# 'delay': 10,
# 'search': 'fmri',
# 'mode': 'direct', # PLoS sends nice usable XML directly
# 'min_pmid': None
# },
# 'Journal of Neuroscience': {
# 'delay': 20,
# 'mode': 'browser',
# 'search': 'fmri',
# 'min_pmid': None,
# 'limit': 100 # We can limit to only N new articles
# }
# }
# Verbose output
ace.set_logging_level('debug')
# Create temporary output dir
output_dir = './tmp/articles'
if not os.path.exists(output_dir):
os.makedirs(output_dir)
# Initialize Scraper
scraper = Scraper(output_dir)
ids = [
"17427209", "21966352", "17475792", "21300162", "20188841", "21382560",
"14960288", "21232548", "20809855", "19651151", "21686071", "19875675",
"20816974", "21782354", "20933020", "18586110", "21499511", "22137505",
"19766936", "19580877"
]
'delay': 10,
'search': 'fmri',
'mode': 'direct', # PLoS sends nice usable XML directly
'min_pmid': None
},
'Journal of Neuroscience': {
'delay': 20,
'mode': 'browser',
'search': 'fmri',
'min_pmid': None,
'limit': 100 # We can limit to only N new articles
}
}
# Verbose output
ace.set_logging_level('debug')
# Create temporary output dir
output_dir = '/tmp/articles'
if not os.path.exists(output_dir):
os.makedirs(output_dir)
# Initialize Scraper
scraper = Scraper('/tmp/articles')
# Loop through journals and
for j, settings in journals.items():
scraper.retrieve_journal_articles(j, **settings)
# In this example we create a new DB file and process a bunch of
# articles. Note that due to copyright restrictions, articles can't
# be included in this package, so you'll need to replace PATH_TO_FILES
# with something that works.
import ace
from ace import database
# Uncomment the next line to seem more information
ace.set_logging_level("info")
# Change this to a valid path to a set of html files.
PATH_TO_FILES = "/Users/tal/tmp/html/*.html"
db = database.Database("example_db.sqlite")
db.add_articles(PATH_TO_FILES)
db.print_stats()
# In this example we create a new DB file and process a bunch of
# articles. Note that due to copyright restrictions, articles can't
# be included in this package, so you'll need to replace PATH_TO_FILES
# with something that works.
import ace
from ace import database
# Uncomment the next line to seem more information
ace.set_logging_level('info')
# Change this to a valid path to a set of html files.
PATH_TO_FILES = "/Users/tal/tmp/html/*.html"
db = database.Database('example_db.sqlite')
db.add_articles(PATH_TO_FILES)
db.print_stats()
# In this example we create a new DB file and process a bunch of
# articles. Note that due to copyright restrictions, articles can't
# be included in this package, so you'll need to replace PATH_TO_FILES
# with something that works.
import ace
from ace import database
from ace import export
from ace.database import Database, Article, Table, Activation
# Uncomment the next line to seem more information
ace.set_logging_level('info')
# Change this to a valid path to a set of html files.
cd /home/jflournoy/Documents/NeuroDebian/code/metanal/ACE
PATH_TO_FILES = "./tmp/articles/html/ids/*.html"
db = database.Database(adapter='sqlite',db_name='sqlite:///example_db.sqlite')
#db.add_articles(PATH_TO_FILES)
db.print_stats()
export.export_database(db,'exported_data_2.csv',groups=True,size=True,statistic=True)
for article in db.session.query(Article).filter(Article.tables.any()).all():
for t in article.tables:
for p in t.activations:
if isinstance(p.size, basestring):
p.size_tmp = [p.size]
elif p.size is None:
p.size_tmp = []