def start(self):
cr = ConfigReader()
self.workflow = Workflow([
IntroStep(
'<h2>Welcome to SmartAnno!</h2><h4>Do you want to start from beginning or continue previous reviewing? </h4>',
name='intro'),
DBInitiater(name='db_initiator'),
DirChooser(name='choosedir'),
ReadFiles(name='readfiles'),
DocsToDB(name='save2db'),
TaskChooser(name='tasknamer'),
DataSetChooser(
name='dataset_chooser',
description='<h4>Choose which dateaset you want to use: </h4>'
),
AnnotationTypeDef(
'<h3>Annotation types:</h3><p>List all the types you want to identify below. Each type per line.<br/>If you'
'have too many types, try set up them separately, so that you won't need to choose from a long list '
'for each sample. </p>',
name='types'),
KeywordsFiltering(name='keywords'),
# PreviousNextIntSlider(value=60, min=0, max=100, step=10,
# description='<h4>Percentage to Filter: </h4><p>Choose how many percent of the samples '
# 'you want to use the keywords filter.</p>', name='percent2filter'),
KeywordsUMLSExtenderSetup(name='umls_extender_setup'),
KeywordsUMLSExtender(
name='umls_extender',
sources=cr.getValue("umls/sources"),
filter_by_length=cr.getValue("umls/filter_by_length"),
filter_by_contains=cr.getValue("umls/filter_by_contains"),
max_query=cr.getValue("umls/max_query")),
KeywordsEmbeddingExtenderSetup(name='w_e_extender_setup'),
KeywordsEmbeddingExtender(name='w_e_extender', max_query=40),
ReviewRBInit(name="rb_review_init"),
ReviewRBLoop(name='rb_review'),
PreviousNextHTML(
description=
'<h2>Congratuations!</h2><h4>You have finished the initial review '
'on the rule-base preannotations. </h4>',
name='rb_review_done'),
ReviewMLInit(name='ml_review_init'),
ReviewMLLoop(name='ml_review',
ml_classifier_cls=self.ml_classifier_cls),
PreviousNextHTML(
name='finish',
description=
'<h3>Well done!</h3><h4>Now you have finished reviewing all the samples. '
)
])
self.workflow.start(False)
pass
def testRBLoop(self):
logging.getLogger().setLevel(logging.WARN)
ConfigReader()
wf = Workflow()
rb = ReviewRBInit(name="rb_review_init")
wf.append(rb)
rv = ReviewRBLoop(name='rb_review')
wf.append(rv)
wf.append(
PreviousNextHTML(
'<h2>Welcome to SmartAnno!</h2><h4>First, let's import txt data from a directory. </h4>',
name='intro'))
wf.filters = {'TypeA': ['heart'], 'TypeB': ['exam']}
wf.types = ['TypeA', 'TypeB']
wf.task_id = 1
wf.umls_extended = {}
wf.we_extended = {}
wf.dao = Dao('sqlite+pysqlite:///data/demo.sqlite',
sqlalchemy_dao.POOL_DISABLED)
wf.start()
if len(rb.branch_buttons) == 0:
# if no records in the db, the optional buttons won't show
rb.sample_size_input.value = 3
rb.complete()
wf.start()
print([doc.DOC_ID for doc in rb.data['docs']])
print([
anno.REVIEWED_TYPE for anno in wf.steps[0].data['annos'].values()
])
rb.sample_size_input.value = 1
rb.navigate(rb.branch_buttons[1])
pass
wf.task_name = 'language'
wf.append(
AnnotationTypeDef(
'<h3>Annotation types:</h3><p>List all the types you want to identify below. Each type per line.<br/>If you'
'have too many types, try set up them separately, so that you won't need to choose from a long list '
'for each sample. </p>',
name='types'))
wf.append(KeywordsFiltering(name='keywords'))
wf.append(
DataSetChooser(
name='dataset_chooser',
description='<h4>Choose which dateaset you want to use: </h4>'))
rb = ReviewRBInit(name="rb_review_init")
wf.append(rb)
rv = ReviewRBLoop(name='rb_review', rush_rule='../conf/rush_rules.tsv')
wf.append(rv)
wf.append(
PreviousNextHTML(
'<h2>Congratuations!</h2><h4>You have finished the initial review on the rule-base preannotations. </h4>',
name='intro'))
wf.append(ReviewMLInit(name='ml_review_init'))
wf.append(
ReviewMLLoop(name='ml_review', ml_classifier_cls=LogisticBOWClassifier))
wf.start()
wf.steps[0].complete()
wf.steps[1].complete()
wf.steps[2].toggle.value = 'n2c2_sents'
wf.steps[2].complete()
wf.steps[3].sample_size_input.value = 100
from SmartAnno.utils.ConfigReader import ConfigReader
from SmartAnno.gui.PreviousNextWidgets import PreviousNextHTML
from SmartAnno.gui.Workflow import Workflow
from SmartAnno.utils.IntroStep import IntroStep
ConfigReader('../conf/smartanno_conf2.json')
intro = IntroStep(
'<h2>Welcome to SmartAnno!</h2><h4>First, let's import txt data from a directory. </h4>',
name='intro')
wf = Workflow([
intro,
PreviousNextHTML(
name='finish',
description=
'<h3>Well done!</h3><h4>Now you have finished reviewing all the samples. '
)
])
wf.start()
intro.navigate(intro.branch_buttons[0])