PatientMatch (PhenoTips - Patient Network - Matching Notification

```
public interface PatientMatch
```
Encapsulates a match between a reference patient and a matched patient.

Version:

$Id: 8a8495a5b4bfce67b5844eda674a374b9913ee1e $

Field Summary

Fields
Modifier and Type Field and Description

static org.xwiki.model.reference.EntityReference DATA_SPACE
The space where matches data is stored.

Fields
Modifier and Type	Field and Description
`static org.xwiki.model.reference.EntityReference`	`DATA_SPACE` The space where matches data is stored.

Method Summary

All Methods Instance Methods Abstract Methods Deprecated Methods
Modifier and Type	Method and Description
`org.json.JSONArray`	`getComments()`
`org.json.JSONArray`	`getFeatureMatchesJSON()`
`Timestamp`	`getFoundTimestamp()`
`Double`	`getGenotypeScore()`
`org.json.JSONArray`	`getGenotypeSimilarityJSON()`
`String`	`getHref()`
`Long`	`getId()`
`PatientInMatch`	`getMatched()`
`String`	`getMatchedDetails()`
`String`	`getMatchedPatientId()`
`String`	`getMatchedServerId()`
`String`	`getNote()`
`org.json.JSONArray`	`getNotes()`
`org.json.JSONObject`	`getNotificationHistory()`
`Double`	`getPhenotypeScore()`
`PatientInMatch`	`getReference()`
`String`	`getReferenceDetails()`
`String`	`getReferencePatientId()`
`String`	`getReferenceServerId()`
`Double`	`getScore()`
`String`	`getStatus()`
`boolean`	`hasSameMatchData(PatientMatch other)` Checks that matches are equivalent (see `isEquivalent()`) and that the match data is the same, meaning that scores are the same, phenotype/genotype is the same, etc.
`boolean`	`isEquivalent(PatientMatch other)` Checks if `other` is equivalent to this.
`boolean`	`isIncoming()` See `isLocal()`.
`boolean`	`isLocal()` Checks if a request is local.
`boolean`	`isMatched(String patientId, String serverId)` Checks if the patient given in parameter is the matched patient of the match.
`boolean`	`isOutgoing()` See `isLocal()`.
`boolean`	`isReference(String patientId, String serverId)` Checks if the patient given in parameter is the reference patient of the match.
`boolean`	`isRejected()` Deprecated. use `getStatus()` instead
`void`	`setComments(org.json.JSONArray comments)` Sets match comments.
`void`	`setExternallyContacted(boolean isExternallyContacted)` Add a record to the notification history in case user contacted regarding this match outside of PhenomeCentral.
`void`	`setFoundTimestamp(Timestamp timestamp)` Set the timestamp when the match was found.
`void`	`setGenotypeScore(Double score)` Set genotype the score.
`void`	`setMatchedDetails(String details)` Set matched details.
`void`	`setMatchedPatientInMatch(PatientInMatch patient)` Set the matched patient in match.
`void`	`setNotes(org.json.JSONArray notes)` Sets match notes as a JSON object, in the following format:
`void`	`setNotificationHistory(org.json.JSONObject notificationHistory)`
`void`	`setPhenotypeScore(Double score)` Set the phenotype score.
`void`	`setReferenceDetails(String details)` Set the reference details.
`void`	`setReferencePatientInMatch(PatientInMatch patient)` Set the reference patient in match when the match was found.
`void`	`setScore(Double score)` Set the match score.
`void`	`setStatus(String status)` Marks status property of match (saved, rejected or uncategorized).
`org.json.JSONObject`	`toJSON()`
`void`	`updateComments(String comment)` Updates match comments JSON log string property with new comment.
`void`	`updateNotes(String note)` Updates a notes JSON with new note record.
`void`	`updateNotificationHistory(org.json.JSONObject notificationRecord)` Updates a notification history JSON log string property with new notification record.

- Field Detail
  - DATA_SPACE
```
static final org.xwiki.model.reference.EntityReference DATA_SPACE
```
    The space where matches data is stored.
- Method Detail
  - getId
```
Long getId()
```
    Returns:
    
    unique id of match
  - getReferencePatientId
```
String getReferencePatientId()
```
    Returns:
    
    id of reference patient.
  - getReferenceServerId
```
String getReferenceServerId()
```
    Returns:
    
    id of server where reference patient is found. Null if local.
  - getMatchedPatientId
```
String getMatchedPatientId()
```
    Returns:
    
    id of other patient.
  - getMatchedServerId
```
String getMatchedServerId()
```
    Returns:
    
    id of server where matched patient is found. Null if local.
  - isRejected
```
@Deprecated
boolean isRejected()
```
    Deprecated. use getStatus() instead
    
    Returns:
    
    true only if match is rejected.
  - setStatus
```
void setStatus(String status)
```
    Marks status property of match (saved, rejected or uncategorized).
    
    Parameters:
    
    status - whether saved, rejected or uncategorized
  - setComments
```
void setComments(org.json.JSONArray comments)
```
    Sets match comments.
    
    Parameters:
    
    comments - comments JSON array
  - updateComments
```
void updateComments(String comment)
```
    Updates match comments JSON log string property with new comment. Comments are stored as a JSON String object, in the following format:
```
         [ { "userinfo":{"id":"xwiki:XWiki.Mary",
                         "name":"Mary Green"},
              "comment":"This is a good match",
              "date":"2018/12/06 15:36"},
            ...
          ]
     
```
    Parameters:
    
    comment - the new comment string
  - setNotes
```
void setNotes(org.json.JSONArray notes)
```
    Sets match notes as a JSON object, in the following format:
```
         [ {"user":"xwiki:XWiki.Pat",
            "note":"This match is very important"}
           ...
          ]
     
```
    Parameters:
    
    notes - notes JSON array
  - updateNotes
```
void updateNotes(String note)
```
    Updates a notes JSON with new note record.
    
    Parameters:
    
    note - the new note string
  - toJSON
```
org.json.JSONObject toJSON()
```
    Returns:
    
    complete match in JSON format.
  - getScore
```
Double getScore()
```
    Returns:
    
    score of match.
  - getPhenotypeScore
```
Double getPhenotypeScore()
```
    Returns:
    
    phenotypical score
  - getGenotypeScore
```
Double getGenotypeScore()
```
    Returns:
    
    genotypical score
  - getHref
```
String getHref()
```
    Returns:
    
    href of remote patient. If this.isLocal() returns null.
  - getStatus
```
String getStatus()
```
    Returns:
    
    status of match: saved, rejected or uncategorized.
  - getComments
```
org.json.JSONArray getComments()
```
    Returns:
    
    all match comments as JSON array.
  - getNote
```
String getNote()
```
    Returns:
    
    currently logged user note about the match in general, if any.
  - getNotes
```
org.json.JSONArray getNotes()
```
    Returns:
    
    all match notes as JSON array.
  - isEquivalent
```
boolean isEquivalent(PatientMatch other)
```
    Checks if other is equivalent to this. A match m1 is equivalent to a match m2 if all the following are true: m1.referencePatientId = m2.matchedPatientId m1.referenceServerId = m2.matchedServerId m2.matchedPatientId = m1.referencePatientId m2.matchedPatientId = m1.referenceServerId
    
    Parameters:
    
    other - match to compare to
    
    Returns:
    
    true if equivalent
  - hasSameMatchData
```
boolean hasSameMatchData(PatientMatch other)
```
    Checks that matches are equivalent (see isEquivalent()) and that the match data is the same, meaning that scores are the same, phenotype/genotype is the same, etc. However all difference in metadata (IDs, timestamps, notificationHistory, notes) is ignored.
    
    Parameters:
    
    other - match to compare to
    
    Returns:
    
    true if matches contain the same data
  - getReference
```
PatientInMatch getReference()
```
    Returns:
    
    PatientInMatch object representing the reference patient.
  - getMatched
```
PatientInMatch getMatched()
```
    Returns:
    
    PatientInMatch object representing the matched patient.
  - isReference
```
boolean isReference(String patientId,
                    String serverId)
```
    Checks if the patient given in parameter is the reference patient of the match.
    
    Parameters:
    
    patientId - id of patient
    
    serverId - id of server where patient is found
    
    Returns:
    
    true if patient is reference patient in match
  - isMatched
```
boolean isMatched(String patientId,
                  String serverId)
```
    Checks if the patient given in parameter is the matched patient of the match.
    
    Parameters:
    
    patientId - id of patient
    
    serverId - id of server where patient is found
    
    Returns:
    
    true if patient is matched patient in match
  - isLocal
```
boolean isLocal()
```
    Checks if a request is local. The relationship between isLocal(), isIncoming() and isOutgoing() is: isLocal()==true ==> isIncoming()==false && isOutgoing()==false and isLocal()==false ==> only one of (isIncoming(), isOutgoing()) is true
    
    Returns:
    
    true if both reference and matched patients are local.
  - isIncoming
```
boolean isIncoming()
```
    See isLocal().
    
    Returns:
    
    true if match request was initiated in remote server.
  - isOutgoing
```
boolean isOutgoing()
```
    See isLocal().
    
    Returns:
    
    true if match was initiated locally and was sent to a remote server.
  - getFoundTimestamp
```
Timestamp getFoundTimestamp()
```
    Returns:
    
    the timestamp when the match was found.
  - setFoundTimestamp
```
void setFoundTimestamp(Timestamp timestamp)
```
    Set the timestamp when the match was found.
    
    Parameters:
    
    timestamp - timestamp
  - setScore
```
void setScore(Double score)
```
    Set the match score.
    
    Parameters:
    
    score - score
  - setGenotypeScore
```
void setGenotypeScore(Double score)
```
    Set genotype the score.
    
    Parameters:
    
    score - score
  - setPhenotypeScore
```
void setPhenotypeScore(Double score)
```
    Set the phenotype score.
    
    Parameters:
    
    score - score
  - setReferenceDetails
```
void setReferenceDetails(String details)
```
    Set the reference details.
    
    Parameters:
    
    details - details
  - setReferencePatientInMatch
```
void setReferencePatientInMatch(PatientInMatch patient)
```
    Set the reference patient in match when the match was found.
    
    Parameters:
    
    patient - patient
  - setMatchedDetails
```
void setMatchedDetails(String details)
```
    Set matched details.
    
    Parameters:
    
    details - details
  - setMatchedPatientInMatch
```
void setMatchedPatientInMatch(PatientInMatch patient)
```
    Set the matched patient in match.
    
    Parameters:
    
    patient - patient
  - getReferenceDetails
```
String getReferenceDetails()
```
    Returns:
    
    the reference details.
  - getMatchedDetails
```
String getMatchedDetails()
```
    Returns:
    
    the matched details.
  - getNotificationHistory
```
org.json.JSONObject getNotificationHistory()
```
    Returns:
    
    the match notification history JSON.
  - setNotificationHistory
```
void setNotificationHistory(org.json.JSONObject notificationHistory)
```
    Parameters:
    
    notificationHistory - the notification history JSON
  - updateNotificationHistory
```
void updateNotificationHistory(org.json.JSONObject notificationRecord)
```
    Updates a notification history JSON log string property with new notification record. Record is a JSON object in the following format:
```
      { "from": {"userinfo":{"id":"xwiki:XWiki.Mary",
                             "name":"Mary"},
                 "emails"  :["mary@blueberry.com"]
                },
         "to":  {"userinfo":{ "id":"xwiki:XWiki.Pat",
                              "name":"Pat Smith",
                              "institution":"Western Hospital San Diego"},
                  "emails":["patcat@catrescuecentre.kom"]
                },
         "cc":  ["mary@blueberry.com"],
         "type":"contact",
         "date":"2018/12/06 14:58"
       }
     
```
    Parameters:
    
    notificationRecord - the new notification record JSON
  - setExternallyContacted
```
void setExternallyContacted(boolean isExternallyContacted)
```
    Add a record to the notification history in case user contacted regarding this match outside of PhenomeCentral.
    
    Parameters:
    
    isExternallyContacted - boolean indicator whether contact regarding this match was done or not
  - getFeatureMatchesJSON
```
org.json.JSONArray getFeatureMatchesJSON()
```
    Returns:
    
    the matched features JSON array in a cluster view.
  - getGenotypeSimilarityJSON
```
org.json.JSONArray getGenotypeSimilarityJSON()
```
    Returns:
    
    the matched genotype JSON array in a cluster view.

Interface PatientMatch

Field Summary

Method Summary

Field Detail

DATA_SPACE

Method Detail

getId

getReferencePatientId

getReferenceServerId

getMatchedPatientId

getMatchedServerId

isRejected

setStatus

setComments

updateComments

setNotes

updateNotes

toJSON

getScore

getPhenotypeScore

getGenotypeScore

getHref

getStatus

getComments

getNote

getNotes

isEquivalent

hasSameMatchData

getReference

getMatched

isReference

isMatched

isLocal

isIncoming

isOutgoing

getFoundTimestamp

setFoundTimestamp

setScore

setGenotypeScore

setPhenotypeScore

setReferenceDetails

setReferencePatientInMatch

setMatchedDetails

setMatchedPatientInMatch

getReferenceDetails

getMatchedDetails

getNotificationHistory

setNotificationHistory

updateNotificationHistory

setExternallyContacted

getFeatureMatchesJSON

getGenotypeSimilarityJSON