def checkDryad(self):
# Test reading data from Dryad
item = ItemFactory.make(self.mydao, app.config["PROVIDERS"])
item.aliases.add_alias('doi', '10.5061/dryad.7898')
item_aliases_list = item.aliases.get_aliases_list()
dryad = Dryad()
new_aliases = dryad.aliases(item_aliases_list)
new_metrics = dryad.metrics(item_aliases_list)
self.check_aliases('dryad.url', new_aliases, ("url", 'http://hdl.handle.net/10255/dryad.7898'))
self.check_aliases('dryad.title', new_aliases, ("title", 'data from: can clone size serve as a proxy for clone age? an exploration using microsatellite divergence in populus tremuloides'))
def first(self):
if self.none_count >= 3:
if self.max_items:
if self.current_item > self.max_items:
return None
# Generate a mock item with initial alias ('mock', id)
item = ItemFactory.make()
item.id = self.current_item
item.aliases['mock'] = str(item.id)
self.items[self.current_item] = item
return item
else:
self.none_count += 1
return None
def checkWikipedia(self):
# Test reading data from Wikipedia
item = ItemFactory.make(self.mydao, app.config["PROVIDERS"])
item.aliases.add_alias("doi", "10.1371/journal.pcbi.1000361")
#item.aliases.add_alias("url", "http://cottagelabs.com")
item_aliases_list = item.aliases.get_aliases_list()
wikipedia = Wikipedia()
# No aliases for wikipedia
#new_aliases = wikipedia.aliases(item_aliases_list)
new_metrics = wikipedia.metrics(item_aliases_list)
self.check_metric('wikipedia:mentions', new_metrics['wikipedia:mentions'], 1)
def create_item(namespace, nid):
logger.debug("In create_item with alias" + str((namespace, nid)))
item = ItemFactory.make()
# set this so we know when it's still updating later on
myredis.set_num_providers_left(item["_id"], ProviderFactory.num_providers_with_metrics(default_settings.PROVIDERS))
item["aliases"][namespace] = [nid]
mydao.save(item)
myredis.add_to_alias_queue(item["_id"], item["aliases"])
logger.info("Created new item '{id}' with alias '{alias}'".format(id=item["_id"], alias=str((namespace, nid))))
try:
return item["_id"]
except AttributeError:
abort(500)
def create_item(namespace, id):
'''Utility function to keep DRY in single/multiple item creation endpoins'''
item = ItemFactory.make(mydao, app.config["PROVIDERS"])
item.aliases.add_alias(namespace, id)
## FIXME - see issue 86
## Should look up this namespace and id and see if we already have a tiid
## If so, return its tiid with a 200.
# right now this makes a new item every time, creating many dupes
# does not filter by whether we actually can process the namespace, since
# we may be able to someday soon. It's user's job to not pass in junk.
item.save()
try:
return item.id
except AttributeError:
abort(500)
def checkGithub(self):
item = ItemFactory.make(self.mydao, app.config["PROVIDERS"])
github = Github()
members = github.member_items("egonw")
self.check_members('github.github_user', members,
[('github', ('egonw', 'blueobelisk.debian')),
('github', ('egonw', 'ron')),
('github', ('egonw', 'pubchem-cdk')),
('github', ('egonw', 'org.openscience.cdk')),
('github', ('egonw', 'java-rdfa')),
('github', ('egonw', 'cdk')),
('github', ('egonw', 'RobotDF')),
('github', ('egonw', 'egonw.github.com')),
('github', ('egonw', 'knime-chemspider')),
('github', ('egonw', 'gtd')),
('github', ('egonw', 'cheminfbenchmark')),
('github', ('egonw', 'cdk-taverna')),
('github', ('egonw', 'groovy-jcp')),
('github', ('egonw', 'jnchem')),
('github', ('egonw', 'acsrdf2010')),
('github', ('egonw', 'Science-3.0')),
('github', ('egonw', 'SNORQL')),
('github', ('egonw', 'ctr-cdk-groovy')),
('github', ('egonw', 'CDKitty')),
('github', ('egonw', 'rednael')),
('github', ('egonw', 'de.ipbhalle.msbi')),
('github', ('egonw', 'collaborative.cheminformatics')),
('github', ('egonw', 'xws-taverna')),
('github', ('egonw', 'cheminformatics.classics')),
('github', ('egonw', 'chembl.rdf')),
('github', ('egonw', 'blueobelisk.userscript')),
('github', ('egonw', 'ojdcheck')),
('github', ('egonw', 'nmrshiftdb-rdf')),
('github', ('egonw', 'bioclipse.ons')),
('github', ('egonw', 'medea_bmc_article'))])
item.aliases.add_alias("github", "egonw,gtd")
item_aliases_list = item.aliases.get_aliases_list()
new_metrics = github.metrics(item_aliases_list)
self.check_metric('github:forks', new_metrics['github:forks'], 0)
self.check_metric('github:watchers', new_metrics['github:watchers'], 7)
def create_or_find_items_from_aliases(clean_aliases):
tiids = []
items = []
for alias in clean_aliases:
(namespace, nid) = alias
existing_tiid = get_tiid_by_alias(namespace, nid)
if existing_tiid:
tiids.append(existing_tiid)
logger.debug(
"found an existing tiid ({tiid}) for alias {alias}".format(tiid=existing_tiid, alias=str(alias))
)
else:
logger.debug("alias {alias} isn't in the db; making a new item for it.".format(alias=alias))
item = ItemFactory.make()
item["aliases"][namespace] = [nid]
items.append(item)
tiids.append(item["_id"])
return (tiids, items)