EMLvp (validator and parser)
EMLvp is a Python 3 library to validate and parse Ecological Metadata Language XML documents for compliance with the EML metadata standard, including XML schema validation and ensuring that references resolve to existing ids. See the EML normative documentation for reference.
The EMLvp package is both a command line interface (CLI) application that can be used in a local environment and an
EML validation and parsing API that may be imported into other Python modules. The CLI application,
emlvp, is also
used as a reference implementation for the EMLvp API. The EMLvp package API provides three object classes that 1)
perform XML schema validation -
Validator, 2) EML compliance parsing -
Parser, and 3) dereference EML
<references> elements into their normalized structures -
Compliance includes the following inspections:
idattributes in all elements are unique,
referenceselements for subject
referencesparent elements with
customUnitfor STMML definitions,
annotationelements for subject
id(sans the annotations element).
referencesattribute of annotation(s) for subject
describesattribute for subject
emlvp application accepts an Ecological Metadata Language XML document file as input or a directory containing
EML XML document files with a “.xml” file extension. Once an EML XML document is identified, the application will
immediately perform a schema validation inspection followed by EML compliance parsing that verifies the
document is compliant with rules that go beyond what is possible with XML schema validation (see above).
EMLvp may be install using pip:
pip install emlvp. You may also install from GitHub by cloning the repository
and then using pip to install EMLvp with
emlvp command line application is installed as part
of the pip installation, as are the XML schema files for EML 2.1.0, 2.1.1, and 2.2.0. EMPvp is dependent on the
following Python packages:
Python >= 3.10,
lxml >= 4.9.2,
click >= 8.1.3, and
daiquiri >= 3.0.0.
EMLvp can be used directly on the command line with the
emlvp application or embedded into another Python
project. Its purpose is to inspect and analyze an EML XML metadata document to ensure it complies with both schema and
emlvp simply follows a three step analysis:
Perform schema validation.
Parse and inspect the document for non-schema requirements (above).
If requested, dereference the “references/ids” of the EML and repeat steps 1 and 2.
If at any point during the analysis an error occurs,
emlvp will either report the error and exit immediately
(fail-fast) or continue to analyze the document and collect all additional errors until the end of the analysis,
at which time the errors are reported (fail-slow). The
emlvp help provides the following description:
Usage: emlvp [OPTIONS] TARGET... Performs validation of EML XML file(s) 1. XML schema validation 2. EML parsing for references/id resolution 3. Dereference references/id into expanded EML XML and re-validate/parse TARGET: EML XML file or directory containing EML XML file(s) (may be repeated) Options: -d, --dereference Dereference EML XML file(s) (default is False). -f, --fail-fast Exit on first exception encountered (default is False). -p, --pretty-print Pretty print output for dereferenced EML XML (default is False). -s, --statistics Show post processing inspection statistics. -v, --verbose Send output to standard out (-v or -vv or -vvv for increasing output). --version Output emlvp version and exit. -h, --help Show this message and exit.
As noted above, the “TARGET” argument may be one or more space separate EML XML files or a directory containing many EML XML files (these files must end with the “.xml” extension). For example:
> emlvp edi.1252.1.xml edi.1252.1.xml Missing custom unit id(s): ['total abundance', 'logarithmic']
If no errors are found,
emlvp ends quietly and with no fanfare.
To use EMLvp in your own Python project, you would need to “import” the necessary class module and perform the appropriate analysis against the EML XML document. For example:
>>> import emlvp.validator as validator >>> from emlvp.validator import Validator >>> >>> with open("edi.1252.1.xml", "r") as f: ... xml = f.read() ... >>> schema_path = validator.schema_path() >>> v = Validator(schema_path + "/EML2.2.0/xsd/eml.xsd") >>> v.validate(xml) >>> >>> from emlvp.parser import Parser >>> p = Parser() >>> p.parse(xml) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/user/anaconda3/envs/emlvp/lib/python3.10/site-packages/emlvp/parser.py", line 185, in parse raise exceptions.ParseError(msg_queue.strip()) emlvp.exceptions.ParseError: Missing custom unit id(s): ['logarithmic', 'total abundance'] >>>
Applications that use the API should rely on exceptions to indicate an error has occurred in either validation or parsing of the EML XML document.
EMLvp Class API
class Validator(object): """ Validates an EML XML document for being well formed and schema syntax correct. """ def __init__(self, schema: str): """ Class init method. :param schema: path to root schema eml.xsd """ def validate(self, xml: str): """ Validates an EML XML document instance :param xml: EML XML document instance as a unicode string :return: None :raises emlvp.exceptions.ValidationError: Raises ValidationError on any invalid content found """
class Parser(object): """ Parses an EML XML document instance inspecting for non-schema related issues. See here for possible issues: https://eml.ecoinformatics.org/validation-and-content-references.html """ def __init__(self, fail_fast: bool = False): """ Class init method. :param fail_fast: Boolean to indicate whether parsing should fail immediately """ def parse(self, xml: str): """ Parses an EML XML document instance inspecting for non-schema related issues. :param xml: EML XML document instance as a unicode string :return: None :raises emlvp.exceptions.ParseError: Raises ParseError on any invalid content found """
class Dereferencer(object): """ Expands EML XML content by dereferencing "references" element to content defined by the "id" attribute of a source element. """ def __init__(self, pretty_print=False): """ Class init method. :param pretty_print: Boolean to indicate if dereferenced EML XML is formatted for viewing """ def dereference(self, xml: str) -> str: """ Dereferences an EML XML document instance. :param xml: EML XML document instance as a unicode string. :return str: Expanded EML XML. """