def on_worker_init(**_):
global bots
global friendly_bots
log.info("Loading the robots...")
# pico span bot must be loaded first i have *no* idea why...
print("LOADING ROBOTS")
bots = {
"pico_span_bot": PICOSpanRobot(),
"bias_bot": BiasRobot(top_k=3),
"pico_bot": PICORobot(),
"pubmed_bot": PubmedRobot(),
# "ictrp_bot": ICTRPRobot(),
"rct_bot": RCTRobot(),
#"pico_viz_bot": PICOVizRobot(),
"punchline_bot": PunchlinesBot(),
"sample_size_bot": SampleSizeBot(),
"bias_ab_bot": BiasAbRobot()
}
friendly_bots = {
"pico_span_bot": "Extracting PICO text from title/abstract",
"bias_bot": "Assessing risks of bias",
"pico_bot": "Extracting PICO information from full text",
"rct_bot": "Assessing study design (is it an RCT?)",
"sample_size_bot": "Extracting sample size",
"punchline_bot": "Extracting main conclusions",
"pubmed_bot": "Looking up meta-data in PubMed",
"bias_ab_bot": "Assessing bias from abstract"
}
print("ROBOTS ALL LOADED")
log.info("Robots loaded successfully! Ready...")
def on_worker_init(**_):
global bots
log.info("Loading the robots...")
bots = {
"bias_bot": BiasRobot(top_k=3),
"pico_bot": PICORobot(),
"pubmed_bot": PubmedRobot(),
# "ictrp_bot": ICTRPRobot(),
"rct_bot": RCTRobot(),
#"pico_viz_bot": PICOVizRobot(),
"sample_size_bot": SampleSizeBot()
}
log.info("Robots loaded successfully! Ready...")
class TestPubmedRobot(unittest.TestCase):
pr = PubmedRobot()
ex_file = ex_path + "pubmedtest.json"
def test_annotate(self):
''' test for PubmedRobot.annotate(data) '''
md = MultiDict()
with open(self.ex_file) as testdata:
data = json.load(testdata)
test = data["annotate"]
md.data["gold"]["title"] = data["title"]
out = self.pr.annotate(md)
self.assertEqual(out.data["pubmed"], test)
def test_query_pubmed(self):
''' test for PubmedRobot.query_pubmed(pmid) '''
with open(self.ex_file) as testdata:
data = json.load(testdata)
pmid = data["pmid"]
q = self.pr.query_pubmed(pmid)
with open(os.path.dirname(__file__) + "/ex/query.json") as f:
query = json.load(f)
self.assertEqual(q, query)
def test_short_citation(self):
''' test for PubmedRobot.short_citation(data) '''
data = {
"authors": [{
"lastname": "Bellman",
"initials": "R"
}, {
"lastname": "Ford",
"initials": "L"
}],
"year":
1958
}
short_cite = self.pr.short_citation(data)
self.assertEqual(short_cite, "Bellman R, 1958")
app.secret_key = os.environ.get("SECRET", "super secret key")
# setting max file upload size 100 mbs
app.config['MAX_CONTENT_LENGTH'] = 100 * 1024 * 1024
csrf = CsrfProtect()
csrf.init_app(app)
######
## default annotation pipeline defined here
######
log.info("Loading the robots...")
bots = {
"bias_bot": BiasRobot(top_k=3),
"pico_bot": PICORobot(),
"pubmed_bot": PubmedRobot(),
# "ictrp_bot": ICTRPRobot(),
"rct_bot": RCTRobot(),
"pico_viz_bot": PICOVizRobot()
}
# "mendeley_bot": MendeleyRobot()}
log.info("Robots loaded successfully! Ready...")
#####
## connect to and set up database
#####
rr_sql_conn = sqlite3.connect(
robotreviewer.get_data('uploaded_pdfs/uploaded_pdfs.sqlite'),
detect_types=sqlite3.PARSE_DECLTYPES)
c = rr_sql_conn.cursor()