def make_record(values, is_dump=True):
"""
Export recjson from drafts
"""
if is_dump:
record = Record(json=values, master_format='marc')
else:
record = Record(master_format='marc')
for k, v in six.iteritems(values):
record[k] = v
return record
def test_marc_export(self):
from invenio.modules.records.api import Record
from invenio.legacy.bibrecord import create_record, record_xml_output
rec = Record(json=test_record, master_format='marc')
# Needed to properly set authors when generating MARC
first = rec['authors'][0]
additional = rec['authors'][1:]
rec['_first_author'] = first
rec['_additional_authors'] = additional
output_marc = record_xml_output(
create_record(rec.legacy_export_as_marc())[0]
)
try:
self.assertEqual(test_marc, output_marc)
except AssertionError:
# Print diff in case of errors.
import difflib
diff = "".join(difflib.unified_diff(
test_marc.splitlines(1),
output_marc.splitlines(1)
))
raise AssertionError(diff)
form_json = rec.produce('json_for_form')
for k, v in test_form_json.items():
self.assertEqual(form_json[k], test_form_json[k])
def test_json_for_ld(self):
from invenio.modules.records.api import Record
r = Record.create({'title': 'Test'}, 'json')
import copy
r = Record(json=copy.copy(test_record), master_format='marc')
r.produce('json_for_ld')
def patch_get_record(self, get_record_patch):
from invenio.modules.records.api import Record
r = Record(json={
self.app.config['PIDSTORE_DATACITE_RECORD_DOI_FIELD']:
'10.1234/invenio.1234',
'recid': 1,
},
master_format='json')
get_record_patch.return_value = r
def create_records_for_workflow(records, **kwargs):
"""Create the record object from the json.
:param records: List of records to be process.
:kwargs:
"""
from invenio.modules.records.api import Record
for i, obj in enumerate(records):
records[i] = (obj[0], Record(json=obj[1]))
def formatter(bwo, **kwargs):
"""Return a formatted version of the data."""
from invenio.modules.formatter.engine import format_record
data = bwo.get_data()
if not data:
return ''
formatter = kwargs.get("formatter", None)
format = kwargs.get("format", None)
if formatter:
# A seperate formatter is supplied
return formatter(data)
from invenio.modules.records.api import Record
if isinstance(data, collections.Mapping):
# Dicts are cool on its own, but maybe its SmartJson (record)
try:
data = Record(data.dumps()).legacy_export_as_marc()
except (TypeError, KeyError):
# Maybe not, submission?
return data
if isinstance(data, string_types):
# Its a string type, lets try to convert
if format:
# We can try formatter!
# If already XML, format_record does not like it.
if format != 'xm':
try:
return format_record(recID=None,
of=format,
xml_record=data)
except TypeError:
# Wrong kind of type
pass
else:
# So, XML then
from xml.dom.minidom import parseString
try:
pretty_data = parseString(data)
return pretty_data.toprettyxml()
except TypeError:
# Probably not proper XML string then
return "Data cannot be parsed: %s" % (data, )
except Exception:
# Some other parsing error
pass
# Just return raw string
return data
if isinstance(data, set):
return list(data)
# Not any of the above types. How juicy!
return data
def formatter(bwo, **kwargs):
"""Nicely format the record."""
from pprint import pformat
from invenio.modules.records.api import Record
data = bwo.get_data()
if not data:
return ''
formatter = kwargs.get("formatter", None)
of = kwargs.get("of", None)
if formatter:
# A separate formatter is supplied
return formatter(data)
if isinstance(data, collections.Mapping):
# Dicts are cool on its own, but maybe its SmartJson (record)
try:
data = Record(data.dumps()).legacy_export_as_marc()
except (TypeError, KeyError):
pass
if isinstance(data, string_types):
# We can try formatter!
# If already XML, format_record does not like it.
if of and of != 'xm':
try:
from invenio.modules.formatter import format_record
formatted_data = format_record(recID=None,
of=of,
xml_record=data)
except TypeError:
# Wrong kind of type
pass
else:
# So, XML then
from xml.dom.minidom import parseString
try:
unpretty_data = parseString(data)
formatted_data = unpretty_data.toprettyxml()
except TypeError:
# Probably not proper XML string then
return "Data cannot be parsed: %s" % (data, )
except Exception:
# Just return raw string
pass
if not formatted_data:
formatted_data = data
if isinstance(formatted_data, dict):
formatted_data = pformat(formatted_data)
return formatted_data
def test_json_for_form(self):
from invenio.modules.records.api import Record
r = Record.create({'title': 'Test'}, 'json')
assert r.produce('json_for_form')['title'] == 'Test'
assert {'245__a': 'Test'} in r.produce('json_for_marc')
import copy
r = Record(json=copy.copy(test_record), master_format='marc')
form_json = r.produce('json_for_form')
for k, v in test_form_json.items():
self.assertEqual(form_json[k], test_form_json[k])
def get_mocked_record():
from invenio.modules.records.api import Record
if RecordMock.record is None:
RecordMock.record = Record(
json={
'doi': '10.1234/invenio.1234',
'files_to_upload': [ # replace with cfg['files_var_name']
('path1.xls', 'this/is/a/long/path/to/the/file/location/path1.xls'),
('path2.csv', 'path2.csv'),
('path3.pdf', 'path3.pdf'), ],
'recid': 1,
# '_files': [ # replace with cfg['files_var_name']
# 'path1',
# 'path2',
# 'path3']
},
master_format='marc'
)
return RecordMock.record
def get_description(bwo):
"""Get the description (identifiers and categories) from the object data."""
from invenio.modules.records.api import Record
from flask import render_template, current_app
record = bwo.get_data()
final_identifiers = {}
try:
identifiers = Record(record.dumps()).persistent_identifiers
for values in identifiers.values():
final_identifiers.extend([i.get("value") for i in values])
except Exception:
current_app.logger.exception("Could not get identifiers")
if hasattr(record, "get"):
final_identifiers = [
record.get("system_control_number",
{}).get("value", 'No ids')
]
else:
final_identifiers = []
categories = []
if hasattr(record, "get"):
if 'subject' in record:
lookup = ["subject", "term"]
elif "subject_term" in record:
lookup = ["subject_term", "term"]
else:
lookup = None
if lookup:
primary, secondary = lookup
category_list = record.get(primary, [])
if isinstance(category_list, dict):
category_list = [category_list]
categories = [subject[secondary] for subject in category_list]
return render_template('workflows/styles/harvesting_record.html',
categories=categories,
identifiers=final_identifiers)
def filter_step(obj, eng):
"""Run an external python script."""
from invenio.modules.records.api import Record
from invenio.utils.shell import run_shell_command
repository = obj.extra_data.get("repository", {})
arguments = repository.get("arguments", {})
script_name = arguments.get("f_filter-file")
if script_name:
marcxml_value = Record(obj.data.dumps()).legacy_export_as_marc()
extract_path = os.path.join(
cfg['CFG_TMPSHAREDDIR'],
str(eng.uuid)
)
if not os.path.exists(extract_path):
os.makedirs(extract_path)
# Now we launch BibUpload tasks for the final MARCXML files
marcxmlfile = extract_path + os.sep + str(obj.id)
file_fd = open(marcxmlfile, 'w')
file_fd.write(marcxml_value)
file_fd.close()
exitcode, cmd_stdout, cmd_stderr = run_shell_command(
cmd="%s '%s'",
args=(str(script_name),
str(marcxmlfile)))
if exitcode != 0 or cmd_stderr != "":
obj.log.error(
"Error while running filtering script on %s\nError:%s"
% (marcxmlfile, cmd_stderr)
)
else:
obj.log.info(cmd_stdout)
else:
obj.log.error("No script file found!")
def get_description(bwo):
"""Get the description column part."""
record = bwo.get_data()
from invenio.modules.records.api import Record
try:
identifiers = Record(record.dumps()).persistent_identifiers
final_identifiers = []
for i in identifiers:
final_identifiers.append(i['value'])
except Exception:
if hasattr(record, "get"):
final_identifiers = [
record.get("system_number_external",
{}).get("value", 'No ids')
]
else:
final_identifiers = [' No ids']
task_results = bwo.get_tasks_results()
results = []
if 'bibclassify' in task_results:
try:
result = task_results['bibclassify'][0]['result']
fast_mode = result.get('fast_mode', False)
result = result['dict']['complete_output']
result_string = "<strong></br>Bibclassify result:"\
"</br></strong>"\
"Number of Core keywords: \t%s</br>"\
"PACS: \t%s</br>"\
% (len(result['Core keywords']),
len(result['Field codes']))
if fast_mode:
result_string += "(This task run at fast mode"\
" taking into consideration"\
" only the title and the abstract)"
results.append(result_string)
except (KeyError, IndexError):
pass
categories = []
if hasattr(record, "get"):
if 'subject' in record:
lookup = ["subject", "term"]
elif "subject_term":
lookup = ["subject_term", "term"]
else:
lookup = None
if lookup:
primary, secondary = lookup
category_list = record.get(primary, [])
if isinstance(category_list, dict):
category_list = [category_list]
for subject in category_list:
category = subject[secondary]
if len(subject) == 2:
if subject.keys()[1] == secondary:
source_list = subject[subject.keys()[0]]
else:
source_list = subject[subject.keys()[1]]
else:
try:
source_list = subject['source']
except KeyError:
source_list = ""
if source_list.lower() == 'inspire':
categories.append(category)
from flask import render_template
return render_template('workflows/styles/harvesting_record.html',
categories=categories,
identifiers=final_identifiers,
results=results)
def quick_match_record(obj, eng):
"""Retrieve the record Id from a record.
Retrieve the record Id from a record by using tag 001 or SYSNO or OAI ID or
DOI tag. opt_mod is the desired mode.
001 fields even in the insert mode
:param obj: Bibworkflow Object to process
:param eng: BibWorkflowEngine processing the object
"""
from invenio.legacy.bibupload.engine import (find_record_from_recid,
find_record_from_sysno,
find_records_from_extoaiid,
find_record_from_oaiid,
find_record_from_doi)
from invenio.modules.records.api import Record
identifier_function_to_check = {
'recid': find_record_from_recid,
'system_number': find_record_from_sysno,
'oaiid': find_record_from_oaiid,
'system_control_number': find_records_from_extoaiid,
'doi': find_record_from_doi
}
record = Record(obj.data.dumps())
try:
identifiers = record.persistent_identifiers
except Exception as e:
# if anything goes wrong, assume we need to get it manually.
eng.log.error("Problem with getting identifiers: %s\n%s" %
(str(e), traceback.format_exc()))
identifiers = []
obj.extra_data["persistent_ids"] = identifiers
identifier_dict = {}
for name, value in identifiers:
value_dict = {}
for dic in value:
value_dict.update(dic)
identifier_dict[name] = value_dict
if "recid" in identifier_dict:
# If there is a recid, we are good, right?
obj.extra_data["persistent_ids"]["recid"] = identifier_dict["recid"]
return True
# So if there is no explicit recid key, then maybe we can find the record
# using any of the other stable identifiers defined.
found_recid = False
for name, func in identifier_function_to_check.iteritems():
if name in identifier_dict:
if name in identifier_dict[name]:
# To get {"doi": {"doi": val}}
found_recid = func(identifier_dict[name][name])
elif "value" in identifier_dict[name]:
# To get {"doi": {"value": val}}
found_recid = func(identifier_dict[name]["value"])
if found_recid:
break
if found_recid:
obj.extra_data["persistent_ids"]["recid"] = found_recid
return True
return False
def upload_step(obj, eng):
"""Perform the upload step.
:param obj: BibWorkflowObject to process
:param eng: BibWorkflowEngine processing the object
"""
from invenio.legacy.oaiharvest.dblayer import create_oaiharvest_log_str
from invenio.modules.records.api import Record
from invenio.legacy.bibsched.bibtask import task_low_level_submission
repository = obj.extra_data.get("repository", {})
sequence_id = random.randrange(1, 60000)
arguments = repository.get("arguments", {})
default_args = []
default_args.extend(['-I', str(sequence_id)])
if arguments.get('u_name', ""):
default_args.extend(['-N', arguments.get('u_name', "")])
if arguments.get('u_priority', 5):
default_args.extend(['-P', str(arguments.get('u_priority', 5))])
extract_path = os.path.join(
cfg['CFG_TMPSHAREDDIR'],
str(eng.uuid)
)
if not os.path.exists(extract_path):
os.makedirs(extract_path)
filepath = extract_path + os.sep + str(obj.id)
if "f" in repository.get("postprocess", []):
# We have a filter.
file_uploads = [
("{0}.insert.xml".format(filepath), ["-i"]),
("{0}.append.xml".format(filepath), ["-a"]),
("{0}.correct.xml".format(filepath), ["-c"]),
("{0}.holdingpen.xml".format(filepath), ["-o"]),
]
else:
# We do not, so we get the data from the record
marcxml_value = Record(obj.data.dumps()).legacy_export_as_marc()
file_fd = open(filepath, 'w')
file_fd.write(marcxml_value)
file_fd.close()
file_uploads = [(filepath, ["-r", "-i"])]
task_id = None
for location, mode in file_uploads:
if os.path.exists(location):
try:
args = mode + [filepath] + default_args
task_id = task_low_level_submission("bibupload",
"oaiharvest",
*tuple(args))
repo_id = repository.get("id")
if repo_id:
create_oaiharvest_log_str(
task_id,
repo_id,
obj.get_data()
)
except Exception as msg:
eng.log.error(
"An exception during submitting oaiharvest task occured : %s " % (
str(msg)))
if task_id is None:
eng.log.error("an error occurred while uploading %s from %s" %
(filepath, repository.get("name", "Unknown")))
else:
eng.log.info(
"material harvested from source %s was successfully uploaded" %
(repository.get("name", "Unknown"),))
eng.log.info("end of upload")