def request_args(request, **overrides):
opts = {}
opts.update(settings.API_OPTS)
opts.update(overrides)
def ispositiveint(v):
ensure(isint(v) and int(v) > 0, "expecting positive integer, got: %s" % v)
return int(v)
def inrange(minpp, maxpp):
def fn(v):
ensure(v >= minpp and v <= maxpp, "value must be between %s and %s" % (minpp, maxpp))
return v
return fn
def asc_or_desc(val):
v = val.strip().upper()
ensure(v in ['ASC', 'DESC'], "expecting either 'asc' or 'desc' for 'order' parameter, got: %s" % val)
return v
desc = {
'page': [p('page', opts['page_num']), ispositiveint],
'per_page': [p('per-page', opts['per_page']), ispositiveint, inrange(opts['min_per_page'], opts['max_per_page'])],
'order': [p('order', opts['order_direction']), str, asc_or_desc]
}
return render_item(desc, request.GET)
def et(struct):
return {
'type': 'external-article',
'articleTitle': p(struct, 'article.title'),
'journal': p(struct, 'journal.name'),
'authorLine': p(struct, 'article.authorLine'),
'uri': 'https://doi.org/%s' % p(struct, 'article.doi'),
}
def et(struct):
return OrderedDict([
('type', 'external-article'),
('articleTitle', p(struct, 'article.title')),
('journal', p(struct, 'journal.name')),
('authorLine', p(struct, 'article.authorLine')),
('uri', 'https://doi.org/%s' % p(struct, 'article.doi')),
])
def et(struct):
return OrderedDict([
('type', 'external-article'),
('articleTitle', p(struct, 'article.title')),
('journal', p(struct, 'journal.name')),
('authorLine', p(struct, 'article.authorLine')),
('uri', 'https://doi.org/%s' % p(struct, 'article.doi')),
])
def request_args(request, **overrides):
opts = {}
opts.update(settings.API_OPTS)
opts.update(overrides)
def ispositiveint(param):
def wrap(v):
ensure(
isint(v) and int(v) > 0,
"expecting positive integer for %r parameter" % param)
return int(v)
return wrap
def inrange(minpp, maxpp):
def fn(v):
ensure(
v >= minpp and v <= maxpp,
"value must be between %s and %s for 'per-page' parameter" %
(minpp, maxpp))
return v
return fn
def asc_or_desc(val):
v = val.strip().upper()[:4]
ensure(v in ['ASC', 'DESC'],
"expecting either 'asc' or 'desc' for 'order' parameter")
return v
desc = {
'page': [p('page', opts['page_num']),
ispositiveint('page')],
'per_page': [
p('per-page', opts['per_page']),
ispositiveint('per-page'),
inrange(opts['min_per_page'], opts['max_per_page'])
],
'order': [p('order', opts['order_direction']), str, asc_or_desc]
}
return render_item(desc, request.GET)
def request_args(request, **overrides):
opts = {}
opts.update(settings.API_OPTS)
opts.update(overrides)
def ispositiveint(v):
ensure(
isint(v) and int(v) > 0, "expecting positive integer, got: %s" % v)
return int(v)
def inrange(minpp, maxpp):
def fn(v):
ensure(v >= minpp and v <= maxpp,
"value must be between %s and %s" % (minpp, maxpp))
return v
return fn
def isin(lst):
def fn(val):
ensure(val in lst, "value is not in %r" % (lst, ))
return val
return fn
desc = {
'page': [p('page', opts['page_num']), ispositiveint],
'per_page': [
p('per-page', opts['per_page']), ispositiveint,
inrange(opts['min_per_page'], opts['max_per_page'])
],
'order': [
p('order', opts['order_direction']), uppercase,
isin(['ASC', 'DESC'])
],
'period': [p('by', 'day'), lowercase,
isin(['day', 'month'])],
}
return render_item(desc, request.GET)
SCHEMA_PATH = join(PROJECT_DIR, 'schema/api-raml/dist')
SCHEMA_IDX = {
'poa': join(SCHEMA_PATH, 'model/article-poa.v1.json'),
'vor': join(SCHEMA_PATH, 'model/article-vor.v1.json'),
'history': join(SCHEMA_PATH, 'model/article-history.v1.json'),
'list': join(SCHEMA_PATH, 'model/article-list.v1.json')
}
API_PATH = join(SCHEMA_PATH, 'api.raml')
def _load_api_raml(path):
# load the api.raml file, ignoring any "!include" commands
yaml.add_multi_constructor('', lambda *args: '[disabled]')
return yaml.load(open(path, 'r'))['traits']['paged']['queryParameters']
API_OPTS = render_item({
'per_page': [p('per-page.default'), int],
'min_per_page': [p('per-page.minimum'), int],
'max_per_page': [p('per-page.maximum'), int],
'page_num': [p('page.default'), int],
'order_direction': [p('order.default')],
}, _load_api_raml(API_PATH))
# KONG gateway options
KONG_AUTH_HEADER = 'KONG-Authenticated'
INTERNAL_NETWORK = '10.0.2.0/24'
#
# ignores any events missing a 'datetime' key
# WARN: if 'datetime' is present but is empty, it *will be given a datetime of now()*
ae_list = utils.lfilter(lambda struct: 'datetime_event' in struct,
ae_list)
return [add(article, **struct) for struct in ae_list]
#
#
#
INGEST_EVENTS = [
# why the list with a single value here? et3.render expects a pipeline of transformations
{
'event': [models.DATE_XML_RECEIVED],
'datetime_event': [p('-history.received', render.EXCLUDE_ME)]
},
{
'event': [models.DATE_XML_ACCEPTED],
'datetime_event': [p('-history.accepted', render.EXCLUDE_ME)]
},
{
'event': [models.DATETIME_ACTION_INGEST],
'datetime_event': [None],
'value': [p('forced?'), lambda v: "forced=%s" % v]
},
]
PUBLISH_EVENTS = [
{
'event': [models.DATETIME_ACTION_PUBLISH],
from et3 import render
from et3.extract import path as p
from django.db import IntegrityError
from functools import partial
from jsonschema import ValidationError
LOG = logging.getLogger(__name__)
class StateError(RuntimeError):
pass
# make the article-json lax compatible
# receives a list of article-json
ARTICLE = {
'manuscript_id': [p('id'), int],
'volume': [p('volume')],
'type': [p('type')],
'doi': [p('id'), utils.msid2doi], # remove when apiv1 is turned off
#'ejp_type': [p('type'), models.EJP_TYPE_REV_SLUG_IDX.get]
}
ARTICLE_VERSION = {
'title': [p('title')],
'version': [p('version')],
'status': [p('status')],
# only v1 article-json has a published date. v2 article-json does not
'datetime_published': [p('published', None), utils.todt],
}
def atomic(fn):
from django.conf import settings
LOG = logging.getLogger(__name__)
# make the article-json lax compatible
# receives a list of article-json
def exclude_if_empty(val):
if not val:
return render.EXCLUDE_ME
return val
ARTICLE = {
'manuscript_id': [p('id'), int],
'volume': [p('volume')],
'type': [p('type')],
'doi': [p('id'), utils.msid2doi], # remove when apiv1 is turned off
'date_received':
[p('-history.received', None), utils.todt, exclude_if_empty],
'date_accepted':
[p('-history.accepted', None), utils.todt, exclude_if_empty],
#'ejp_type': [p('type'), models.EJP_TYPE_REV_SLUG_IDX.get]
}
ARTICLE_VERSION = {
'title': [p('title')],
'version': [p('version')],
'status': [p('status')],
# only v1 article-json has a published date. v2 article-json does not
'metric': join(SCHEMA_PATH, 'model/metric.v1.json'),
}
API_PATH = join(SCHEMA_PATH, 'api.raml')
def _load_api_raml(path):
# load the api.raml file, ignoring any "!include" commands
yaml.add_multi_constructor('', lambda *args: '[disabled]')
return yaml.load(
open(path, 'r'),
Loader=yaml.FullLoader)['traits']['paged']['queryParameters']
API_OPTS = render_item(
{
'per_page': [p('per-page.default'), int],
'min_per_page': [p('per-page.minimum'), int],
'max_per_page': [p('per-page.maximum'), int],
'page_num': [p('page.default'), int],
'order_direction': [p('order.default')],
}, _load_api_raml(API_PATH))
LOG_FILE = join(PROJECT_DIR, 'elife-metrics.log')
if ENV != DEV:
LOG_FILE = join('/var/log/', 'elife-metrics.log')
DEBUG_LOG_FILE = join(PROJECT_DIR, 'debugme.log')
# whereever our log files are, ensure they are writable before we do anything else.
def writable(path):
from django.db import IntegrityError
from functools import partial
from jsonschema import ValidationError
LOG = logging.getLogger(__name__)
class StateError(RuntimeError):
pass
# make the article-json lax compatible
# receives a list of article-json
ARTICLE = {
"manuscript_id": [p("id"), int],
"volume": [p("volume")],
"type": [p("type")],
"doi": [p("id"), utils.msid2doi], # remove when apiv1 is turned off
#'ejp_type': [p('type'), models.EJP_TYPE_REV_SLUG_IDX.get]
}
ARTICLE_VERSION = {
"title": [p("title")],
"version": [p("version")],
"status": [p("status")],
# only v1 article-json has a published date. v2 article-json does not
"datetime_published": [p("published", None), utils.todt],
}
types = {
'RA': 'Research article',
'AV': 'Short report',
'RR': 'Research advance',
'SR': 'Registered report',
'TR': 'Tools and resources',
'RE': 'Research exchange', # deprecated in favour of SC
'SC': 'Scientific Correspondence',
'RS': 'Replication study',
'RC': 'Research communication',
}
assert mstype in types.keys(), "unknown paper type %r" % mstype
return mstype
DESCRIPTION = OrderedDict([
('manuscript_id', [p('ms'), int, str]), # yes, str->int->str, I know.
('ejp_type', [p('type'), paper_type]),
('date_initial_qc', [p('initial_qc_dt', None), todt]),
('date_initial_decision', [p('initial_decision_dt', None), todt]),
('initial_decision', [p('initial_decision', None), tfield]),
('date_full_qc', [p('full_qc_dt', None), todt]),
('date_full_decision', [p('full_decision_dt', None), todt]),
('decision', [p('full_decision', None), tfield]),
('date_rev1_qc', [p('rev1_qc_dt', None), todt]),
('date_rev1_decision', [p('rev1_decision_dt', None), todt]),
('rev1_decision', [p('rev1_decision', None), tfield]),
