org.phenotips.matchingnotification.storage

Interface MatchStorageManager

@Role
public interface MatchStorageManager

Version:

$Id: 0dcae06b1c1acd45e11fee5b910e823e206774b8 $

Method Summary

Modifier and Type	Method and Description
boolean	addNote(PatientMatch match, String note) Saves a note to a match.
boolean	deleteMatchesForLocalPatient(String patientId) Deletes all matches (including those that users have been notified about, and MME matches) for the given local patient (e.g.
Long	getNumberOfRemoteMatches() Calculates the number of matches that were found by all remote outgoing/incoming requests where at least one patient in the match is remote.
List<PatientMatch>	loadMatches(String patientId, double score, double phenScore, double genScore, boolean onlyCurrentUserAccessible, Timestamp fromDate, Timestamp toDate) Loads matches filtered by the parameters.
List<PatientMatch>	loadMatchesByIds(Set<Long> matchesIds) Load all matches with ids in matchesIds.
boolean	saveComment(PatientMatch match, String comment) Saves comment to a match.
List<PatientMatch>	saveLocalMatches(Collection<? extends PatientSimilarityView> similarityViews, String patientId) Saves a list of local matches.
List<PatientMatch>	saveRemoteMatches(Collection<? extends PatientSimilarityView> similarityViews, String patientId, String serverId, boolean isIncoming) Saves a list of matches that were found by a remote outgoing/incoming request.
boolean	setStatus(PatientMatch match, String status) Sets status to a match.
boolean	setUserContacted(PatientMatch match, boolean isUserContacted) Marks a match as user-contacted or not.
boolean	updateNotes(PatientMatch match, String note) Updates match notes string property with new note record.
Collection<PatientMatch>	updateNotificationHistory(PatientMatch match, org.json.JSONObject notificationRecord) Updates a notification history JSON log string with new notification record.

Method Detail

loadMatches

List<PatientMatch> loadMatches(String patientId,
                               double score,
                               double phenScore,
                               double genScore,
                               boolean onlyCurrentUserAccessible,
                               Timestamp fromDate,
                               Timestamp toDate)

Loads matches filtered by the parameters.

Parameters:

patientId - the patient ID if null, then all matches will be returned

score - threshold for matches

phenScore - only matches with phenotypical score higher or equal to this value are returned

genScore - only matches with genotypical score higher or equal to this value are returned

onlyCurrentUserAccessible - when true only matches that current user has access to are returned

fromDate - if passed a date, then only matches found on or after this date will be returned; if null, then no lower limit on the match date is considered

toDate - if passed a date, then only matches found on or before this date will be returned; if null, then no upper limit on the match date is considered

Returns:

a list of matches

loadMatchesByIds

List<PatientMatch> loadMatchesByIds(Set<Long> matchesIds)

Load all matches with ids in matchesIds.

Parameters:

matchesIds - list of ids of matches to load

Returns:

list of matches

setUserContacted

boolean setUserContacted(PatientMatch match,
                         boolean isUserContacted)

Marks a match as user-contacted or not.

Parameters:

match - match to mark as user-contacted.

isUserContacted - boolean user-contacted status to set for a match

Returns:

true if successful

setStatus

boolean setStatus(PatientMatch match,
                  String status)

Sets status to a match.

Parameters:

match - match to mark as notified.

status - whether a match should be marked as saved, rejected or uncategorized

Returns:

true if successful

saveComment

boolean saveComment(PatientMatch match,
                    String comment)

Saves comment to a match.

Parameters:

match - match to save comment.

comment - comment text

Returns:

true if successful

addNote

boolean addNote(PatientMatch match,
                String note)

Saves a note to a match.

Parameters:

match - match to save note to.

note - note text

Returns:

true if successful

deleteMatchesForLocalPatient

boolean deleteMatchesForLocalPatient(String patientId)

Deletes all matches (including those that users have been notified about, and MME matches) for the given local patient (e.g. when a patient is deleted).

Parameters:

patientId - local patient ID for whom to delete matches.

Returns:

true if successful

saveLocalMatches

List<PatientMatch> saveLocalMatches(Collection<? extends PatientSimilarityView> similarityViews,
                                    String patientId)

Saves a list of local matches.

Parameters:

similarityViews - list of matches as "similarity views" between two local patients

patientId - local patient ID for whom to save matches

Returns:

null if saving failed, otherwise list of saved PatientMatches

saveRemoteMatches

List<PatientMatch> saveRemoteMatches(Collection<? extends PatientSimilarityView> similarityViews,
                                     String patientId,
                                     String serverId,
                                     boolean isIncoming)

Saves a list of matches that were found by a remote outgoing/incoming request.

Parameters:

similarityViews - list of similarity views between a local patient and a remote patient

patientId - remote patient ID for whom to save matches

serverId - id of remote server

isIncoming - whether we are saving results of incoming (then true) or outgoing request

Returns:

null if saving failed, otherwise list of saved PatientMatches

getNumberOfRemoteMatches

Long getNumberOfRemoteMatches()

Calculates the number of matches that were found by all remote outgoing/incoming requests where at least one patient in the match is remote.

Returns:

the total number of remote matches in matches database

updateNotificationHistory

Collection<PatientMatch> updateNotificationHistory(PatientMatch match,
                                                   org.json.JSONObject notificationRecord)

Updates a notification history JSON log string with new notification record.

Parameters:

match - subject match

notificationRecord - the new notification record JSON

Returns:

collection of successfully updated matches

updateNotes

boolean updateNotes(PatientMatch match,
                    String note)

Updates match notes string property with new note record.

Parameters:

match - subject match

note - the new note record JSON string

Returns:

true if successful