def _getter(field):
if field.data:
val = get_kb_mapping("json_projects", str(field.data))
if val:
data = json_projects_kb_mapper(val)
return data["fields"][key_name]
return ""
def _getter(field):
if field.data:
val = get_kb_mapping('json_projects', str(field.data))
if val:
data = json_projects_kb_mapper(val)
return data['fields'][key_name]
return ''
def _getter(field):
if field.data:
val = get_kb_mapping('json_projects', str(field.data))
if val:
data = json_projects_kb_mapper(val)
return data['fields'][key_name]
return ''
def grants_validator(form, field):
if field.data:
for item in field.data:
val = get_kb_mapping('json_projects', str(item['id']))
if val:
data = json_projects_kb_mapper(val)
item['acronym'] = data['fields']['acronym']
item['title'] = data['fields']['title']
continue
raise ValidationError("Invalid grant identifier %s" % item['id'])
def grants_validator(form, field):
if field.data:
for item in field.data:
val = get_kb_mapping('json_projects', str(item['id']))
if val:
data = json_projects_kb_mapper(val)
item['acronym'] = data['fields']['acronym']
item['title'] = data['fields']['title']
continue
raise ValidationError("Invalid grant identifier %s" % item['id'])
def grants_validator(form, field):
if field.data:
for item in field.data:
val = get_kb_mapping("json_projects", str(item["id"]))
if val:
data = json_projects_kb_mapper(val)
item["acronym"] = data["fields"]["acronym"]
item["title"] = data["fields"]["title"]
continue
raise ValidationError("Invalid grant identifier %s" % item["id"])
def _f1(x):
info = get_kb_mapping('json_projects', str(x))
data = json.loads(info['value'])
return {'id': x, 'title': data.get('title', ''), 'acronym': data.get('acronym', '')}
def process_recjson(deposition, recjson):
"""
Process exported recjson (common for both new and edited records)
"""
# ================
# ISO format dates
# ================
for k in recjson.keys():
if isinstance(recjson[k], date):
recjson[k] = recjson[k].isoformat()
# =======
# Authors
# =======
if 'authors' in recjson and recjson['authors']:
recjson['_first_author'] = recjson['authors'][0]
recjson['_additional_authors'] = recjson['authors'][1:]
if 'keywords' in recjson and recjson['keywords']:
recjson['keywords'] = sorted(
set([item.strip() for item in recjson['keywords'].split(',')]))
# ===========
# Communities
# ===========
try:
communities = recjson.get('provisional_communities', [])
# Extract identifier (i.e. elements are mapped from dict ->
# string)
recjson['provisional_communities'] = map(
lambda x: x['identifier'],
filter(lambda x: x.get('provisional', False), communities)
)
recjson['communities'] = map(
lambda x: x['identifier'],
filter(lambda x: not x.get('provisional', False), communities)
)
except TypeError:
# Happens on re-run
pass
# ===========
# Access groups
# ===========
try:
access_groups = recjson.get('access_groups', [])
# Extract identifier (i.e. elements are mapped from dict ->
# string)
recjson['access_groups'] = map(
lambda x: x['identifier'], access_groups
)
recjson['access_groups_title'] = map(
lambda x: x['title'], access_groups
)
except TypeError:
# Happens on re-run
pass
# ==============
# Related inputs
# ==============
for rel_input_type in ['rel_dataset', 'rel_software']:
try:
rel_input = recjson.get(rel_input_type, [])
# Extract identifier (i.e. elements are mapped from dict ->
# string)
recjson[rel_input_type] = map(
lambda x: x['identifier'], rel_input
)
except TypeError:
# Happens on re-run
pass
# =============================
# Related/alternate identifiers
# =============================
if recjson.get('related_identifiers', []):
related_identifiers = recjson.get('related_identifiers', [])
recjson['related_identifiers'] = filter(
lambda x: x.get('relation', '') != 'isAlternativeIdentifier',
related_identifiers
)
recjson['alternate_identifiers'] = map(
lambda x: {'scheme': x['scheme'], 'identifier': x['identifier']},
filter(
lambda x: x.get('relation', '') == 'isAlternativeIdentifier',
related_identifiers
)
)
# =================
# License
# =================
if recjson['access_right'] in ["open", "embargoed"]:
info = get_kb_mapping(CFG_LICENSE_KB, str(recjson['license']))
if info:
info = json.loads(info['value'])
recjson['license'] = dict(
identifier=recjson['license'],
source=CFG_LICENSE_SOURCE,
license=info['title'],
url=info['url'],
)
elif 'license' in recjson:
del recjson['license']
# =================
# Project info
# =================
if recjson.get('project'):
if 'record_curated_in_project' in recjson:
if recjson['upload_type'] != 'dataset':
recjson['record_curated_in_project'] = True
else:
curated = _get_bool_value_from_bool_or_str(
recjson['record_curated_in_project'])
recjson['record_curated_in_project'] = curated
if 'record_public_from_project' in recjson:
public = _get_bool_value_from_bool_or_str(
recjson['record_public_from_project'])
recjson['record_public_from_project'] = public
else:
for k in ['record_curated_in_project', 'record_public_from_project']:
if k in recjson:
del recjson[k]
if 'record_selected_for_archive' in recjson:
archived = _get_bool_value_from_bool_or_str(
recjson['record_selected_for_archive'])
recjson['record_selected_for_archive'] = archived
# Requirements
# =================
# if recjson.get('os', []):
# info = get_kb_mapping(CFG_REQUIREMENT_KB, str(recjson['os']))
# if info:
# info = json.loads(info['value'])
# recjson['os'] = dict(
# identifier=recjson['os'],
# os=info['title'],
# )
# elif 'os' in recjson:
# del recjson['os']
# if recjson.get('flavor', []):
# info = get_kb_mapping(CFG_REQUIREMENT_KB, str(recjson['flavor']))
# if info:
# info = json.loads(info['value'])
# recjson['flavor'] = dict(
# identifier=recjson['flavor'],
# flavor=info['title'],
# )
# elif 'flavor' in recjson:
# del recjson['flavor']
# =======================
# Filter out empty fields
# =======================
filter_empty_elements(recjson)
# ==================================
# Map dot-keys to their dictionaries
# ==================================
for k in recjson.keys():
if '.' in k:
mainkey, subkey = k.split('.')
if mainkey not in recjson:
recjson[mainkey] = {}
recjson[mainkey][subkey] = recjson.pop(k)
return recjson
def process_recjson(deposition, recjson):
"""
Process exported recjson (common for both new and edited records)
"""
# ================
# ISO format dates
# ================
for k in recjson.keys():
if isinstance(recjson[k], date):
recjson[k] = recjson[k].isoformat()
# =======
# Authors
# =======
if 'authors' in recjson and recjson['authors']:
recjson['_first_author'] = recjson['authors'][0]
recjson['_additional_authors'] = recjson['authors'][1:]
# ===========
# Communities
# ===========
try:
communities = recjson.get('provisional_communities', [])
# Extract identifier (i.e. elements are mapped from dict ->
# string)
recjson['provisional_communities'] = map(
lambda x: x['identifier'],
filter(lambda x: x.get('provisional', False), communities)
)
recjson['communities'] = map(
lambda x: x['identifier'],
filter(lambda x: not x.get('provisional', False), communities)
)
except TypeError:
# Happens on re-run
pass
# =============================
# Related/alternate identifiers
# =============================
if recjson.get('related_identifiers', []):
related_identifiers = recjson.get('related_identifiers', [])
recjson['related_identifiers'] = filter(
lambda x: x.get('relation', '') != 'isAlternativeIdentifier',
related_identifiers
)
recjson['alternate_identifiers'] = map(
lambda x: {'scheme': x['scheme'], 'identifier': x['identifier']},
filter(
lambda x: x.get('relation', '') == 'isAlternativeIdentifier',
related_identifiers
)
)
# =================
# License
# =================
if recjson['access_right'] in ["open", "embargoed"]:
info = get_kb_mapping(CFG_LICENSE_KB, str(recjson['license']))
if info:
info = json.loads(info['value'])
recjson['license'] = dict(
identifier=recjson['license'],
source=CFG_LICENSE_SOURCE,
license=info['title'],
url=info['url'],
)
elif 'license' in recjson:
del recjson['license']
# =======================
# Journal
# =======================
# Set year or delete fields if no title is provided
if recjson.get('journal.title', None):
recjson['journal.year'] = recjson['publication_date'][:4]
# =======================
# References
# =======================
if recjson.get('references', []):
recjson['references'] = map(
lambda x: dict(raw_reference=x),
recjson['references']
)
# =======================
# Book/chaper/report
# =======================
if 'imprint.publisher' in recjson and 'imprint.place' in recjson:
recjson['imprint.year'] = recjson['publication_date'][:4]
if 'part_of.title' in recjson:
mapping = [
('part_of.publisher', 'imprint.publisher'),
('part_of.place', 'imprint.place'),
('part_of.year', 'imprint.year'),
('part_of.isbn', 'isbn'),
]
for new, old in mapping:
if old in recjson:
try:
recjson[new] = recjson[old]
del recjson[old]
except KeyError:
pass
# =================
# Grants
# =================
# Remap incoming dictionary
recjson['grants'] = map(
lambda x: dict(
title="%s - %s (%s)" % (x['acronym'], x['title'], x['id']),
identifier=x['id']
),
recjson.get('grants', [])
)
# =======================
# Filter out empty fields
# =======================
filter_empty_elements(recjson)
# ==================================
# Map dot-keys to their dictionaries
# ==================================
for k in recjson.keys():
if '.' in k:
mainkey, subkey = k.split('.')
if mainkey not in recjson:
recjson[mainkey] = {}
recjson[mainkey][subkey] = recjson.pop(k)
return recjson
def process_recjson(deposition, recjson):
"""
Process exported recjson (common for both new and edited records)
"""
# ================
# ISO format dates
# ================
for k in recjson.keys():
if isinstance(recjson[k], date):
recjson[k] = recjson[k].isoformat()
# =======
# Authors
# =======
if 'authors' in recjson and recjson['authors']:
recjson['first_author'] = recjson['authors'][0]
recjson['additional_authors'] = recjson['authors'][1:]
del recjson['authors']
# ===========
# Communities
# ===========
# FIXME: Properly deal with provisional/non-provisional
try:
# Extract identifier (i.e. elements are mapped from dict ->
# string)
recjson['provisional_communities'] = list(set(map(
lambda x: x['identifier'],
recjson.get('provisional_communities', [])
)))
recjson['communities'] = list(set(map(
lambda x: x['identifier'],
recjson.get('communities', [])
)))
except TypeError:
# Happens on re-run
pass
# =================
# License
# =================
if recjson['access_right'] in ["open", "embargoed"]:
info = get_kb_mapping(CFG_LICENSE_KB, str(recjson['license']))
if info:
info = json.loads(info['value'])
recjson['license'] = dict(
identifier=recjson['license'],
source=CFG_LICENSE_SOURCE,
license=info['title'],
url=info['url'],
)
elif 'license' in recjson:
del recjson['license']
# =======================
# Journal
# =======================
# Set year or delete fields if no title is provided
if recjson.get('journal.title', None):
recjson['journal.year'] = recjson['publication_date'][:4]
# =======================
# Book/chaper/report
# =======================
if 'imprint.publisher' in recjson and 'imprint.place' in recjson:
recjson['imprint.year'] = recjson['publication_date'][:4]
if 'part_of.title' in recjson:
mapping = [
('part_of.publisher', 'imprint.publisher'),
('part_of.place', 'imprint.place'),
('part_of.year', 'imprint.year'),
('part_of.isbn', 'isbn'),
]
for new, old in mapping:
if old in recjson:
try:
recjson[new] = recjson[old]
del recjson[old]
except KeyError:
pass
# =================
# Grants
# =================
# Remap incoming dictionary
recjson['grants'] = map(
lambda x: dict(
title="%s - %s (%s)" % (x['acronym'], x['title'], x['id']),
identifier=x['id']
),
recjson.get('grants', [])
)
# =======================
# Filter out empty fields
# =======================
filter_empty_elements(recjson)
# ==================================
# Map dot-keys to their dictionaries
# ==================================
for k in recjson.keys():
if '.' in k:
mainkey, subkey = k.split('.')
if mainkey not in recjson:
recjson[mainkey] = {}
recjson[mainkey][subkey] = recjson.pop(k)
return recjson
def _f1(x):
info = get_kb_mapping('json_projects', str(x))
data = json.loads(info['value'])
return {'id': x, 'title': data.get('title', ''), 'acronym': data.get('acronym', '')}
def format_element(bfo, req_id=''):
info = get_kb_mapping('requirements', req_id)
if info:
info = json.loads(info['value'])
return info['title']
def format_element(bfo, req_id=""):
info = get_kb_mapping("requirements", req_id)
if info:
info = json.loads(info["value"])
return info["title"]
