).merge_schema(self.base_view.schema)
return self.schema

def _tidy_slot_usage(self):
Expand Down Expand Up @@ -660,10 +669,12 @@ def ensure_csvreader(self, file_name: str, delimiter=None) -> str:
help="Auto-repair schema")
@click.option("--gsheet-id",
help="Google sheets ID. If this is specified then the arguments MUST be sheet names")
@click.option("--base-schema-path",
help="Base schema yaml file, the base-schema will be merged with the generated schema")
@click.option("-v", "--verbose", count=True)
@click.argument('tsv_files', nargs=-1)
def convert(tsv_files, gsheet_id, output: TextIO, name, repair, table_config_path: str, use_attributes: bool,
unique_slots: bool, verbose: int, sort_keys: bool):
unique_slots: bool, verbose: int, sort_keys: bool, base_schema_path: str):
"""
Convert schemasheets to a LinkML schema

Expand All @@ -688,7 +699,8 @@ def convert(tsv_files, gsheet_id, output: TextIO, name, repair, table_config_pat
unique_slots=unique_slots,
gsheet_id=gsheet_id,
default_name=name,
table_config_path=table_config_path)
table_config_path=table_config_path,
base_schema_path=base_schema_path)
schema = sm.create_schema(list(tsv_files))
if repair:
schema = sm.repair_schema(schema)
Expand Down
Loading