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epiph/app/lib/collections/patients.coffee
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patients.coffee
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class @Patient
constructor: (doc) ->
_.extend this, doc
caseManagers: ->
return null unless @caseManagerIds?
Meteor.users.find(_id: $in: @caseManagerIds).map((x) -> x)
study: ->
return null unless @studyId?
Studies.findOne _id: @studyId
studyDesigns: ->
return [] unless @studyDesignIds?
StudyDesigns.find
_id: $in: @studyDesignIds
,
sort: createdAt: 1
languages: ->
langs = ""
langs += @primaryLanguage if @primaryLanguage?
if @secondaryLanguage
langs += ", #{@secondaryLanguage}"
langs
@Patients = new Meteor.Collection("patients",
transform: (doc) ->
new Patient(doc)
)
if Meteor.isServer
Patients._ensureIndex( { id: 1 }, { unique: true } )
Patients.before.insert BeforeInsertTimestampHook
Patients.before.update BeforeUpdateTimestampHook
schema =
'id':
type: String
'hrid':
type: String
optional: true
unique: true
index: true
'creatorId':
type: String
'studyId':
type: String
'studyDesignId':
type: String
optional: true
'studyDesignIds':
type: [String]
optional: true
defaultValue: []
'caseManagerId': # TODO remove it at some point
type: String
optional: true
'caseManagerIds':
type: [String]
optional: true
'primaryLanguage':
type: String
optional: true
'secondaryLanguage':
type: String
optional: true
'hasData':
type: Boolean
defaultValue: false
'hasDataForDesignIds':
type: [String]
optional: true
'isExcluded':
type: Boolean
defaultValue: false
'excludesIncludes':
type: [Object]
optional: true
'excludesIncludes.$.reason':
type: String
'excludesIncludes.$.createdAt':
type: Number
'updatedAt':
type: Number
optional: true
'createdAt':
type: Number
optional: true
Patients.attachSchema new SimpleSchema(schema)
if Meteor.isServer
Meteor.methods
"createPatient": (studyId) ->
canAddPatient(studyId)
check studyId, String
study = Studies.findOne studyId
throw new Meteor.Error(403, "study not found.") unless study?
throw new Meteor.Error(400, "Study is locked. Please unlock it first.") if study.isLocked
_id = null
tries = 0
loop
try
_id = Patients.insert
id: readableRandom(6)
creatorId: Meteor.userId()
studyId: studyId
hasData: false
caseManagerIds: [Meteor.userId()]
catch e
console.log "Error: createPatient"
console.log e
finally
tries += 1
break if _id or tries >= 10
throw new Meteor.Error(500, "Can't create patient, id space seems to be full.") unless _id?
return _id
Meteor.methods
'updatePatients': (ids, update) ->
check ids, [String]
check update, Object
ids.forEach((patientId) -> canUpdatePatient(patientId))
allowedKeys = [
"$set.caseManagerIds",
"$set.studyDesignIds",
"$set.primaryLanguage",
"$set.secondaryLanguage",
"$unset.primaryLanguage",
"$unset.secondaryLanguage",
]
if Roles.userIsInRole(Meteor.user(), 'admin')
allowedKeys = [
allowedKeys...,
"$unset.caseManagerIds",
"$unset.studyDesignIds"
]
if ids.length > 1
if update['$set']? #don't overwrite with empty values
delete update['$unset']
else if ids.length is 1
allowedKeys = _.union allowedKeys, [
"$set.hrid",
"$unset.hrid"
]
# If no study designs are selected store an empty array
if update['$unset']? and update['$set']? and update['$unset']['studyDesignIds']?
delete update['$unset']['studyDesignIds']
update['$set']['studyDesignIds'] = []
#pick whitelisted keys
update = _.pickDeep update, allowedKeys
Patients.find(_id: $in: ids).forEach (p) ->
study = Studies.findOne p.studyId
throw new Meteor.Error(403, "study not found.") unless study?
throw new Meteor.Error(400, "Study is locked. Please unlock it first.") if study.isLocked
#check if changing studyDesign for a patient which has data
if update['$set']?['studyDesignIds']? or update['$unset']?['studyDesignIds']?
patientIds = []
Patients.find(_id: $in: ids).forEach (p) ->
# unset is always a string
if update['$unset']?['studyDesignIds']? and p.hasData
patientIds.push p.id
if p.hasDataForDesignIds?
if update['$set']?['studyDesignIds']?
allFound = true
p.hasDataForDesignIds.forEach (sDId) ->
if update['$set']['studyDesignIds'].indexOf(sDId) is -1
allFound = false
if !allFound
patientIds.push p.id
if patientIds.length > 0
throw new Meteor.Error(400, "You have removed one or more study designs from patient(s) (#{patientIds.join(', ')}) which have already entered data for one of these designs. This is not allowed and your changes are therefore discarded.")
#remove already created visits with no data
Patients.find(_id: $in: ids).forEach (p) ->
Visits.find( patientId: p._id ).forEach (v) ->
if Answers.find( visitId: v._id).count() is 0
Visits.remove _id: v._id
ids.forEach (id) ->
try
Patients.update _id: id, update
catch e
if e.code is 11000 #MongoError: E11000 duplicate key error
throw new Meteor.Error(400, "The HRID you entered exists already, please choose a unique value.")
else
throw e
return
"excludePatient": (patientId, reason) ->
checkIfAdmin()
check patientId, String
check reason, String
patient = Patients.findOne patientId
throw new Meteor.Error(500, "Patient can't be found.") unless patient?
throw new Meteor.Error(500, "Patient is already excluded.") if patient.isExcluded
study = Studies.findOne patient.studyId
throw new Meteor.Error(403, "study not found.") unless study?
throw new Meteor.Error(400, "Study is locked. Please unlock it first.") if study.isLocked
Patients.update patientId,
$push: excludesIncludes:
reason: reason
createdAt: Date.now()
Patients.update patientId,
$set: isExcluded: true
return
"includePatient": (patientId, reason) ->
checkIfAdmin()
check patientId, String
check reason, String
patient = Patients.findOne patientId
throw new Meteor.Error(500, "Patient can't be found.") unless patient?
throw new Meteor.Error(500, "Patient isn't excluded.") if !patient.isExcluded
study = Studies.findOne patient.studyId
throw new Meteor.Error(403, "study not found.") unless study?
throw new Meteor.Error(400, "Study is locked. Please unlock it first.") if study.isLocked
Patients.update patientId,
$push: excludesIncludes:
reason: reason
createdAt: Date.now()
Patients.update patientId,
$set: isExcluded: false
return
"removePatient": (patientId, forceReason) ->
check patientId, String
canUpdatePatient(patientId)
patient = Patients.findOne patientId
throw new Meteor.Error(500, "Patient can't be found.") unless patient?
study = Studies.findOne patient.studyId
throw new Meteor.Error(403, "study not found.") unless study?
throw new Meteor.Error(400, "Study is locked. Please unlock it first.") if study.isLocked
if patient.hasData and !forceReason
throw new Meteor.Error(500, "patientHasData")
if patient.hasData
Meteor.call "logActivity", "remove patient (#{patient.id}) which has data", "critical", forceReason, patient
else
Meteor.call "logActivity", "remove patient (#{patient.id}) which has no data", "notice", null, patient
Visits.find(patientId: patientId).forEach (v) ->
Answers.remove visitId: v._id
Visits.remove v._id
Patients.remove
_id: patientId
return
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