org.phenotips.matchingnotification.storage

Interface MatchStorageManager

@Role
public interface MatchStorageManager

Version:

$Id: fb2dccee575c44213fef80ca00cb268e21542661 $

Method Summary

Modifier and Type	Method and Description
boolean	addNote(List<PatientMatch> matches, String note) Saves a note to all matches in matches.
boolean	deleteMatchesForLocalPatient(String patientId) Deletes all matches (including those that users have been notified about, and MME matches) for the given local patient.
List<PatientMatch>	getMatchesToBePlacedIntoNotificationTable(List<PatientSimilarityView> matches) Converts a list of local SimilarityViews into a list of PatientMatches, keeping only those matches which should be saved into the notification table (i.e.
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(double score, double phenScore, double genScore, boolean onlyCurrentUserAccessible, Timestamp fromDate, Timestamp toDate) Loads matches filtered by the parameters.
List<PatientMatch>	loadMatchesBetweenPatients(String patientId1, String serverId1, String patientId2, String serverId2) Load all matches where reference/matched patient ID is same as one of parameters.
List<PatientMatch>	loadMatchesByIds(Set<Long> matchesIds) Load all matches with ids in matchesIds.
boolean	saveComment(List<PatientMatch> matches, String comment) Saves comment to all matches in matches to a passed status string.
boolean	saveLocalMatches(List<PatientMatch> matches, String patientId) Saves a list of local matches.
boolean	saveRemoteMatches(List<? extends PatientSimilarityView> similarityViews, String patientId, String serverId, boolean isIncoming) Saves a list of matches that were found by a remote outgoing/incoming request.
boolean	setNotifiedStatus(List<PatientMatch> matches, boolean isNotified) Marks all matches in matches as notified or not notified.
boolean	setStatus(List<PatientMatch> matches, String status) Sets status to all matches in matches to a passed status string.
boolean	setUserContacted(List<PatientMatch> matches, boolean isUserContacted) Marks all matches with ids in matchesIds as user-contacted or not.
boolean	updateNotes(PatientMatch match, String note) Updates match notes string property with new note record.
boolean	updateNotificationHistory(PatientMatch match, org.json.JSONObject notificationRecord) Updates a notification history JSON log string with new notification record.

Method Detail

loadMatches

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

Loads matches filtered by the parameters.

Parameters:

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

loadMatchesBetweenPatients

List<PatientMatch> loadMatchesBetweenPatients(String patientId1,
                                              String serverId1,
                                              String patientId2,
                                              String serverId2)

Load all matches where reference/matched patient ID is same as one of parameters.

Parameters:

patientId1 - id of reference/matched patient to load matches for

serverId1 - id of the server that hosts patientId1

patientId2 - id of reference/matched patient to load matches for

serverId2 - id of the server that hosts patientId2

Returns:

list of matches

setNotifiedStatus

boolean setNotifiedStatus(List<PatientMatch> matches,
                          boolean isNotified)

Marks all matches in matches as notified or not notified.

Parameters:

matches - list of matches to mark as notified.

isNotified - boolean notified status to set for matches

Returns:

true if successful

setUserContacted

boolean setUserContacted(List<PatientMatch> matches,
                         boolean isUserContacted)

Marks all matches with ids in matchesIds as user-contacted or not.

Parameters:

matches - list of matches to mark as user-contacted.

isUserContacted - boolean user-contacted status to set for matches

Returns:

true if successful

setStatus

boolean setStatus(List<PatientMatch> matches,
                  String status)

Sets status to all matches in matches to a passed status string.

Parameters:

matches - list of matches to mark as notified.

status - whether the matches should be marked as saved, rejected or uncategorized

Returns:

true if successful

saveComment

boolean saveComment(List<PatientMatch> matches,
                    String comment)

Saves comment to all matches in matches to a passed status string.

Parameters:

matches - list of matches to save comment.

comment - comment text

Returns:

true if successful

addNote

boolean addNote(List<PatientMatch> matches,
                String note)

Saves a note to all matches in matches.

Parameters:

matches - list of matches 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.

Parameters:

patientId - local patient ID for whom to delete matches.

Returns:

true if successful

getMatchesToBePlacedIntoNotificationTable

@Unstable
List<PatientMatch> getMatchesToBePlacedIntoNotificationTable(List<PatientSimilarityView> matches)

Converts a list of local SimilarityViews into a list of PatientMatches, keeping only those matches which should be saved into the notification table (i.e. filters out self-matches). FIXME: this method should be part of saveLocalMatches(), however a larger refactoring is needed for that, since one of the two codepaths that use saveLocalMatches() needs a filtered list of matches (while another one does not). We should unify both codepaths.

Parameters:

matches - a list of matches assumed ot be matches between local patients

Returns:

a list of PatientMatches

saveLocalMatches

boolean saveLocalMatches(List<PatientMatch> matches,
                         String patientId)

Saves a list of local matches.

Parameters:

matches - list of similarity views

patientId - local patient ID for whom to save matches

Returns:

true if successful

saveRemoteMatches

boolean saveRemoteMatches(List<? 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

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:

true if successful

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

boolean 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:

true if successful

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