class RelatedOrders(BaseDynamicData):
"""Simple script to (dynamically) relay query and result data
from the ItemRecommendation module in URL request then HTML table format.
"""
def __init__(self):
BaseDynamicData.__init__(self)
self.requestData["searchStr"] = ""
self.requestData["analysisStatus"] = "1"
self.requestData["sim_patient_id"] = ""
self.requestData["sim_time"] = ""
self.requestData["sourceTables"] = "stride_order_proc,stride_order_med"
# Default comma-separated list of source tables to expect orders to reside in
self.requestData["queryItemIds"] = ""
self.requestData["targetItemIds"] = ""
self.requestData["excludeItemIds"] = ""
self.requestData["excludeCategoryIds"] = ""
self.requestData["timeDeltaMax"] = "86400"
# Look for recommendations likely within 24 hours
self.requestData["sortField"] = ""
self.requestData["enableRecommender"] = "True"
# By default, asssume recommender is enabled
self.requestData["displayFields"] = ""
#"prevalence","PPV","RR","P-YatesChi2"
self.requestData["sortReverse"] = "True"
self.requestData["nPreCols"] = "1"
self.requestData["groupByCategory"] = "True"
self.requestData["resultCount"] = "10"
# Default for related order search
self.requestData["invertQuery"] = ""
self.requestData["showCounts"] = ""
self.requestData["countPrefix"] = "patient_"
self.requestData["aggregationMethod"] = "weighted"
self.requestData["title"] = "Order Search Results"
self.requestData["fieldHeaders"] = ""
self.requestData[
"dataRows"] = '<tr><td colspan=100 align=center height=200><img src="../../resource/ajax-loader.gif"></td></tr>'
self.addHandler("searchStr", RelatedOrders.action_orderSearch.__name__)
self.addHandler("RelatedOrders", RelatedOrders.action_default.__name__)
def action_orderSearch(self):
"""Search for orders by query string"""
manager = SimManager()
query = ClinicalItemQuery()
query.parseParams(self.requestData)
query.sourceTables = self.requestData["sourceTables"].split(",")
results = manager.clinicalItemSearch(query)
lastModel = None
for dataModel in results:
dataModel["controls"] = CONTROLS_TEMPLATE % dataModel
dataModel["nPreCols"] = self.requestData["nPreCols"]
dataModel["category_description.format"] = ""
if lastModel is None or lastModel[
"category_description"] != dataModel[
"category_description"]:
dataModel[
"category_description.format"] = "<b>%s</b>" % dataModel[
"category_description"]
# Only show category if new
lastModel = dataModel
colNames = ["controls", "description"]
# "name" for order code. ,"category_description.format"
lastModel = None
htmlLines = list()
for dataModel in results:
newCategory = (lastModel is None
or lastModel["category_description"] !=
dataModel["category_description"])
showCategory = (self.requestData["groupByCategory"]
and newCategory)
# Limit category display if many repeats
if showCategory:
htmlLines.append(CATEGORY_HEADER_TEMPLATE % dataModel)
htmlLines.append(
self.formatRowHTML(dataModel, colNames, showCategory))
lastModel = dataModel
self.requestData["dataRows"] = str.join("\n", htmlLines)
def action_default(self):
"""Look for related orders by association / recommender methods"""
# If patient is specified then modify query and exclusion list based on items already ordered for patient
recentItemIds = set()
if self.requestData["sim_patient_id"]:
patientId = int(self.requestData["sim_patient_id"])
simTime = int(self.requestData["sim_time"])
# Track recent item IDs (orders, diagnoses, unlocked results, etc. that related order queries will be based off of)
manager = SimManager()
recentItemIds = manager.recentItemIds(patientId, simTime)
# Recommender Instance to test on
self.recommender = ItemAssociationRecommender()
self.recommender.dataManager.dataCache = webDataCache
# Allow caching of data for rapid successive queries
query = RecommenderQuery()
if self.requestData["sortField"] == "":
self.requestData["sortField"] = "P-YatesChi2-NegLog"
# P-Fisher-NegLog should yield better results, but beware, much longer to calculate
query.parseParams(self.requestData)
if len(query.excludeItemIds) == 0:
query.excludeItemIds = self.recommender.defaultExcludedClinicalItemIds(
)
if len(query.excludeCategoryIds) == 0:
query.excludeCategoryIds = self.recommender.defaultExcludedClinicalItemCategoryIds(
)
#query.fieldList.extend( ["prevalence","PPV","RR"] );
displayFields = list()
if self.requestData["displayFields"] != "":
displayFields = self.requestData["displayFields"].split(",")
# Exclude items already ordered for the patient from any recommended list
query.excludeItemIds.update(recentItemIds)
if not query.queryItemIds: # If no specific query items specified, then use the recent patient item IDs
query.queryItemIds.update(recentItemIds)
recommendedData = self.recommender(query)
if len(recommendedData) > 0:
# Denormalize results with links to clinical item descriptions
self.recommender.formatRecommenderResults(recommendedData)
# Display fields should append Format suffix to identify which version to display, but use original for header labels
(self.requestData["fieldHeaders"], displayFieldsFormatSuffixed
) = self.prepareDisplayHeaders(displayFields)
# Format for HTML and add a control field for interaction with the data
for dataModel in recommendedData:
self.prepareResultRow(dataModel, displayFields)
# Try organize by category
if self.requestData["groupByCategory"]:
recommendedData = self.recommender.organizeByCategory(
recommendedData)
colNames = ["controls"]
# "name" for code. ,"category_description"
colNames.extend(displayFieldsFormatSuffixed)
colNames.extend(["description"])
lastModel = None
htmlLines = list()
for dataModel in recommendedData:
newCategory = (lastModel is None
or lastModel["category_description"] !=
dataModel["category_description"])
showCategory = (self.requestData["groupByCategory"]
and newCategory)
# Limit category display if many repeats
if showCategory:
htmlLines.append(CATEGORY_HEADER_TEMPLATE % dataModel)
htmlLines.append(
self.formatRowHTML(dataModel, colNames, showCategory))
lastModel = dataModel
self.requestData["dataRows"] = str.join("\n", htmlLines)
def prepareDisplayHeaders(self, displayFields):
showCounts = (self.requestData["showCounts"].lower()
not in FALSE_STRINGS)
fieldHeadersHTML = ""
for displayField in displayFields:
fieldHeadersHTML += '<th nowrap>' + displayField + '</th>'
if showCounts:
fieldHeadersHTML += '<th>' + str.join('</th><th>',
CORE_FIELDS) + '</th>'
displayFieldsFormatSuffixed = list()
for field in displayFields:
displayFieldsFormatSuffixed.append('%sFormat' % field)
if showCounts:
for field in CORE_FIELDS:
displayFieldsFormatSuffixed.append('%sFormat' % field)
return (fieldHeadersHTML, displayFieldsFormatSuffixed)
def prepareResultRow(self, dataModel, displayFields):
dataModel["controls"] = CONTROLS_TEMPLATE % dataModel
dataModel["nPreCols"] = len(displayFields) + 1
# Track spacer columns leading up to order description. +1 for control column
dataModel["name"] = dataModel["name"].replace(",", "-")
if "nB" in dataModel:
if "nAB" not in dataModel:
# Baseline query without query items, use matching numbers to ensure calculations will have something to process
dataModel["nAB"] = dataModel["nB"]
dataModel["nA"] = dataModel["N"]
nAB = dataModel["nAB"]
nA = dataModel["nA"]
nB = dataModel["nB"]
N = dataModel["N"]
contStats = ContingencyStats(nAB, nA, nB, N)
contStats.normalize(truncateNegativeValues=False)
for field in displayFields:
if field not in dataModel:
# Unavailable field, see if it is a derived field that can be calculated
dataModel[field] = contStats[field]
if field in CORE_FIELDS:
pass
elif field in PERCENT_FIELDS:
# Format as a percentage
dataModel["%sFormat" %
field] = "%d%%" % (dataModel[field] * 100)
elif abs(dataModel[field]) < 0.01:
# Allow formatting for very small values
dataModel["%sFormat" % field] = "%.0e" % dataModel[field]
elif abs(dataModel[field]) < 1:
# Smaller value, show more significant digits
dataModel["%sFormat" % field] = "%.2f" % dataModel[field]
else:
# Default just format as limited floating point values
dataModel["%sFormat" % field] = "%.1f" % dataModel[field]
for field in CORE_FIELDS:
# Count fields express as integers, assuming available at all
if field in BASELINE_FIELDS:
dataModel["%sFormat" % field] = "%d" % dataModel[field]
else:
# May have small virtual counts from derived scenarios
if dataModel[field] > 10:
dataModel["%sFormat" % field] = "%.1f" % dataModel[field]
else:
dataModel["%sFormat" % field] = "%.2f" % dataModel[field]
def formatRowHTML(self, dataModel, colNames, showCategory=True):
"""Specific formatting for row data elements
"""
htmlList = list()
htmlList.append('<tr valign=top>')
for col in colNames:
if col == "category_description": # Blank out repeat categories
if showCategory:
htmlList.append(
'<td align=center><b>%(category_description)s</b></td>'
% dataModel)
else:
htmlList.append('<td></td>')
elif col == "description":
htmlList.append('<td align=left>')
htmlList.append(DESCRIPTION_TEMPLATE % dataModel)
# Only include related link if recommender is enabled
if self.requestData['enableRecommender'] == "True":
htmlList.append(RELATED_LINK_TEMPLATE % dataModel)
htmlList.append('</td>')
else:
htmlList.append('<td align=right>%s</td>' % dataModel[col])
htmlList.append('</tr>')
return str.join("\n", htmlList)
admitDxIdSectionGuidelineNameTuples = set()
# Keep track of each guideline name set
itemIdsByAdmitDxId = dict()
for admitDxId, sectionName, guidelineName, itemId, itemName, itemDescription, itemCount in resultsTable:
if admitDxId not in itemIdsByAdmitDxId:
itemIdsByAdmitDxId[admitDxId] = set()
itemIdsByAdmitDxId[admitDxId].add(itemId)
admitDxIdSectionGuidelineNameTuples.add(
(admitDxId, sectionName, guidelineName))
recommender = ItemAssociationRecommender()
for admitDxId, itemIds in itemIdsByAdmitDxId.iteritems():
print >> sys.stderr, admitDxId, len(itemIds)
recQuery = RecommenderQuery()
recQuery.excludeItemIds = recommender.defaultExcludedClinicalItemIds()
recQuery.excludeCategoryIds = recommender.defaultExcludedClinicalItemCategoryIds(
)
recQuery.queryItemIds = [admitDxId]
recQuery.timeDeltaMax = timedelta(1)
# Within one day
recQuery.countPrefix = "patient_"
recQuery.limit = TOP_ITEM_COUNT
# Top results by P-value
recQuery.sortField = "P-YatesChi2-NegLog"
results = recommender(recQuery)
#recommender.formatRecommenderResults(results);
for result in results:
itemIds.add(result["clinical_item_id"])
#print >> sys.stderr, result["description"];