FAILED                               [ 30%]
test_schema_exporter.py:174 (test_types)
self = SchemaMaker(schema=SchemaDefinition(name='TEMP', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None...), element_map=None, metamodel=None, cardinality_vocabulary=None, default_name=None, unique_slots=None, gsheet_id=None)
file_name = '/Users/MAM/Documents/gitrepos/schemasheets/tests/output/mini.tsv'
delimiter = '\t'

    def merge_sheet(self, file_name: str, delimiter='\t') -> None:
        """
        Merge information from the given schema sheet into the current schema
    
        :param file_name: schema sheet
        :param delimiter: default is tab
        :return:
        """
        logging.info(f'READING {file_name} D={delimiter}')
        #with self.ensure_file(file_name) as tsv_file:
        #    reader = csv.DictReader(tsv_file, delimiter=delimiter)
        with self.ensure_csvreader(file_name, delimiter=delimiter) as reader:
            schemasheet = SchemaSheet.from_dictreader(reader)
            line_num = schemasheet.start_line_number
            # TODO: check why this doesn't work
            #while rows and all(x for x in rows[-1] if not x):
            #    print(f'TRIMMING: {rows[-1]}')
            #    rows.pop()
            logging.info(f'ROWS={len(schemasheet.rows)}')
            for row in schemasheet.rows:
                try:
>                   self.add_row(row, schemasheet.table_config)

../schemasheets/schemamaker.py:105: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = SchemaMaker(schema=SchemaDefinition(name='TEMP', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None...), element_map=None, metamodel=None, cardinality_vocabulary=None, default_name=None, unique_slots=None, gsheet_id=None)
row = {'Desc': 'my string', 'Extends': 'string', 'Type': '', 'base': '', ...}
table_config = TableConfig(name=None, columns={'Type': ColumnConfig(name='Type', maps_to='type', settings=ColumnSettings(curie_prefix...], all_of=[]), is_element_type=None)}, column_by_element_type={'type': 'Type'}, metatype_column=None, name_column=None)

    def add_row(self, row: Dict[str, Any], table_config: TableConfig):
>       for element in self.row_focal_element(row, table_config):

../schemasheets/schemamaker.py:111: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = SchemaMaker(schema=SchemaDefinition(name='TEMP', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None...), element_map=None, metamodel=None, cardinality_vocabulary=None, default_name=None, unique_slots=None, gsheet_id=None)
row = {'Desc': 'my string', 'Extends': 'string', 'Type': '', 'base': '', ...}
table_config = TableConfig(name=None, columns={'Type': ColumnConfig(name='Type', maps_to='type', settings=ColumnSettings(curie_prefix...], all_of=[]), is_element_type=None)}, column_by_element_type={'type': 'Type'}, metatype_column=None, name_column=None)
column = None

    def row_focal_element(self, row: Dict[str, Any], table_config: TableConfig,
                          column: COL_NAME = None) -> Generator[None, Element, None]:
        """
        Each row must have a single focal element, i.e the row is about a class, a slot, an enum, ...
    
        :param row:
        :param table_config:
        :return:
        """
        vmap = {}
        main_elt = None
        if table_config.metatype_column:
            tc = table_config.metatype_column
            if tc in row:
                typ = self.normalize_value(row[tc], table_config.columns[tc])
                if not table_config.name_column:
                    raise ValueError(f'name column must be set when type column ({tc}) is set; row={row}')
                name_val = row[table_config.name_column]
                if not name_val:
                    raise ValueError(f'name column must be set when type column ({tc}) is set')
                if typ == 'class':
                    vmap[T_CLASS] = [self.get_current_element(ClassDefinition(name_val))]
                elif typ == 'slot':
                    vmap[T_SLOT] = [self.get_current_element(SlotDefinition(name_val))]
                else:
                    raise ValueError(f'Unknown metatype: {typ}')
        if table_config.column_by_element_type is None:
            raise ValueError(f'No table_config.column_by_element_type')
        for k, elt_cls in tmap.items():
            if k in table_config.column_by_element_type:
                col = table_config.column_by_element_type[k]
                if col in row:
                    v = self.normalize_value(row[col])
                    if v:
                        if '|' in v:
                            vs = v.split('|')
                        else:
                            vs = [v]
                        if elt_cls == Prefix:
                            if len(vs) != 1:
                                raise ValueError(f'Cardinality of prefix col must be 1; got: {vs}')
                            pfx = Prefix(vs[0], 'TODO')
                            self.schema.prefixes[pfx.prefix_prefix] = pfx
                            vmap[k] = [pfx]
                        elif elt_cls == SchemaDefinition:
                            if len(vs) != 1:
                                raise ValueError(f'Cardinality of schema col must be 1; got: {vs}')
                            self.schema.name = vs[0]
                            vmap[k] = [self.schema]
                        else:
                            vmap[k] = [self.get_current_element(elt_cls(v)) for v in vs]
        def check_excess(descriptors):
            diff = set(vmap.keys()) - set(descriptors + [T_SCHEMA])
            if len(diff) > 0:
                raise ValueError(f'Excess slots: {diff}')
        if column:
            cc = table_config.columns[column]
            if cc.settings.applies_to_class:
                if T_CLASS in vmap and vmap[T_CLASS]:
                    raise ValueError(f'Cannot use applies_to_class in class-focused row')
                else:
                    cls = self.get_current_element(ClassDefinition(cc.settings.applies_to_class))
                    vmap[T_CLASS] = [cls]
        if T_SLOT in vmap:
            check_excess([T_SLOT, T_CLASS])
            if len(vmap[T_SLOT]) != 1:
                raise ValueError(f'Cardinality of slot field must be 1; got {vmap[T_SLOT]}')
            main_elt = vmap[T_SLOT][0]
            if T_CLASS in vmap:
                # TODO: attributes
                c: ClassDefinition
                for c in vmap[T_CLASS]:
                    #c: ClassDefinition = vmap[T_CLASS]
                    if main_elt.name not in c.slots:
                        c.slots.append(main_elt.name)
                    if self.unique_slots:
                        yield main_elt
                    else:
                        c.slot_usage[main_elt.name] = SlotDefinition(main_elt.name)
                        main_elt = c.slot_usage[main_elt.name]
                        yield main_elt
            else:
                yield main_elt
        elif T_CLASS in vmap:
            check_excess([T_CLASS])
            for main_elt in vmap[T_CLASS]:
                yield main_elt
        elif T_ENUM in vmap:
            check_excess([T_ENUM, T_PV])
            if len(vmap[T_ENUM]) != 1:
                raise ValueError(f'Cardinality of enum field must be 1; got {vmap[T_ENUM]}')
            this_enum: EnumDefinition = vmap[T_ENUM][0]
            if T_PV in vmap:
                for pv in vmap[T_PV]:
                    #pv = PermissibleValue(text=v)
                    this_enum.permissible_values[pv.text] = pv
                    yield pv
            else:
                yield this_enum
        elif T_PREFIX in vmap:
            for main_elt in vmap[T_PREFIX]:
                yield main_elt
        elif T_TYPE in vmap:
            for main_elt in vmap[T_TYPE]:
                yield main_elt
        elif T_SUBSET in vmap:
            for main_elt in vmap[T_SUBSET]:
                yield main_elt
        elif T_SCHEMA in vmap:
            for main_elt in vmap[T_SCHEMA]:
                yield main_elt
        else:
>           raise ValueError(f'Could not find a focal element for {row}')
E           ValueError: Could not find a focal element for {'Type': '', 'base': '', 'uri': '', 'Desc': 'my string', 'Extends': 'string'}

../schemasheets/schemamaker.py:318: ValueError

The above exception was the direct cause of the following exception:

    def test_types():
        """
        tests a specification that is dedicated to types
        """
        sb = SchemaBuilder()
        schema = sb.schema
        # TODO: add this functionality to SchemaBuilder
        t = TypeDefinition('MyString', description='my string', typeof='string')
        schema.types[t.name] = t
>       _roundtrip(schema, TYPES_SPEC)

test_schema_exporter.py:184: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
test_schema_exporter.py:94: in _roundtrip
    schema2 = sm.create_schema(MINISHEET)
../schemasheets/schemamaker.py:61: in create_schema
    self.merge_sheet(f, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = SchemaMaker(schema=SchemaDefinition(name='TEMP', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None...), element_map=None, metamodel=None, cardinality_vocabulary=None, default_name=None, unique_slots=None, gsheet_id=None)
file_name = '/Users/MAM/Documents/gitrepos/schemasheets/tests/output/mini.tsv'
delimiter = '\t'

    def merge_sheet(self, file_name: str, delimiter='\t') -> None:
        """
        Merge information from the given schema sheet into the current schema
    
        :param file_name: schema sheet
        :param delimiter: default is tab
        :return:
        """
        logging.info(f'READING {file_name} D={delimiter}')
        #with self.ensure_file(file_name) as tsv_file:
        #    reader = csv.DictReader(tsv_file, delimiter=delimiter)
        with self.ensure_csvreader(file_name, delimiter=delimiter) as reader:
            schemasheet = SchemaSheet.from_dictreader(reader)
            line_num = schemasheet.start_line_number
            # TODO: check why this doesn't work
            #while rows and all(x for x in rows[-1] if not x):
            #    print(f'TRIMMING: {rows[-1]}')
            #    rows.pop()
            logging.info(f'ROWS={len(schemasheet.rows)}')
            for row in schemasheet.rows:
                try:
                    self.add_row(row, schemasheet.table_config)
                    line_num += 1
                except ValueError as e:
>                   raise SchemaSheetRowException(f'Error in line {line_num}, row={row}') from e
E                   schemasheets.schemamaker.SchemaSheetRowException: Error in line 2, row={'Type': '', 'base': '', 'uri': '', 'Desc': 'my string', 'Extends': 'string'}

../schemasheets/schemamaker.py:108: SchemaSheetRowException

Summarizing requests related to Web documentation content and format in this ticket. Providing as one long list for now, but happy to break out into tickets for specific feature requests as needed. @sujaypatil96 @sierra-moxon hope we can coordinate soon on these!

Content/Sections I’d like to see in each Class page (in the following order):

1. Definition: a. already provided, and looks fine b. content comes from the s/s "description" field.

2. UML-style diagram: a. already provided using YUML, but I find these YUML diagrams hard to read and not all that useful. b. It sounds like a new framework will be used to generate diagrams in the near future, so I will hold off on and requests here until I see how the new diagrams look.

3. Parents: a. already present as a section on the page, and looks fine

4. Description:
   a. A new section with the title "Description". b. This should contain content in the 'comments' field of the s/s. Ideally as a bulleted list of sentences rather than one long paragraph/block of text, for improved readability. c. At present text form the 'comments' column is in a table at the end of each Class page - but I’d like it front and center directly under the Definition.

5. Implementation and Use: a. A new section with the title "Implementation and Use" b. content would ideally be derived from the s/s - but not sure how to do this in practice? . . . I hear that the Annotations feature might let me just create a new 'Implementation and Use' column and give it whatever name I want. Not sure what tooling would be needed to generate a proper section in the Class web page that holds the content. d. I'd also want this presented as a bulleted list of sentences/short paragraphs, rather than one long blob of text.

6. Own Attributes: a. This section already exists in each Class page b. content of course comes from the s/s c. prefer 'expanded' form - not tables - as this better accommodates the types and amount of text I want to provide in describing each attribute. (see below) d. don't think we need the class -> attribute pattern for 'own' attributes (no need class context when you are already on the class page and the section says 'own' )

7. Inherited Attributes a. This section already exists in each Class page b. content generated from s/s but pulling in all attributes from parents of a given class

8. Data Examples: a. A new section called "Data Examples" b. content would be nicely formatted yaml or json data examples - e.g. like those in the VRS RTD docs here), Ideally with some lead in text that describes what is being represented (but this could be part of the data example text block, as a # comment preceding the data itself) c. Chris suggested a housing these in a 'Data Examples' directory in the repo - and pulling relevant examples in to a Class web page from these example files automatically. These data examples could then serve multiple purposes (documentation, texting/validation, etc.)

Content/Fields I’d like to see in for each Attribute of a class, as shown in a Class page

1. The attribute name, description, cardinality, and range are already provided and look good as is.
2. I’d also like to include a 'Comments:' field that holds text from the ‘comments’ column in the s/s - to provide additional clarification on meaning and usage of an attribute.

This works

sheets2linkml \
		--output $@ \
		--gsheet-id 1zsxvjvifDcmkt72v9m1_VKa2m73_THDJapJYK6dqidw core 

In that sheet, I protected numerical values and Booleans in the examples column by preceding them with '. I think the same thing is required for dates, and the affirmative boolean value must be represented as 'true, not the magic value of TRUE.

But switch term MIXS:0000001's example to 555, and you get

sheets2linkml \
		--output $@ \
		--gsheet-id 1zsxvjvifDcmkt72v9m1_VKa2m73_THDJapJYK6dqidw core_example_555_num 

Traceback (most recent call last): File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 105, in merge_sheet self.add_row(row, schemasheet.table_config) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 111, in add_row for element in self.row_focal_element(row, table_config): File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 233, in row_focal_element raise ValueError(f'No table_config.column_by_element_type') ValueError: No table_config.column_by_element_type

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/bin/sheets2linkml", line 8, in sys.exit(convert()) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/click/core.py", line 1130, in call return self.main(*args, **kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 578, in convert schema = sm.create_schema(list(tsv_files)) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 61, in create_schema self.merge_sheet(f, **kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 108, in merge_sheet raise SchemaSheetRowException(f'Error in line {line_num}, row={row}') from e schemasheets.schemamaker.SchemaSheetRowException: Error in line 1, row={'Structured comment name > slot > >': 'samp_size', 'Item (rdfs:label) title ': 'amount or size of sample collected', 'Definition description ': 'The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.', 'Expected value annotations inner_key: expected_value': 'measurement value', 'Value syntax structured_pattern ': '{float} {unit}', 'Example examples internal_separator: "|"': '555', 'Section slot_group ': 'nucleic acid sequence source', 'migs_eu annotations applies_to_class: migs_eu inner_key: cardinality': 'X', 'migs_ba annotations applies_to_class: migs_ba inner_key: cardinality': 'X', 'migs_pl annotations applies_to_class: migs_pl inner_key: cardinality': 'X', 'migs_vi annotations applies_to_class: migs_vi inner_key: cardinality': 'X', 'migs_org annotations applies_to_class: migs_org inner_key: cardinality': 'X', 'mims annotations applies_to_class: mims inner_key: cardinality': 'C', 'mimarks_s annotations applies_to_class: mimarks_s inner_key: cardinality': 'C', 'mimarks_c annotations applies_to_class: mimarks_c inner_key: cardinality': 'X', 'misag annotations applies_to_class: misag inner_key: cardinality': 'C', 'mimag annotations applies_to_class: mimag inner_key: cardinality': 'C', 'miuvig annotations applies_to_class: miuvig inner_key: cardinality': 'C', 'Preferred unit annotations inner_key: preferred_unit': 'millliter, gram, milligram, liter', 'Occurrence multivalued vmap: {s: false, m: true}': 's', 'MIXS ID slot_uri ': 'MIXS:0000001', 'MIGS ID (mapping to GOLD) annotations inner_key: gold_migs_id': ''} make: *** [generated/MIxS6_from_gsheet_templates_bad.yaml] Error 1

https://linkml.io/schemasheets/intro/converting/ link Edit on GitHub uses branch name "master" but the correct branch is "main".

Please fix the mkdoc configuration.

when running schemasheets/get_metaclass_slotvals.py or schemasheets/verbatim_sheets.py

/Users/MAM/Library/Caches/pypoetry/virtualenvs/schemasheets-FMUhH2LU-py3.9/lib/python3.9/site-packages/requests/init.py:109: RequestsDependencyWarning: urllib3 (1.26.9) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version! warnings.warn(

I have found that the experimental linkml2sheets can't sheetify several of the elements and attributes I care about, and it can't seem to do even a minimal dump on complex/large schemas like MIxS. I have written some code that approximate a LinkML/sheets round trip on the following metaclasses:

See the turbomam/linkml-abuse project.Makefile

• annotations
• class_definitions
• enum_definitions
• prefixes
• schema_definitions
• slot_definitions
• subset_definitions
• type_definitions

The prefixes and subsets don't seem to include the content of imports

I'm not using a template to determine what gets written to the sheets. I'm iterating over all slots, except for the skipped slots listed below.

If my code was going to be included in any LinkML repo, it would need refactoring for performance and readability. I can do some of that. Even as it is, I have already used this for QC'ing the MIxS schema and plan to use it for round-tripping the NMDC submission portal schema (within sheets_and_friends)

There are some minor systematic changes between the before and after schemas. Thats crudely reported in target/roundtrip.yaml

skipped slots:

• all_of
• alt_descriptions
• annotations
• any_of
• attributes
• classes
• classification_rules
• default_curi_maps
• enum_range
• enums
• exactly_one_of
• extensions
• from_schema
• implicit_prefix
• imports
• local_names
• name
• none_of
• prefixes
• rules
• slot_definitions
• slot_usage
• slots
• structured_aliases
• subsets
• unique_keys
• type_uri

Notes from @cmungall:

metatype is useful for cases where you want to have a single column always represent the element name, and the element type to switch depending on the row. If you do it this style, you always need a “name” column. Further up in the stack trace it was complaining about the name field missing.

issue #25

My contributions from #24 also got committed here

The range override and OWL consequences are triggered by make examples/output/range_override_examples_reasoned.ttl

% poetry run sheets2linkml --help

gives the output below, but the script is called sheets2linkml, not schemasheets and the -d option doesn't seem to be implemented

/usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( Usage: sheets2linkml [OPTIONS] [TSV_FILES]...

Convert schemasheets to a LinkML schema

schemasheets -d . my_schema/*tsv

Options: -o, --output FILENAME output file -v, --verbose --help Show this message and exit.

As opposed to schemasheets? See #10

% sheets2linkml --help

Traceback (most recent call last): File "/Users/MAM/my_first_ss/venv/bin/sheets2linkml", line 5, in from fairstructure.schemamaker import convert ModuleNotFoundError: No module named 'fairstructure'

% make all

poetry run pytest /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( Creating virtualenv schemasheets-FMUhH2LU-py3.9 in /Users/MAM/Library/Caches/pypoetry/virtualenvs

FileNotFoundError

[Errno 2] No such file or directory: b'/Users/MAM/edirect/pytest'

at /usr/local/Cellar/[email protected]/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py:607 in _execvpe 603│ path_list = map(fsencode, path_list) 604│ for dir in path_list: 605│ fullname = path.join(dir, file) 606│ try: → 607│ exec_func(fullname, *argrest) 608│ except (FileNotFoundError, NotADirectoryError) as e: 609│ last_exc = e 610│ except OSError as e: 611│ last_exc = e make: *** [test] Error 1

I love the ignore column specification. Is there some way to ignore rows? That would help illustrate content from an upstream provider that is being excluded from the model.

Could the metatype specification be repurposed to allow for ignoring rows? (If it doesn't support that already?)

For example, if a user wants to use the "test enums" tab from https://docs.google.com/spreadsheets/d/1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ/edit#gid=823426713 , then their sheets2linkml command would look like this

sheets2linkml --gsheet-id 1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ test+enums

We should discourage tab names that contain characters requiring more aggressive URL encoding than -> +

#76

@cmungall I wrote test_schema_metadata and added

elif t == T_SCHEMA and isinstance(element, SchemaDefinition)

to schemasheets/schema_exporter.py, following your https://github.com/linkml/schemasheets/pull/77

but I think the exporting steps may have to be different, because we won't be iterating over a multiple schema rows, like we would for slots, classes or prefixes.

@putmantime and I have observed that running linkml2sheets on a directory of templates doesn't work, even when all of the individual templates do work

the linkml2sheets help gives this example:

linkml2sheets -s my_schema.yaml sheets/*.tsv -d sheets --overwrite

In the nmdc-schema repo, the following two work

schemasheets/tsv_output/slots.tsv: clean_schemasheets
	linkml2sheets \
		--schema src/schema/nmdc.yaml \
		--output-directory schemasheets/tsv_output/ \
		schemasheets/templates/slots.tsv

schemasheets/tsv_output/classes.tsv: clean_schemasheets
	linkml2sheets \
		--schema src/schema/nmdc.yaml \
		--output-directory schemasheets/tsv_output/ \
		schemasheets/templates/classes.tsv

but this doesn't work

schemasheets/tsv_output/all.tsv: clean_schemasheets
	linkml2sheets \
		--schema src/schema/nmdc.yaml \
		--output-directory schemasheets/tsv_output/ \
		schemasheets/templates/*.tsv

Even though

ls -l schemasheets/templates 

-rw-r--r--@ 1 MAM staff 71 Aug 16 17:22 classes.tsv -rw-r--r--@ 1 MAM staff 58 Aug 16 17:26 prefixes.tsv -rw-r--r--@ 1 MAM staff 2005 Aug 16 18:01 slots.tsv

The error is

Traceback (most recent call last): File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/nmdc-schema-MTtWF7zd-py3.9/bin/linkml2sheets", line 8, in sys.exit(export_schema()) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/nmdc-schema-MTtWF7zd-py3.9/lib/python3.9/site-packages/click/core.py", line 1130, in call return self.main(*args, **kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/nmdc-schema-MTtWF7zd-py3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/nmdc-schema-MTtWF7zd-py3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/nmdc-schema-MTtWF7zd-py3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/nmdc-schema-MTtWF7zd-py3.9/lib/python3.9/site-packages/schemasheets/schema_exporter.py", line 297, in export_schema exporter.export(sv, specification=f, to_file=outpath) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/nmdc-schema-MTtWF7zd-py3.9/lib/python3.9/site-packages/schemasheets/schema_exporter.py", line 90, in export writer.writerow(row) File "/usr/local/Cellar/[email protected]/3.9.13_2/Frameworks/Python.framework/Versions/3.9/lib/python3.9/csv.py", line 154, in writerow return self.writer.writerow(self._dict_to_list(rowdict)) File "/usr/local/Cellar/[email protected]/3.9.13_2/Frameworks/Python.framework/Versions/3.9/lib/python3.9/csv.py", line 149, in _dict_to_list raise ValueError("dict contains fields not in fieldnames: " ValueError: dict contains fields not in fieldnames: 'class' make: *** [schemasheets/tsv_output/all.tsv] Error 1

FAILED tests/test_schema_exporter.py::test_types - schemasheets.schemamaker.SchemaSheetRowException: Error in line 2, row={'Type': '', 'base': '', 'uri': '', 'Desc': 'my string', 'Extends': 'string'} FAILED tests/test_schemamaker.py::test_types - AttributeError: 'TypeDefinition' object has no attribute 'type' FAILED tests/test_schemamaker.py::test_combined - AttributeError: 'TypeDefinition' object has no attribute 'type'