Пример #1
0
def run_trials(run_id):
	""" Returns the trials from a given run-id.
	You can filter the returned trias by supplying 'intv' for intervention
	types to be included and 'phases' for trial phases to be active """
	
	# from pycallgraph import PyCallGraph
	# from pycallgraph.output import GraphvizOutput
	# with PyCallGraph(output=GraphvizOutput()):
	runner = Runner.get(run_id)
	if runner is None:
		bottle.abort(404)
	
	if not runner.done:
		bottle.abort(400, "Trials are not yet available")
	
	# get request vars
	intv = bottle.request.query.intv
	intv = intv.split('|') if intv else []
	phases = bottle.request.query.phases
	phases = phases.split('|') if phases else []
	reload_phases = bottle.request.query.reload_phases
	
	ret_dict = {
		'trials': runner.trials_json(intv, phases)
	}
	if reload_phases:
		ret_dict['drug_phases'] = runner.trial_phases(intv)
	
	return json.dumps(ret_dict)
Пример #2
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def run_trials(run_id):
    """ Returns the trials from a given run-id.
	You can filter the returned trias by supplying 'intv' for intervention
	types to be included and 'phases' for trial phases to be active """

    # from pycallgraph import PyCallGraph
    # from pycallgraph.output import GraphvizOutput
    # with PyCallGraph(output=GraphvizOutput()):
    runner = Runner.get(run_id)
    if runner is None:
        bottle.abort(404)

    if not runner.done:
        bottle.abort(400, "Trials are not yet available")

    # get request vars
    intv = bottle.request.query.intv
    intv = intv.split('|') if intv else []
    phases = bottle.request.query.phases
    phases = phases.split('|') if phases else []
    reload_phases = bottle.request.query.reload_phases

    ret_dict = {'trials': runner.trials_json(intv, phases)}
    if reload_phases:
        ret_dict['drug_phases'] = runner.trial_phases(intv)

    return json.dumps(ret_dict)
Пример #3
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def trial_progress(run_id):
    """ Returns text status from the file corresponding to the given run-id, if
	it's missing returns a 404. """

    runner = Runner.get(run_id)
    if runner is None:
        bottle.abort(404)

    return runner.status
Пример #4
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def trial_progress(run_id):
	""" Returns text status from the file corresponding to the given run-id, if
	it's missing returns a 404. """
	
	runner = Runner.get(run_id)
	if runner is None:
		bottle.abort(404)
	
	return runner.status
Пример #5
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def run_overview(run_id):
    """ Overview results for a run. """

    runner = Runner.get(run_id)
    if runner is None:
        bottle.abort(404)

    try:
        overview = runner.overview()
    except Exception as e:
        bottle.abort(400, e)

    return json.dumps(overview)
Пример #6
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def run_overview(run_id):
	""" Overview results for a run. """
	
	runner = Runner.get(run_id)
	if runner is None:
		bottle.abort(404)
	
	try:
		overview = runner.overview()
	except Exception as e:
		bottle.abort(400, e)
	
	return json.dumps(overview)
Пример #7
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#!/usr/bin/python
# -*- coding: utf-8 -*-

import logging
from ClinicalTrials.runner import Runner

logging.basicConfig(level=logging.DEBUG)

# setup the runner
run = Runner(666, 'run-alternative')
run.catch_exceptions = False
#run.limit = 3
run.discard_cached = False

run.term = "pulmonary arterial hypertension"
# run.term = "juvenile rheumatoid arthritis"
run.analyze_eligibility = False
run.analyze_keypaths = set([
    'condition_browse', 'intervention_browse', 'intervention', 'keyword',
    'primary_outcome', 'arm_group'
])


# create a callback
def cb(success, trials):
    if success:

        # loop trials
        for trial in trials:
            doc = trial.doc or {}
            print 'Trial "%s"  [ %s ]' % (trial.title, trial.nct)
Пример #8
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def trials_filter_by(run_id, filter_by):
    runner = Runner.get(run_id)
    if runner is None:
        bottle.abort(404)

    if not runner.done:
        bottle.abort(400, "Trial results are not available")

    ncts = runner.get_ncts(restrict='none')
    sess = _get_session()
    run_data = sess.get('runs', {}).get(run_id, {})

    # demographics - get age and gender
    if 'demographics' == filter_by:
        f_gender = run_data.get('gender')
        f_age = int(run_data.get('age', 0))

        for tpl in ncts:
            nct = tpl[0]
            reason = tpl[1] if len(tpl) > 1 else None

            if not reason:
                trial = Trial(nct)
                trial.load()

                # filter gender
                if f_gender:
                    if 'male' == f_gender:
                        if trial.eligibility.gender == 2:
                            reason = "Limited to women"
                    else:
                        if trial.eligibility.gender == 1:
                            reason = "Limited to men"

                # filter age
                if f_age > 0:
                    if trial.eligibility.min_age and trial.eligibility.min_age > f_age:
                        reason = "Patient is too young (min age %d)" % trial.eligibility.min_age
                    elif trial.eligibility.max_age and trial.eligibility.max_age < f_age:
                        reason = "Patient is too old (max age %d)" % trial.eligibility.max_age

            # TODO: REFACTOR into runner class!
            if reason:
                runner.write_trial_reason(nct, reason)

        runner.commit_transactions()

    # problems (only if NLP is on)
    elif 'problems' == filter_by:
        if USE_NLP:
            probs = problems().get('problems', [])

            # extract snomed codes from patient's problem list
            snomed = SNOMEDLookup()
            exclusion_codes = []
            for problem in probs:
                snomed_url = problem.get('sp:problemName',
                                         {}).get('sp:code', {}).get('@id')
                if snomed_url is not None:
                    snomed_code = os.path.basename(snomed_url)
                    exclusion_codes.append(snomed_code)

            # look at trial criteria
            for tpl in ncts:
                nct = tpl[0]
                reason = tpl[1] if len(tpl) > 1 else None

                # if we already have a reason, this trial has already been filtered
                if not reason:
                    trial = Trial(nct)
                    trial.load()

                    # exclusion criterion matched
                    if trial.filter_snomed(exclusion_codes) is not None:
                        reason = 'Matches exclusion criterium "%s" (SNOMED %s)' % (
                            snomed.lookup_code_meaning(match, True,
                                                       True), match)
                        break

                # TODO: REFACTOR
                # runner.write_trial_reason(nct, reason)

    # unknown filtering property
    else:
        return '{"error": "We can not filter by %s"}' % filter_by

    return '{"status": "ok"}'
Пример #9
0
def find_trials():
    """ Initiates the chain to find trials for the given condition or search-
	term. Supply with parameters:
	- "cond" or "term", the prior taking precedence
	- "gender" ('male' or 'female')
	- "age" (in years)
	- "latlng", comma-separated latitude and longituted of the patient
	- "remember_input" if the condition or term should be stored in the session
	
	This method forks off and prints the status to a file which can be read by
	calling /trials_status/<run-id>. "run-id" is returned from this call.
	"""

    # get the runner
    run_id = datetime.now().isoformat()
    runner = Runner.get(run_id)
    if runner is None:
        runner = Runner(run_id, "run-server")
        runner.in_background = True

    # configure
    cond = bottle.request.query.get('cond')
    term = bottle.request.query.get('term')
    if cond:
        cond = re.sub(r'\s+\((disorder|finding)\)', '', cond)
        runner.condition = cond
    elif term:
        term = re.sub(r'\s+-(\w+)', r' NOT \1', term)
        term = re.sub(r'\s*([^\w\d])\s+([^-])', r' AND \2', term)
        runner.term = term
    else:
        bottle.abort(400, 'You need to specify "cond" or "term"')

    # latitude and longitude
    latlng = bottle.request.query.get('latlng')
    if latlng is None or 0 == len(latlng):
        latlng = '42.358,-71.06'  # default to Boston
    parts = latlng.split(',', 2)
    if parts is None or 2 != len(parts):
        bottle.abort(400, '"latlng" must be two numbers separated by a comma')

    lat = parts[0]
    lng = parts[1]
    runner.reference_location = (lat, lng)

    # store in session
    age = bottle.request.query.get('age')

    sess = _get_session()
    runs = sess.get('runs', {})
    runs[run_id] = {
        'cond': cond,
        'gender': bottle.request.query.get('gender'),
        'age': int(age) if age else None,
        'latlng': latlng
    }
    sess['runs'] = runs

    if 'true' == bottle.request.query.get('remember_input'):
        if cond or term:
            sess['last_manual_input'] = cond or term
        elif 'last_manual_input' in sess:
            del sess['last_manual_input']

    # launch and return id
    runner.run([
        'id', 'acronym', 'keyword', 'brief_title', 'official_title',
        'brief_summary', 'overall_contact', 'eligibility', 'location',
        'attributes', 'intervention', 'intervention_browse', 'phase',
        'study_design', 'primary_outcome'
    ])

    return run_id
Пример #10
0
def trials_filter_by(run_id, filter_by):
	runner = Runner.get(run_id)
	if runner is None:
		bottle.abort(404)
	
	if not runner.done:
		bottle.abort(400, "Trial results are not available")
	
	ncts = runner.get_ncts(restrict='none')
	sess = _get_session()
	run_data = sess.get('runs', {}).get(run_id, {})
	
	# demographics - get age and gender
	if 'demographics' == filter_by:
		f_gender = run_data.get('gender')
		f_age = int(run_data.get('age', 0))
		
		for tpl in ncts:
			nct = tpl[0]
			reason = tpl[1] if len(tpl) > 1 else None
			
			if not reason:
				trial = Trial(nct)
				trial.load()
				
				# filter gender
				if f_gender:
					if 'male' == f_gender:
						if trial.eligibility.gender == 2:
							reason = "Limited to women"
					else:
						if trial.eligibility.gender == 1:
							reason = "Limited to men"
				
				# filter age
				if f_age > 0:
					if trial.eligibility.min_age and trial.eligibility.min_age > f_age:
						reason = "Patient is too young (min age %d)" % trial.eligibility.min_age
					elif trial.eligibility.max_age and trial.eligibility.max_age < f_age:
						reason = "Patient is too old (max age %d)" % trial.eligibility.max_age
			
			# TODO: REFACTOR into runner class!
			if reason:
				runner.write_trial_reason(nct, reason)
		
		runner.commit_transactions()
	
	# problems (only if NLP is on)
	elif 'problems' == filter_by:
		if USE_NLP:
			probs = problems().get('problems', [])
			
			# extract snomed codes from patient's problem list
			snomed = SNOMEDLookup()
			exclusion_codes = []
			for problem in probs:
				snomed_url = problem.get('sp:problemName', {}).get('sp:code', {}).get('@id')
				if snomed_url is not None:
					snomed_code = os.path.basename(snomed_url)
					exclusion_codes.append(snomed_code)
			
			# look at trial criteria
			for tpl in ncts:
				nct = tpl[0]
				reason = tpl[1] if len(tpl) > 1 else None
				
				# if we already have a reason, this trial has already been filtered
				if not reason:
					trial = Trial(nct)
					trial.load()
					
					# exclusion criterion matched
					if trial.filter_snomed(exclusion_codes) is not None:
						reason = 'Matches exclusion criterium "%s" (SNOMED %s)'  % (snomed.lookup_code_meaning(match, True, True), match)
						break
				
				# TODO: REFACTOR
				# runner.write_trial_reason(nct, reason)
	
	# unknown filtering property
	else:
		return '{"error": "We can not filter by %s"}' % filter_by
	
	return '{"status": "ok"}'
Пример #11
0
def find_trials():
	""" Initiates the chain to find trials for the given condition or search-
	term. Supply with parameters:
	- "cond" or "term", the prior taking precedence
	- "gender" ('male' or 'female')
	- "age" (in years)
	- "latlng", comma-separated latitude and longituted of the patient
	- "remember_input" if the condition or term should be stored in the session
	
	This method forks off and prints the status to a file which can be read by
	calling /trials_status/<run-id>. "run-id" is returned from this call.
	"""
	
	# get the runner
	run_id = datetime.now().isoformat()
	runner = Runner.get(run_id)
	if runner is None:
		runner = Runner(run_id, "run-server")
		runner.in_background = True
	
	# configure
	cond = bottle.request.query.get('cond')
	term = bottle.request.query.get('term')
	if cond:
		cond = re.sub(r'\s+\((disorder|finding)\)', '', cond)
		runner.condition = cond
	elif term:
		term = re.sub(r'\s+-(\w+)', r' NOT \1', term)
		term = re.sub(r'\s*([^\w\d])\s+([^-])', r' AND \2', term)
		runner.term = term
	else:
		bottle.abort(400, 'You need to specify "cond" or "term"')
	
	# latitude and longitude
	latlng = bottle.request.query.get('latlng')
	if latlng is None or 0 == len(latlng):
		latlng = '42.358,-71.06'		# default to Boston
	parts = latlng.split(',', 2)
	if parts is None or 2 != len(parts):
		bottle.abort(400, '"latlng" must be two numbers separated by a comma')
	
	lat = parts[0]
	lng = parts[1]
	runner.reference_location = (lat, lng)
	
	# store in session
	age = bottle.request.query.get('age')
	
	sess = _get_session()
	runs = sess.get('runs', {})
	runs[run_id] = {
		'cond': cond,
		'gender': bottle.request.query.get('gender'),
		'age': int(age) if age else None,
		'latlng': latlng
	}
	sess['runs'] = runs
	
	if 'true' == bottle.request.query.get('remember_input'):
		if cond or term:
			sess['last_manual_input'] = cond or term
		elif 'last_manual_input' in sess:
			del sess['last_manual_input']
	
	# launch and return id
	runner.run(['id', 'acronym', 'keyword', 'brief_title', 'official_title', 'brief_summary', 'overall_contact', 'eligibility', 'location', 'attributes', 'intervention', 'intervention_browse', 'phase', 'study_design', 'primary_outcome'])
	
	return run_id
Пример #12
0
#!/usr/bin/python
# -*- coding: utf-8 -*-

import logging
from ClinicalTrials.runner import Runner

logging.basicConfig(level=logging.DEBUG)

# setup the runner
run = Runner(666, 'run-alternative')
run.catch_exceptions = False
#run.limit = 3
run.discard_cached = False

run.term = "pulmonary arterial hypertension"
# run.term = "juvenile rheumatoid arthritis"
run.analyze_eligibility = False
run.analyze_keypaths = set(['condition_browse', 'intervention_browse', 'intervention', 'keyword', 'primary_outcome', 'arm_group'])

# create a callback
def cb(success, trials):
	if success:
		
		# loop trials
		for trial in trials:
			doc = trial.doc or {}
			print 'Trial "%s"  [ %s ]' % (trial.title, trial.nct)
			print '    keyw: %s' % '; '.join(doc.get('keyword') or [])
			print '    cond: %s' % '; '.join(doc.get('condition_browse', {}).get('mesh_term', []))
			print '    intr: %s' % '; '.join(doc.get('intervention_browse', {}).get('mesh_term', []))
			print '    intn: %s' % "\n    ----> ".join([p.get('intervention_name') or '' for p in doc.get('intervention', [])])
Пример #13
0
from ClinicalTrials.runner import Runner
from ClinicalTrials.umls import UMLSLookup
from ClinicalTrials.ctakes import cTAKES
from ClinicalTrials.metamap import MetaMap
from ClinicalTrials.nltktags import NLTKTags

logging.basicConfig(level=logging.DEBUG)

# setup NLP pipelines
nlp_ctakes = cTAKES()
nlp_metamap = MetaMap()
nlp_nltkt = NLTKTags()
#nlp_nltkt.cleanup = False

# setup the runner
run = Runner(666, 'run-test')
run.catch_exceptions = False
#run.limit = 3
run.discard_cached = False

run.term = "juvenile rheumatoid arthritis"
run.analyze_eligibility = False
run.analyze_keypaths = set(['brief_summary'])
# run.analyze_keypaths = set(['eligibility_inclusion', 'eligibility_exclusion', 'brief_summary', 'detailed_description'])

run.add_pipeline(nlp_metamap)
# run.add_pipeline(nlp_nltkt)

# create a callback
def cb(success, trials):
	if success:
Пример #14
0
    if term is None or len(term) < 1:
        term = "diabetic cardiomyopathy"

        # recruiting = None
        # if _use_recruiting:
        # 	recruiting = raw_input("Recruiting: [no] ")
        # 	if recruiting is None or len(recruiting) < 1:
        # 		recruiting = False
        # 	else:
        # 		recruiting = recruiting[:1] is 'y' or recruiting[:1] is 'Y'

        # run the runner
    now = date.today()
    run_id = now.isoformat()
    run_dir = "run-%s-%s" % (re.sub(r"[^\w\d\-]+", "_", term.lower()), run_id)
    runner = Runner(run_id, run_dir)
    runner.run_ctakes = True
    runner.run_metamap = True
    runner.term = term
    runner.log_status = True
    runner.run()

    # generate HTML report
    if _generate_report:
        print "Generating report..."
        recr_status = ""
        if _use_recruiting:
            recr_status = ", recruiting" if recruiting else ", not recruiting"

        html = """<html>
		<head>
Пример #15
0
    if term is None or len(term) < 1:
        term = 'diabetic cardiomyopathy'

    # recruiting = None
    # if _use_recruiting:
    # 	recruiting = raw_input("Recruiting: [no] ")
    # 	if recruiting is None or len(recruiting) < 1:
    # 		recruiting = False
    # 	else:
    # 		recruiting = recruiting[:1] is 'y' or recruiting[:1] is 'Y'

    # run the runner
    now = date.today()
    run_id = now.isoformat()
    run_dir = "run-%s-%s" % (re.sub(r'[^\w\d\-]+', '_', term.lower()), run_id)
    runner = Runner(run_id, run_dir)
    runner.run_ctakes = True
    runner.run_metamap = True
    runner.term = term
    runner.log_status = True
    runner.run()

    # generate HTML report
    if _generate_report:
        print 'Generating report...'
        recr_status = ''
        if _use_recruiting:
            recr_status = ', recruiting' if recruiting else ', not recruiting'

        html = """<html>
		<head>