def formdata_to_model(obj, formdata):
"""Manipulate form data to match authors data model."""
form_fields = copy.deepcopy(formdata)
filter_empty_elements(
form_fields,
['institution_history', 'advisors', 'websites', 'experiments'])
data = updateform.do(form_fields)
# ======
# Schema
# ======
if '$schema' not in data and '$schema' in obj.data:
data['$schema'] = obj.data.get('$schema')
if '$schema' in data and not data['$schema'].startswith('http'):
data['$schema'] = url_for('invenio_jsonschemas.get_schema',
schema_path="records/{0}".format(
data['$schema']))
author_name = ''
if 'family_name' in form_fields and form_fields['family_name']:
author_name = form_fields['family_name'].strip() + ', '
if 'given_names' in form_fields and form_fields['given_names']:
author_name += form_fields['given_names']
if author_name:
data.get('name', {})['value'] = author_name
# Add comments to extra data
if 'extra_comments' in form_fields and form_fields['extra_comments']:
data['_private_note'] = form_fields['extra_comments']
# Add email to extra data
if "public_email" in form_fields and form_fields["public_email"]:
obj.extra_data["public_email"] = form_fields["public_email"]
data["public_email"] = form_fields["public_email"]
# Add HEPNAMES collection
data["collections"] = [{"primary": "HEPNAMES"}]
# ==========
# Owner Info
# ==========
try:
user_email = User.query.get(obj.id_user).email
except AttributeError:
user_email = ''
source = "{0}{1}".format('inspire:uid:', obj.id_user)
data['acquisition_source'] = dict(
source=source,
email=user_email,
date=date.today().isoformat(),
method="submission",
submission_number=str(obj.id),
)
# Finally, set data
return data
def formdata_to_model(obj, formdata):
"""Manipulate form data to match authors data model."""
form_fields = copy.deepcopy(formdata)
filter_empty_elements(
form_fields,
['institution_history', 'advisors',
'websites', 'experiments']
)
data = updateform.do(form_fields)
# ======
# Schema
# ======
if '$schema' in data and not data['$schema'].startswith('http'):
data['$schema'] = url_for(
'invenio_jsonschemas.get_schema',
schema_path="records/{0}".format(data['$schema'])
)
author_name = ''
if 'family_name' in form_fields and form_fields['family_name']:
author_name = form_fields['family_name'].strip() + ', '
if 'given_names' in form_fields and form_fields['given_names']:
author_name += form_fields['given_names']
if author_name:
data.get('name', {})['value'] = author_name
# Add comments to extra data
if "comments" in form_fields and form_fields["comments"]:
obj.extra_data["comments"] = form_fields["comments"]
data["_private_note"] = form_fields["comments"]
# Add HEPNAMES collection
data["collections"] = [{
"primary": "HEPNAMES"
}]
# ==========
# Owner Info
# ==========
try:
user_email = User.query.get(obj.id_user).email
except AttributeError:
user_email = ''
sources = ["{0}{1}".format('inspire:uid:', obj.id_user)]
data['acquisition_source'] = dict(
source=sources,
email=user_email,
date=date.today().isoformat(),
method="submission",
submission_number=str(obj.id),
)
# Finally, set data
return data
def convert_data_to_model(obj, eng):
"""Manipulate form data to match author model keys."""
# Save original form data for later access
form_fields = copy.deepcopy(obj.data)
obj.extra_data["formdata"] = copy.deepcopy(form_fields)
filter_empty_elements(
obj.data,
['institution_history', 'advisors',
'websites', 'experiments']
)
converted = updateform.do(obj.data)
obj.data.update(converted)
author_name = ''
if 'family_name' in form_fields and form_fields['family_name']:
author_name = form_fields['family_name'].strip() + ', '
if 'given_names' in form_fields and form_fields['given_names']:
author_name += form_fields['given_names']
if author_name:
obj.data.get('name', {})['value'] = author_name
# Add comments to extra data
if "comments" in form_fields and form_fields["comments"]:
obj.extra_data["comments"] = form_fields["comments"]
obj.data["_private_note"] = form_fields["comments"]
# Add HEPNAMES collection
obj.data["collections"] = [{
"primary": "HEPNAMES"
}]
# ==========
# Owner Info
# ==========
try:
user_email = User.query.get(obj.id_user).email
except AttributeError:
user_email = ''
sources = ["{0}{1}".format('inspire:uid:', obj.id_user)]
obj.data['acquisition_source'] = dict(
source=sources,
email=user_email,
date=date.today().isoformat(),
method="submission",
submission_number=obj.id,
)
def formdata_to_model(obj, formdata):
"""Manipulate form data to match authors data model."""
form_fields = copy.deepcopy(formdata)
filter_empty_elements(
form_fields,
['institution_history', 'advisors',
'websites', 'experiments']
)
data = updateform.do(form_fields)
# ======
# Schema
# ======
if '$schema' not in data and '$schema' in obj.data:
data['$schema'] = obj.data.get('$schema')
if '$schema' in data and not data['$schema'].startswith('http'):
data['$schema'] = url_for(
'invenio_jsonschemas.get_schema',
schema_path="records/{0}".format(data['$schema'])
)
author_name = ''
if 'family_name' in form_fields and form_fields['family_name']:
author_name = form_fields['family_name'].strip() + ', '
if 'given_names' in form_fields and form_fields['given_names']:
author_name += form_fields['given_names']
if author_name:
data.get('name', {})['value'] = author_name
# Add comments to extra data
if 'extra_comments' in form_fields and form_fields['extra_comments']:
data.setdefault('_private_notes', []).append({
'source': 'submitter',
'value': form_fields['extra_comments']
})
data['stub'] = False
# ==========
# Submitter Info
# ==========
try:
user_email = User.query.get(obj.id_user).email
except AttributeError:
user_email = ''
try:
orcid = UserIdentity.query.filter_by(
id_user=obj.id_user,
method='orcid'
).one().id
except NoResultFound:
orcid = ''
data['acquisition_source'] = dict(
email=user_email,
datetime=datetime.datetime.utcnow().isoformat(),
method="submitter",
orcid=orcid,
submission_number=str(obj.id),
internal_uid=int(obj.id_user),
)
strip_empty_values(data)
validate(data, 'authors')
return data
def formdata_to_model(obj, formdata):
"""Manipulate form data to match literature data model."""
def _is_arxiv_url(url):
return 'arxiv.org' in url
form_fields = copy.deepcopy(formdata)
filter_empty_elements(form_fields,
['authors', 'supervisors', 'report_numbers'])
builder = LiteratureBuilder(source='submitter')
for author in form_fields.get('authors', []):
builder.add_author(
builder.make_author(author['full_name'],
affiliations=force_list(author['affiliation'])
if author['affiliation'] else None,
roles=['author']))
for supervisor in form_fields.get('supervisors', []):
builder.add_author(
builder.make_author(
supervisor['full_name'],
affiliations=force_list(supervisor['affiliation'])
if author['affiliation'] else None,
roles=['supervisor']))
builder.add_title(title=form_fields.get('title'))
document_type = 'conference paper' if form_fields.get('conf_name') \
else form_fields.get('type_of_doc', [])
if document_type == 'chapter':
document_type = 'book chapter'
builder.add_document_type(document_type=document_type)
builder.add_abstract(
abstract=form_fields.get('abstract'),
source='arXiv' if form_fields.get('categories') else None)
if form_fields.get('arxiv_id') and form_fields.get('categories'):
builder.add_arxiv_eprint(
arxiv_id=form_fields.get('arxiv_id'),
arxiv_categories=form_fields.get('categories').split())
builder.add_doi(doi=form_fields.get('doi'))
builder.add_inspire_categories(
subject_terms=form_fields.get('subject_term'), source='user')
for key in ('extra_comments', 'nonpublic_note', 'hidden_notes',
'conf_name'):
builder.add_private_note(private_notes=form_fields.get(key))
year = form_fields.get('year')
try:
year = int(year)
except (TypeError, ValueError):
year = None
builder.add_preprint_date(
preprint_date=form_fields.get('preprint_created'))
if form_fields.get('type_of_doc') == 'thesis':
builder.add_thesis(defense_date=form_fields.get('defense_date'),
degree_type=form_fields.get('degree_type'),
institution=form_fields.get('institution'),
date=form_fields.get('thesis_date'))
if form_fields.get('type_of_doc') == 'chapter':
if not form_fields.get('journal_title'):
builder.add_book_series(title=form_fields.get('series_title'))
if form_fields.get('type_of_doc') == 'book':
if form_fields.get('journal_title'):
form_fields['volume'] = form_fields.get('series_volume')
else:
builder.add_book_series(title=form_fields.get('series_title'),
volume=form_fields.get('series_volume'))
builder.add_book(publisher=form_fields.get('publisher_name'),
place=form_fields.get('publication_place'),
date=form_fields.get('publication_date'))
builder.add_publication_info(
year=year,
cnum=form_fields.get('conference_id'),
journal_issue=form_fields.get('issue'),
journal_title=form_fields.get('journal_title'),
journal_volume=form_fields.get('volume'),
page_start=form_fields.get('start_page'),
page_end=form_fields.get('end_page'),
artid=form_fields.get('artid'),
parent_record=form_fields.get('parent_book'))
builder.add_accelerator_experiments_legacy_name(
legacy_name=form_fields.get('experiment'))
language = form_fields.get('other_language') \
if form_fields.get('language') == 'oth' \
else form_fields.get('language')
builder.add_language(language=language)
if form_fields.get('title_translation'):
builder.add_title_translation(
title=form_fields['title_translation'],
language='en',
)
builder.add_title(title=form_fields.get('title_arXiv'), source='arXiv')
builder.add_title(title=form_fields.get('title_crossref'),
source='crossref')
builder.add_license(url=form_fields.get('license_url'))
builder.add_public_note(public_note=form_fields.get('public_notes'))
builder.add_public_note(
public_note=form_fields.get('note'),
source='arXiv' if form_fields.get('categories') else 'CrossRef')
form_url = form_fields.get('url')
form_additional_url = form_fields.get('additional_url')
if form_url and not _is_arxiv_url(form_url):
obj.extra_data['submission_pdf'] = form_url
if not form_additional_url:
builder.add_url(url=form_url)
if form_additional_url and not _is_arxiv_url(form_additional_url):
builder.add_url(url=form_additional_url)
[
builder.add_report_number(
report_number=report_number.get('report_number'))
for report_number in form_fields.get('report_numbers', [])
]
builder.add_collaboration(collaboration=form_fields.get('collaboration'))
builder.add_acquisition_source(
datetime=datetime.datetime.utcnow().isoformat(),
submission_number=obj.id,
internal_uid=int(obj.id_user),
email=form_fields.get('email'),
orcid=form_fields.get('orcid'),
method='submitter')
return builder.record
def formdata_to_model(obj, formdata):
"""Manipulate form data to match literature data model."""
def _is_arxiv_url(url):
return 'arxiv.org' in url
form_fields = copy.deepcopy(formdata)
filter_empty_elements(
form_fields, ['authors', 'supervisors', 'report_numbers']
)
builder = LiteratureBuilder(source='submitter')
for author in form_fields.get('authors', []):
builder.add_author(builder.make_author(
author['full_name'],
affiliations=force_list(author['affiliation'])
if author['affiliation'] else None,
roles=['author']
))
for supervisor in form_fields.get('supervisors', []):
builder.add_author(builder.make_author(
supervisor['full_name'],
affiliations=force_list(supervisor['affiliation'])
if author['affiliation'] else None,
roles=['supervisor']
))
builder.add_title(title=form_fields.get('title'))
document_type = 'conference paper' if form_fields.get('conf_name') \
else form_fields.get('type_of_doc', [])
builder.add_document_type(
document_type=document_type
)
builder.add_abstract(
abstract=form_fields.get('abstract'),
source='arXiv' if form_fields.get('categories') else None
)
if form_fields.get('arxiv_id') and form_fields.get('categories'):
builder.add_arxiv_eprint(
arxiv_id=form_fields.get('arxiv_id'),
arxiv_categories=form_fields.get('categories').split()
)
builder.add_doi(doi=form_fields.get('doi'))
builder.add_inspire_categories(
subject_terms=form_fields.get('subject_term'),
source='user'
)
for key in ('extra_comments', 'nonpublic_note',
'hidden_notes', 'conf_name', 'references'):
builder.add_private_note(
private_notes=form_fields.get(key)
)
year = form_fields.get('year')
try:
year = int(year)
except (TypeError, ValueError):
year = None
builder.add_publication_info(
year=year,
cnum=form_fields.get('conference_id'),
journal_issue=form_fields.get('issue'),
journal_title=form_fields.get('journal_title'),
journal_volume=form_fields.get('volume'),
page_start=form_fields.get('page_start'),
page_end=form_fields.get('page_end'),
artid=form_fields.get('artid')
)
builder.add_preprint_date(
preprint_date=form_fields.get('preprint_created')
)
if form_fields.get('type_of_doc') == 'thesis':
builder.add_thesis(
defense_date=form_fields.get('defense_date'),
degree_type=form_fields.get('degree_type'),
institution=form_fields.get('institution'),
date=form_fields.get('thesis_date')
)
builder.add_accelerator_experiments_legacy_name(
legacy_name=form_fields.get('experiment')
)
language = form_fields.get('other_language') \
if form_fields.get('language') == 'oth' \
else form_fields.get('language')
builder.add_language(language=language)
builder.add_title_translation(title=form_fields.get('title_translation'))
builder.add_title(
title=form_fields.get('title_arXiv'),
source='arXiv'
)
builder.add_title(
title=form_fields.get('title_crossref'),
source='crossref'
)
builder.add_license(url=form_fields.get('license_url'))
builder.add_public_note(public_note=form_fields.get('public_notes'))
builder.add_public_note(
public_note=form_fields.get('note'),
source='arXiv' if form_fields.get('categories') else 'CrossRef'
)
form_url = form_fields.get('url')
form_additional_url = form_fields.get('additional_url')
if form_url and not _is_arxiv_url(form_url):
obj.extra_data['submission_pdf'] = form_url
if not form_additional_url:
builder.add_url(url=form_url)
if form_additional_url and not _is_arxiv_url(form_additional_url):
builder.add_url(url=form_additional_url)
[builder.add_report_number(
report_number=report_number.get('report_number')
) for report_number in form_fields.get('report_numbers', [])]
builder.add_collaboration(collaboration=form_fields.get('collaboration'))
builder.add_acquisition_source(
datetime=datetime.datetime.utcnow().isoformat(),
submission_number=obj.id,
internal_uid=int(obj.id_user),
email=form_fields.get('email'),
orcid=form_fields.get('orcid'),
method='submitter'
)
builder.validate_record()
return builder.record
def formdata_to_model(obj, formdata):
"""Manipulate form data to match literature data model."""
form_fields = copy.deepcopy(formdata)
filter_empty_elements(
form_fields, ['authors', 'supervisors', 'report_numbers']
)
obj.extra_data["submission_data"] = {}
data = literature.do(form_fields)
# Add extra fields that need to be computed or depend on other
# fields.
#
# ======
# Schema
# ======
if '$schema' in data and not data['$schema'].startswith('http'):
data['$schema'] = url_for(
'invenio_jsonschemas.get_schema',
schema_path="records/{0}".format(data['$schema'])
)
# ============================
# Collection
# ============================
data['collections'] = [{'primary': "HEP"}]
if form_fields['type_of_doc'] == 'thesis':
data['collections'].append({'primary': "THESIS"})
if "field_categories" in data:
# Check if it was imported from arXiv
if any([x["scheme"] == "arXiv" for x in data["field_categories"]]):
data['collections'].extend([{'primary': "arXiv"},
{'primary': "Citeable"}])
# Add arXiv as source
if data.get("abstracts"):
data['abstracts'][0]['source'] = 'arXiv'
if form_fields.get("arxiv_id"):
data['external_system_numbers'] = [{
'value': 'oai:arXiv.org:' + form_fields['arxiv_id'],
'institute': 'arXiv'
}]
if "publication_info" in data:
if all([key in data['publication_info'][0].keys() for key in
('year', 'journal_issue', 'journal_volume', 'page_start',
'page_end', 'artid')]):
# NOTE: Only peer reviewed journals should have this collection
# we are adding it here but ideally should be manually added
# by a curator.
data['collections'].append({'primary': "Published"})
# Add Citeable collection if not present
collections = [x['primary'] for x in data['collections']]
if "Citeable" not in collections:
data['collections'].append({'primary': "Citeable"})
# ============================
# Title source and cleanup
# ============================
try:
# Clean up all extra spaces in title
data['titles'][0]['title'] = " ".join(
data['titles'][0]['title'].split()
)
title = data['titles'][0]['title']
except (KeyError, IndexError):
title = ""
if form_fields.get('title_arXiv'):
title_arxiv = " ".join(form_fields.get('title_arXiv').split())
if title == title_arxiv:
data['titles'][0]["source"] = "arXiv"
else:
data['titles'].append({
'title': title_arxiv,
'source': "arXiv"
})
if form_fields.get('title_crossref'):
title_crossref = " ".join(
form_fields.get('title_crossref').split()
)
if title == title_crossref:
data['titles'][0]["source"] = "CrossRef"
else:
data['titles'].append({
'title': title_crossref,
'source': "CrossRef"
})
try:
data['titles'][0]['source']
except KeyError:
# Title has no source, so should be the submitter
data['titles'][0]['source'] = "submitter"
# ============================
# Conference name
# ============================
if 'conf_name' in form_fields:
if 'nonpublic_note' in form_fields:
data.setdefault("hidden_notes", []).append({
"value": form_fields['conf_name']
})
data['hidden_notes'].append({
'value': form_fields['nonpublic_note']
})
else:
data.setdefault("hidden_notes", []).append({
"value": form_fields['conf_name']
})
data['collections'].extend([{'primary': "ConferencePaper"}])
# ============================
# Page number
# ============================
if 'page_nr' not in data:
first_publication_info = data.get('publication_info', [{}])[0]
page_start = first_publication_info.get('page_start')
page_end = first_publication_info.get('page_end')
if page_start and page_end:
try:
data['page_nr'] = int(page_end) - int(page_start) + 1
except (TypeError, ValueError):
pass
# ============================
# Language
# ============================
if data.get("languages", []) and data["languages"][0] == "oth":
if form_fields.get("other_language"):
data["languages"] = [form_fields["other_language"]]
# ==========
# Owner Info
# ==========
# TODO Make sure we are getting the email correctly
userid = obj.id_user
try:
email = User.query.get(userid).email
except AttributeError:
email = ''
try:
# TODO Make sure we are getting the ORCID id correctly
source = UserIdentity.query.filter_by(id_user=userid, method='orcid').one()
except NoResultFound:
source = ''
if source:
source = source.method + ':' + source.id
data['acquisition_source'] = dict(
source=source,
email=email,
date=date.today().isoformat(),
method="submission",
submission_number=str(obj.id),
)
# ==============
# References
# ==============
if form_fields.get('references'):
obj.extra_data["submission_data"]['references'] = form_fields.get('references')
# ==============
# Extra comments
# ==============
if form_fields.get('extra_comments'):
data.setdefault('hidden_notes', []).append(
{
'value': form_fields['extra_comments'],
'source': 'submitter'
}
)
obj.extra_data["submission_data"]["extra_comments"] = form_fields.get("extra_comments")
# ======================================
# Journal name Knowledge Base conversion
# ======================================
if data.get("publication_info", [{}])[0].get("journal_title"):
# journals_kb = dict([(x['key'].lower(), x['value'])
# for x in get_kb_mappings(current_app.config.get("DEPOSIT_INSPIRE_JOURNALS_KB"))])
# data['publication_info']['journal_title'] = journals_kb.get(data['publication_info']['journal_title'].lower(),
# data['publication_info']['journal_title'])
# TODO convert using journal records
pass
if 'pdf' in data:
obj.extra_data["submission_data"]["pdf"] = data.pop("pdf")
# Finally, return the converted data
return data
def formdata_to_model(obj, formdata):
"""Manipulate form data to match literature data model."""
form_fields = copy.deepcopy(formdata)
filter_empty_elements(form_fields,
['authors', 'supervisors', 'report_numbers'])
obj.extra_data["submission_data"] = {}
data = literature.do(form_fields)
# Add extra fields that need to be computed or depend on other
# fields.
#
# ======
# Schema
# ======
if '$schema' in data and not data['$schema'].startswith('http'):
data['$schema'] = url_for('invenio_jsonschemas.get_schema',
schema_path="records/{0}".format(
data['$schema']))
# ============================
# Collection
# ============================
data['collections'] = [{'primary': "HEP"}]
if form_fields['type_of_doc'] == 'thesis':
data['collections'].append({'primary': "THESIS"})
if "field_categories" in data:
# Check if it was imported from arXiv
if any([x["scheme"] == "arXiv" for x in data["field_categories"]]):
data['collections'].extend([{
'primary': "arXiv"
}, {
'primary': "Citeable"
}])
# Add arXiv as source
if data.get("abstracts"):
data['abstracts'][0]['source'] = 'arXiv'
if form_fields.get("arxiv_id"):
data['external_system_numbers'] = [{
'value':
'oai:arXiv.org:' + form_fields['arxiv_id'],
'institute':
'arXiv'
}]
if "publication_info" in data:
if all([
key in data['publication_info'][0].keys()
for key in ('year', 'journal_issue', 'journal_volume',
'page_start', 'page_end', 'artid')
]):
# NOTE: Only peer reviewed journals should have this collection
# we are adding it here but ideally should be manually added
# by a curator.
data['collections'].append({'primary': "Published"})
# Add Citeable collection if not present
collections = [x['primary'] for x in data['collections']]
if "Citeable" not in collections:
data['collections'].append({'primary': "Citeable"})
# ============================
# Title source and cleanup
# ============================
try:
# Clean up all extra spaces in title
data['titles'][0]['title'] = " ".join(
data['titles'][0]['title'].split())
title = data['titles'][0]['title']
except (KeyError, IndexError):
title = ""
if form_fields.get('title_arXiv'):
title_arxiv = " ".join(form_fields.get('title_arXiv').split())
if title == title_arxiv:
data['titles'][0]["source"] = "arXiv"
else:
data['titles'].append({'title': title_arxiv, 'source': "arXiv"})
if form_fields.get('title_crossref'):
title_crossref = " ".join(form_fields.get('title_crossref').split())
if title == title_crossref:
data['titles'][0]["source"] = "CrossRef"
else:
data['titles'].append({
'title': title_crossref,
'source': "CrossRef"
})
try:
data['titles'][0]['source']
except KeyError:
# Title has no source, so should be the submitter
data['titles'][0]['source'] = "submitter"
# ============================
# Conference name
# ============================
if 'conf_name' in form_fields:
if 'nonpublic_note' in form_fields:
data.setdefault("hidden_notes",
[]).append({"value": form_fields['conf_name']})
data['hidden_notes'].append(
{'value': form_fields['nonpublic_note']})
else:
data.setdefault("hidden_notes",
[]).append({"value": form_fields['conf_name']})
data['collections'].extend([{'primary': "ConferencePaper"}])
# ============================
# Page number
# ============================
if 'page_nr' not in data:
first_publication_info = data.get('publication_info', [{}])[0]
page_start = first_publication_info.get('page_start')
page_end = first_publication_info.get('page_end')
if page_start and page_end:
try:
data['page_nr'] = int(page_end) - int(page_start) + 1
except (TypeError, ValueError):
pass
# ============================
# Language
# ============================
if data.get("languages", []) and data["languages"][0] == "oth":
if form_fields.get("other_language"):
data["languages"] = [form_fields["other_language"]]
# ==========
# Owner Info
# ==========
# TODO Make sure we are getting the email correctly
userid = obj.id_user
try:
email = User.query.get(userid).email
except AttributeError:
email = ''
try:
# TODO Make sure we are getting the ORCID id correctly
source = UserIdentity.query.filter_by(id_user=userid,
method='orcid').one()
except NoResultFound:
source = ''
if source:
source = source.method + ':' + source.id
data['acquisition_source'] = dict(
source=source,
email=email,
date=date.today().isoformat(),
method="submission",
submission_number=str(obj.id),
)
# ==============
# References
# ==============
if form_fields.get('references'):
obj.extra_data["submission_data"]['references'] = form_fields.get(
'references')
# ==============
# Extra comments
# ==============
if form_fields.get('extra_comments'):
data.setdefault('hidden_notes', []).append({
'value':
form_fields['extra_comments'],
'source':
'submitter'
})
obj.extra_data["submission_data"]["extra_comments"] = form_fields.get(
"extra_comments")
# ======================================
# Journal name Knowledge Base conversion
# ======================================
if data.get("publication_info", [{}])[0].get("journal_title"):
# journals_kb = dict([(x['key'].lower(), x['value'])
# for x in get_kb_mappings(current_app.config.get("DEPOSIT_INSPIRE_JOURNALS_KB"))])
# data['publication_info']['journal_title'] = journals_kb.get(data['publication_info']['journal_title'].lower(),
# data['publication_info']['journal_title'])
# TODO convert using journal records
pass
if 'pdf' in data:
obj.extra_data["submission_data"]["pdf"] = data.pop("pdf")
# Finally, return the converted data
return data
def formdata_to_model(obj, formdata):
"""Manipulate form data to match authors data model."""
form_fields = copy.deepcopy(formdata)
filter_empty_elements(
form_fields,
['institution_history', 'advisors',
'websites', 'experiments']
)
data = updateform.do(form_fields)
# ===========
# Collections
# ===========
data['_collections'] = ['Authors']
# ======
# Schema
# ======
# FIXME it's not clear whether $schema is ever present at this stage
if '$schema' not in data and '$schema' in obj.data:
data['$schema'] = obj.data.get('$schema')
if '$schema' in data:
ensure_valid_schema(data)
author_name = ''
if 'family_name' in form_fields and form_fields['family_name']:
author_name = form_fields['family_name'].strip() + ', '
if 'given_names' in form_fields and form_fields['given_names']:
author_name += form_fields['given_names']
if author_name:
data.get('name', {})['value'] = author_name
# Add comments to extra data
if 'extra_comments' in form_fields and form_fields['extra_comments']:
data.setdefault('_private_notes', []).append({
'source': 'submitter',
'value': form_fields['extra_comments']
})
data['stub'] = False
# ==========
# Submitter Info
# ==========
try:
user_email = User.query.get(obj.id_user).email
except AttributeError:
user_email = ''
try:
orcid = UserIdentity.query.filter_by(
id_user=obj.id_user,
method='orcid'
).one().id
except NoResultFound:
orcid = ''
data['acquisition_source'] = dict(
email=user_email,
datetime=datetime.datetime.utcnow().isoformat(),
method="submitter",
orcid=orcid,
submission_number=str(obj.id),
internal_uid=int(obj.id_user),
)
data = strip_empty_values(data)
return data
def formdata_to_model(obj, formdata):
"""Manipulate form data to match authors data model."""
form_fields = copy.deepcopy(formdata)
filter_empty_elements(
form_fields,
['institution_history', 'advisors', 'websites', 'experiments'])
data = updateform.do(form_fields)
# ===========
# Collections
# ===========
data['_collections'] = ['Authors']
# ======
# Schema
# ======
if '$schema' not in data and '$schema' in obj.data:
data['$schema'] = obj.data.get('$schema')
if '$schema' in data and not data['$schema'].startswith('http'):
data['$schema'] = url_for('invenio_jsonschemas.get_schema',
schema_path="records/{0}".format(
data['$schema']))
author_name = ''
if 'family_name' in form_fields and form_fields['family_name']:
author_name = form_fields['family_name'].strip() + ', '
if 'given_names' in form_fields and form_fields['given_names']:
author_name += form_fields['given_names']
if author_name:
data.get('name', {})['value'] = author_name
# Add comments to extra data
if 'extra_comments' in form_fields and form_fields['extra_comments']:
data.setdefault('_private_notes', []).append({
'source':
'submitter',
'value':
form_fields['extra_comments']
})
data['stub'] = False
# ==========
# Submitter Info
# ==========
try:
user_email = User.query.get(obj.id_user).email
except AttributeError:
user_email = ''
try:
orcid = UserIdentity.query.filter_by(id_user=obj.id_user,
method='orcid').one().id
except NoResultFound:
orcid = ''
data['acquisition_source'] = dict(
email=user_email,
datetime=datetime.datetime.utcnow().isoformat(),
method="submitter",
orcid=orcid,
submission_number=str(obj.id),
internal_uid=int(obj.id_user),
)
data = strip_empty_values(data)
validate(data, 'authors')
return data
def formdata_to_model(obj, formdata):
"""Manipulate form data to match literature data model."""
form_fields = copy.deepcopy(formdata)
filter_empty_elements(form_fields,
['authors', 'supervisors', 'report_numbers'])
data = literature.do(form_fields)
# Add extra fields that need to be computed or depend on other
# fields.
#
# ======
# Schema
# ======
if '$schema' in data and not data['$schema'].startswith('http'):
jsonschemas_ext = current_app.extensions.get('invenio-jsonschemas')
data['$schema'] = jsonschemas_ext.path_to_url("records/{0}".format(
data['$schema']))
# ============================
# Collection
# ============================
data['collections'] = [{'primary': "HEP"}]
if form_fields['type_of_doc'] == 'thesis':
data['collections'].append({'primary': "THESIS"})
if get_value(form_fields, "arxiv_eprints.categories", None):
# Check if it was imported from arXiv
data['collections'].extend([{
'primary': "arXiv"
}, {
'primary': "Citeable"
}])
# Add arXiv as source
if data.get("abstracts"):
data['abstracts'][0]['source'] = 'arXiv'
if form_fields.get("arxiv_id"):
data['external_system_numbers'] = [{
'value':
'oai:arXiv.org:' + form_fields['arxiv_id'],
'institute':
'arXiv'
}]
if "publication_info" in data:
pub_keys = data['publication_info'][0].keys()
has_pub_info = all([
key in pub_keys
for key in ('year', 'journal_issue', 'journal_volume')
])
has_page_or_artid = any(
[key in pub_keys for key in ('page_start', 'page_end', 'artid')])
if has_pub_info and has_page_or_artid:
# NOTE: Only peer reviewed journals should have this collection
# we are adding it here but ideally should be manually added
# by a curator.
data['collections'].append({'primary': "Published"})
# Add Citeable collection if not present
collections = [x['primary'] for x in data['collections']]
if "Citeable" not in collections:
data['collections'].append({'primary': "Citeable"})
# ============================
# Title source and cleanup
# ============================
try:
# Clean up all extra spaces in title
data['titles'][0]['title'] = " ".join(
data['titles'][0]['title'].split())
title = data['titles'][0]['title']
except (KeyError, IndexError):
title = ""
if form_fields.get('title_arXiv'):
title_arxiv = " ".join(form_fields.get('title_arXiv').split())
if title == title_arxiv:
data['titles'][0]["source"] = "arXiv"
else:
data['titles'].append({'title': title_arxiv, 'source': "arXiv"})
if form_fields.get('title_crossref'):
title_crossref = " ".join(form_fields.get('title_crossref').split())
if title == title_crossref:
data['titles'][0]["source"] = "CrossRef"
else:
data['titles'].append({
'title': title_crossref,
'source': "CrossRef"
})
try:
data['titles'][0]['source']
except KeyError:
# Title has no source, so should be the submitter
data['titles'][0]['source'] = "submitter"
# ============================
# Conference name
# ============================
if 'conf_name' in form_fields:
if 'nonpublic_note' in form_fields:
data.setdefault("hidden_notes",
[]).append({"value": form_fields['conf_name']})
data['hidden_notes'].append(
{'value': form_fields['nonpublic_note']})
else:
data.setdefault("hidden_notes",
[]).append({"value": form_fields['conf_name']})
data['collections'].extend([{'primary': "ConferencePaper"}])
# ============================
# Page number
# ============================
if 'page_nr' not in data:
first_publication_info = data.get('publication_info', [{}])[0]
page_start = first_publication_info.get('page_start')
page_end = first_publication_info.get('page_end')
if page_start and page_end:
try:
data['page_nr'] = int(page_end) - int(page_start) + 1
except (TypeError, ValueError):
pass
# ============================
# Language
# ============================
if form_fields.get('language') == 'oth':
if form_fields.get("other_language"):
data["languages"] = [form_fields["other_language"]]
# ==========
# Owner Info
# ==========
# TODO Make sure we are getting the email correctly
userid = obj.id_user
try:
email = User.query.get(userid).email
except AttributeError:
email = ''
try:
# TODO Make sure we are getting the ORCID id correctly
source = UserIdentity.query.filter_by(id_user=userid,
method='orcid').one()
except NoResultFound:
source = ''
if source:
source = source.method + ':' + source.id
data['acquisition_source'] = dict(
source=source,
email=email,
date=date.today().isoformat(),
method="submission",
submission_number=str(obj.id),
)
# ==============
# Extra comments
# ==============
if form_fields.get('extra_comments'):
data.setdefault('hidden_notes', []).append({
'value':
form_fields['extra_comments'],
'source':
'submitter'
})
# ==========================
# Journal name normalization
# ==========================
journal_title = get_value(data, 'publication_info[0].journal_title')
if journal_title:
hits = JournalsSearch().query(
'match',
title_variants__title__lowercased=journal_title).execute()
if hits:
try:
short_title = hits[0].short_titles[0].title
data['publication_info'][0]['journal_title'] = short_title
except (AttributeError, IndexError):
pass
# Finally, return the converted data
return data
