@nishad I noticed today that the last three RTD builds had failed - see https://readthedocs.org/projects/dctap-python/builds/14275110/ .

The builds started failing when we changed the hand-entered version number in conf.py to be dctap.__version__. At first it failed because this variable was unfindable until I added import dctap to conf.py. But I did not realize until today that import dctap was now causing the build to "fail", perhaps because the documentation online looked perfectly fine.

Now that I have reverted to hand-entering the version number (from dctap/__init__.py), the build is passing again.

I do not think that hand-entering the version number imposes an undue burden, but do you see a way to make it work with dctap.__version__?

See dcmi/dctap#28

The program should verify that the input file as valid as CSV:

• each row has the same number of columns

If errors found:

• stop program with message to user

At https://github.com/dcmi/dctap-python/blob/main/dctap/utils.py#L22

def is_uri_or_prefixed_uri(uri):
    """True if string is URI or superficially looks like a prefixed URI."""
    if is_uri(uri):
        return True
    if re.match("[A-Za-z0-9_]*:[A-Za-z0-9_]*", uri):  # looks like prefixed URI
        return True

Pylint says: "R1710: Either all return statements in a function should return an expression, or none of them should. (inconsistent-return-statements)"

@nishad Can you advise?

The program issues a warning for each use of a shapeID that is not in URL form:

  "warnings": {
    "Scholarly Resource": {
      "shapeID": [
        "Value 'Scholarly Resource' does not look like a URI.",
        "Value 'Scholarly Resource' does not look like a URI.",

Because we do not require the shapeID to be a URI, this warning could be confusing. I think it should be removed.

At huggingFace, the default text output does not have line ends:

['Tabular Application Profile (TAP)', '    Shape', '        shapeID                  Scholarly Resource', '        Statement Template', '            propertyID           dct:abstract', '            propertyLabel        Abstract', '            valueDataType        xsd:string', '            note                 Free text', '        Statement Template', '            propertyID           dct:accessRights', '            propertyLabel        Access rights', '            valueDataType        xsd:anyURI', "            valueConstraint      ['http://vocabularies.coar-repositories.org/documentation/access_rights/']", '            valueConstraintType  iristem', '            note                 A term from COAR vocabulary (http://vocabularies.coar-repositories.org

In a text program it looks like:

I assume this is a question of carriage return types, as I think that huggingface doesn't make any modifications to output.

pyproject.toml currently requires Python 3.9, but I'm not at all sure that the version needs to be so recent.

dctap can now be installed with pip (see PyPI project), it would be good to adjust the version required to the lowest possible.

@nishad Do you have a way to test whether it will work with earlier Python versions?

There is an alternative option to install from GitHub using pip.

pip install git+https://github.com/dcmi/dctap-python.git

Works with recent versions of pip.

.*rc files are a standard convention, but using “.dctaprc” raises some issues.

• It is a hidden file in NIX OSs as a dotfile, which may be tricky for many users to find or modify, especially within the working directory. In the long run, this implementation can raise a lot of unexpected side effects.
• Keeping the file extension yaml or yml helps the text editors to syntax highlight and validate while editing these files.

CLI argument generate has changed to read, but example commands in the README Quick start have not been updated to reflect this.

Attaching 20231218_dctap-python_cli_copy_paste.txt for "No such command" error message and other details. Python 3.11.7 in Windows PowerShell.

Ran successfully with dctap read --warnings my_profile.csv.

If ignore::PendingDeprecationWarning is commented out in pytest.ini one gets:

tests/test_config/test_config_get_config_dict.py::test_exit_if_configfile_has_bad_yaml
  /Users/tbaker/github/dcmi/dctap-python/dctap/config.py:73: PendingDeprecationWarning:
  safe_load will be removed, use

    yaml=YAML(typ='safe', pure=True)
    yaml.load(...)

  instead
    return yaml.safe_load(default_config_yaml)

-- Docs: https://docs.pytest.org/en/stable/warnings.html

The function dctap._get_rows reads CSV from a file, but could there be an alternative function to read the CSV from stdin?

One easy way to do this could be to use click.Path, which allows the use of a single dash to read input from stdin.

Running the latest version of dctap with a dctap.yml that sets an element alias causes the error
Valid DCTAP CSV must have a 'propertyID' column.

to repeat use:
dctap.yaml:

### dctap configuration file (in YAML format)
extra_statement_template_elements:
 - severity

element_aliases:
     "Mand": "mandatory"
     "Rep": "repeatable"

tap.csv:

shapeID,propertyID,propertyLabel,Mand,Rep,valueNodeType,valueDataType,valueConstraint,valueConstraintType,valueShape,note,severity
BookShape,dct:title,Title,TRUE,FALSE,Literal,rdf:langString,,,,,Violation
BookShape,dct:creator,Author,FALSE,TRUE,IRI BNODE,,,,AuthorShape,,Warning
BookShape,sdo:isbn,ISBN-13,FALSE,FALSE,Literal,xsd:string,^(\\d{13})?$,pattern,,"Just the 13 numbers, no spaces or separators.",Violation
BookShape,rdf:type,Type,TRUE,FALSE,IRI,,sdo:Book,,,,Warning
AuthorShape,rdf:type,Type,TRUE,TRUE,IRI,,foaf:Person,,,,Warning
AuthorShape,foaf:givenName,Given name,FALSE,TRUE,Literal,xsd:string,,,,,Warning
AuthorShape,foaf:familyName,Family name,FALSE,TRUE,Literal,xsd:string,,,,,Warning

Removing the element_alias block from dctap.yaml fixes the error message.

I'm using the csvreader() method in another program. The TAP I am reading has one entry of valueNodeType of IRI BNODE (line 8). The dctap yaml config I am using has

extra_value_node_types:
 - iri bnode

but still I get {'valueNodeType': ["'iri bnode' is not a valid node type."]} in the "warnings_dict"

(I understand the values should be case-insensitive, but I've also tried IRI BNODE in the YAML config and it made no difference.)

The file loads fine and I can use it, but I think this is a spurious warning.

@nishad The current version number is 0.2, but that seems low. Can you point me to guidelines we might follow?

In dctap/utils.py, line 27:

    if re.match("[A-Za-z0-9_]*:[A-Za-z0-9_]*", uri):  # looks like prefixed URI
        return True

Pylint suggests: R1703: The if statement can be replaced with 'return bool(test)' (simplifiable-if-statement)