Source code for swh.indexer.codemeta

# Copyright (C) 2018  The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU General Public License version 3, or any later version
# See top-level LICENSE file for more information

import collections
import csv
import itertools
import json
import os.path
import re

from pyld import jsonld

import swh.indexer

_DATA_DIR = os.path.join(os.path.dirname(swh.indexer.__file__), "data")

CROSSWALK_TABLE_PATH = os.path.join(_DATA_DIR, "codemeta", "crosswalk.csv")

CODEMETA_CONTEXT_PATH = os.path.join(_DATA_DIR, "codemeta", "codemeta.jsonld")


with open(CODEMETA_CONTEXT_PATH) as fd:
    CODEMETA_CONTEXT = json.load(fd)

CODEMETA_CONTEXT_URL = "https://doi.org/10.5063/schema/codemeta-2.0"
CODEMETA_ALTERNATE_CONTEXT_URLS = {
    ("https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld")
}
CODEMETA_URI = "https://codemeta.github.io/terms/"
SCHEMA_URI = "http://schema.org/"


PROPERTY_BLACKLIST = {
    # CodeMeta properties that we cannot properly represent.
    SCHEMA_URI + "softwareRequirements",
    CODEMETA_URI + "softwareSuggestions",
    # Duplicate of 'author'
    SCHEMA_URI + "creator",
}

_codemeta_field_separator = re.compile(r"\s*[,/]\s*")


[docs]def make_absolute_uri(local_name): definition = CODEMETA_CONTEXT["@context"][local_name] if isinstance(definition, str): return definition elif isinstance(definition, dict): prefixed_name = definition["@id"] (prefix, local_name) = prefixed_name.split(":") if prefix == "schema": canonical_name = SCHEMA_URI + local_name elif prefix == "codemeta": canonical_name = CODEMETA_URI + local_name else: assert False, prefix return canonical_name else: assert False, definition
def _read_crosstable(fd): reader = csv.reader(fd) try: header = next(reader) except StopIteration: raise ValueError("empty file") data_sources = set(header) - {"Parent Type", "Property", "Type", "Description"} assert "codemeta-V1" in data_sources codemeta_translation = {data_source: {} for data_source in data_sources} terms = set() for line in reader: # For each canonical name local_name = dict(zip(header, line))["Property"] if not local_name: continue canonical_name = make_absolute_uri(local_name) if canonical_name in PROPERTY_BLACKLIST: continue terms.add(canonical_name) for (col, value) in zip(header, line): # For each cell in the row if col in data_sources: # If that's not the parentType/property/type/description for local_name in _codemeta_field_separator.split(value): # For each of the data source's properties that maps # to this canonical name if local_name.strip(): codemeta_translation[col][local_name.strip()] = canonical_name return (terms, codemeta_translation) with open(CROSSWALK_TABLE_PATH) as fd: (CODEMETA_TERMS, CROSSWALK_TABLE) = _read_crosstable(fd) def _document_loader(url, options=None): """Document loader for pyld. Reads the local codemeta.jsonld file instead of fetching it from the Internet every single time.""" if url == CODEMETA_CONTEXT_URL or url in CODEMETA_ALTERNATE_CONTEXT_URLS: return { "contextUrl": None, "documentUrl": url, "document": CODEMETA_CONTEXT, } elif url == CODEMETA_URI: raise Exception( "{} is CodeMeta's URI, use {} as context url".format( CODEMETA_URI, CODEMETA_CONTEXT_URL ) ) else: raise Exception(url)
[docs]def compact(doc): """Same as `pyld.jsonld.compact`, but in the context of CodeMeta.""" return jsonld.compact( doc, CODEMETA_CONTEXT_URL, options={"documentLoader": _document_loader} )
[docs]def expand(doc): """Same as `pyld.jsonld.expand`, but in the context of CodeMeta.""" return jsonld.expand(doc, options={"documentLoader": _document_loader})
[docs]def merge_values(v1, v2): """If v1 and v2 are of the form `{"@list": l1}` and `{"@list": l2}`, returns `{"@list": l1 + l2}`. Otherwise, make them lists (if they are not already) and concatenate them. >>> merge_values('a', 'b') ['a', 'b'] >>> merge_values(['a', 'b'], 'c') ['a', 'b', 'c'] >>> merge_values({'@list': ['a', 'b']}, {'@list': ['c']}) {'@list': ['a', 'b', 'c']} """ if v1 is None: return v2 elif v2 is None: return v1 elif isinstance(v1, dict) and set(v1) == {"@list"}: assert isinstance(v1["@list"], list) if isinstance(v2, dict) and set(v2) == {"@list"}: assert isinstance(v2["@list"], list) return {"@list": v1["@list"] + v2["@list"]} else: raise ValueError("Cannot merge %r and %r" % (v1, v2)) else: if isinstance(v2, dict) and "@list" in v2: raise ValueError("Cannot merge %r and %r" % (v1, v2)) if not isinstance(v1, list): v1 = [v1] if not isinstance(v2, list): v2 = [v2] return v1 + v2
[docs]def merge_documents(documents): """Takes a list of metadata dicts, each generated from a different metadata file, and merges them. Removes duplicates, if any.""" documents = list(itertools.chain.from_iterable(map(expand, documents))) merged_document = collections.defaultdict(list) for document in documents: for (key, values) in document.items(): if key == "@id": # @id does not get expanded to a list value = values # Only one @id is allowed, move it to sameAs if "@id" not in merged_document: merged_document["@id"] = value elif value != merged_document["@id"]: if value not in merged_document[SCHEMA_URI + "sameAs"]: merged_document[SCHEMA_URI + "sameAs"].append(value) else: for value in values: if isinstance(value, dict) and set(value) == {"@list"}: # Value is of the form {'@list': [item1, item2]} # instead of the usual [item1, item2]. # We need to merge the inner lists (and mostly # preserve order). merged_value = merged_document.setdefault(key, {"@list": []}) for subvalue in value["@list"]: # merged_value must be of the form # {'@list': [item1, item2]}; as it is the same # type as value, which is an @list. if subvalue not in merged_value["@list"]: merged_value["@list"].append(subvalue) elif value not in merged_document[key]: merged_document[key].append(value) return compact(merged_document)