4.0.0 org.phenotips phenotips-components 1.3.6 patient-network 1.1.9 pom PhenoTips - Patient network scm:git:git://github.com/phenotips/patient-network.git scm:git:git@github.com:phenotips/patient-network.git https://github.com/phenotips/remote-matching.git/tree/stable-1.1.x/ patient-network-1.1.9 phenotips-releases PhenoTips Releases repository https://nexus.phenotips.org/nexus/content/repositories/releases/ true fail false fail phenotips-snapshots PhenoTips Snapshots repository https://nexus.phenotips.org/nexus/content/repositories/snapshots/ false fail true fail 1.0 access-rules similarity-data-api similarity-data-impl similarity-genotype-view similarity-phenotype-view similarity-data-rest similarity-search communication ui matching-notification-resources matching-notification-ui matching-notification-api matching-notification-migrations matching-notification-rest org.codehaus.mojo clirr-maven-plugin ${project.version.previous} org/phenotips/data/similarity/Exome 7004 java.util.List getTopVariants(java.lang.String) Allow to specify _how many_ top variants to return. org/phenotips/data/similarity/PatientSimilarityView 7002 org.json.JSONObject getOwnerJSON() Removed for better patient contact acces via getData() method. org/phenotips/data/similarity/PatientGenotype 7012 java.lang.String getGenesStatus() Provide a status of genes stored in the class. org/phenotips/matchingnotification/match/PatientInMatch 7012 java.lang.String getHref() Provide a contact url for patient owner. org/phenotips/matchingnotification/match/PatientInMatch 7012 org.phenotips.data.Patient getPatient() Provide a patient object of patient in match. org/phenotips/matchingnotification/MatchingNotificationManager 7002 boolean markRejected(java.util.List, boolean) Removed in favour setStatus(). org/phenotips/matchingnotification/MatchingNotificationManager 7012 boolean setStatus(java.util.List, java.lang.String) Added in place of markRejected(). org/phenotips/matchingnotification/match/PatientMatch 7012 java.lang.String getStatus() Provide a status of the match (rejected, saved or uncategorized). org/phenotips/matchingnotification/match/PatientMatch 7002 boolean isRejected() Removed in favour of getStatus(). org/phenotips/matchingnotification/match/PatientMatch 7002 void setRejected(boolean) Removed in favour of setStatus(). org/phenotips/matchingnotification/match/PatientMatch 7012 void setStatus(java.lang.String) Added in place of setRejected(). org/phenotips/matchingnotification/script/MatchingNotificationScriptService 7002 java.lang.String rejectMatches(java.lang.String, boolean) Removed in favour of setStatus(). org/phenotips/matchingnotification/storage/MatchStorageManager 7002 boolean markRejected(org.hibernate.Session, java.util.List, boolean) Removed in favour of setStatus(). org/phenotips/matchingnotification/storage/MatchStorageManager 7012 boolean setStatus(org.hibernate.Session, java.util.List, java.lang.String) Added in place of markRejected(). org/phenotips/data/similarity/PatientSimilarityView 7012 org.json.JSONArray getFeatureMatchesJSON() Added to have access to structured phenotypes similarity list brokedown by cateries for email notification UI. org/phenotips/matchingnotification/MatchingNotificationManager 7005 java.util.List sendNotifications(java.util.List) java.util.List sendNotifications(java.util.Map) Add option to send matching notification to one user only. org/phenotips/matchingnotification/notification/PatientMatchNotifier 7004 java.util.List createEmails(java.util.List) Add option to send matching notification to one user only. org/phenotips/data/similarity/Variant 7012 void setAnnotation(java.lang.String, java.lang.String) Allow setting annotation properties after Variant creation. org/phenotips/matchingnotification/match/PatientMatch 7012 java.sql.Timestamp getFoundTimestamp() Allow access to the timestamp of the match. org/phenotips/matchingnotification/storage/MatchStorageManager 7012 boolean deleteMatches(org.hibernate.Session, java.util.List) Allow bulk delete for matches. org/phenotips/matchingnotification/match/PatientMatch 7012 java.lang.String getMatchedDetails() Added to have access to matched details. org/phenotips/matchingnotification/match/PatientMatch 7012 java.lang.String getReferenceDetails() Added to have access to reference details. org/phenotips/matchingnotification/match/PatientMatch 7012 void setFoundTimestamp(java.sql.Timestamp) Added to set match found timestamp. org/phenotips/matchingnotification/match/PatientMatch 7012 void setGenotypeScore(java.lang.Double) Added to set genotype score. org/phenotips/matchingnotification/match/PatientMatch 7012 void setMatchedDetails(java.lang.String) Added to set reference details. org/phenotips/matchingnotification/match/PatientMatch 7012 void setMatchedPatientInMatch(org.phenotips.matchingnotification.match.PatientInMatch) Added to set matched patient in match. org/phenotips/matchingnotification/match/PatientMatch 7012 void setPhenotypeScore(java.lang.Double) Added set phenotype score. org/phenotips/matchingnotification/match/PatientMatch 7012 void setReferenceDetails(java.lang.String) Added to set reference details. org/phenotips/matchingnotification/match/PatientMatch 7012 void setReferencePatientInMatch(org.phenotips.matchingnotification.match.PatientInMatch) Added to set reference patient in match. org/phenotips/matchingnotification/match/PatientMatch 7012 void setScore(java.lang.Double) Added to set score. org/phenotips/data/similarity/PatientGenotype 7012 boolean hasExomeData() Added to determine whether patient has any exome data. org/phenotips/data/similarity/PatientGenotypeSimilarityView 7012 boolean hasExomeData() Added to determine whether patient has any exome data. org/phenotips/matchingnotification/match/PatientInMatch 7012 boolean hasExomeData() Added to determine whether patient has any exome data. org/phenotips/matchingnotification/match/PatientInMatch 7012 org.phenotips.data.permissions.AccessLevel getAccess() Added to determine what type of access does the user have to this patient profile. org/phenotips/data/similarity/FeatureClusterView 7012 java.lang.String getId() Added to determine the root/ancestor id of the cluster. org/phenotips/data/similarity/FeatureClusterView 7012 java.lang.String getName() Added to determine the root/ancestor name of the cluster. org/phenotips/data/similarity/FeatureClusterView 7002 double getScore() Relocated to PatientSimilarityView. org/phenotips/data/similarity/FeatureClusterView 4001 org/phenotips/data/Feature Removed org.phenotips.data.Feature from the set of implemented interfaces org/phenotips/data/similarity/FeatureClusterView 4001 org/phenotips/data/VocabularyProperty Removed org.phenotips.data.VocabularyProperty from the set of implemented interfaces org/phenotips/matchingnotification/match/PhenotypesMap 8001 Relocating PhenotypesMap to new phenotype-view component. org/phenotips/matchingnotification/match/PatientInMatch 7006 org.phenotips.matchingnotification.match.PhenotypesMap getPhenotypes() org.phenotips.data.similarity.phenotype.PhenotypesMap Relocating PhenotypesMap to new phenotype-view component. org/phenotips/matchingnotification/MatchingNotificationManager 7012 boolean saveOutgoingMatches(java.util.List, java.lang.String, java.lang.String) Added to save outgoing remote matches ffom remore server. org/phenotips/matchingnotification/MatchingNotificationManager 7012 boolean saveLocalMatchesViews(java.util.List, java.lang.String) Added to save local remote matches. org/phenotips/matchingnotification/storage/MatchStorageManager 7002 java.util.List loadMatchesByReferencePatientId(java.lang.String) Renamed to loadMatchesByPatientId(). org/phenotips/matchingnotification/storage/MatchStorageManager 7002 void saveMatches(java.util.List) Removed, substituted by saveLocalMatchesViews() and saveLocalMatches(). org/phenotips/matchingnotification/storage/MatchStorageManager 7012 boolean deleteMatches(java.lang.String) Added to delete all matches by this local patient ID. org/phenotips/matchingnotification/storage/MatchStorageManager 7012 java.util.List loadMatchesBetweenPatients(java.lang.String, java.lang.String, java.lang.String, java.lang.String) Used to collect matches for notifications. org/phenotips/matchingnotification/storage/MatchStorageManager 7012 java.util.List loadMatchesByPatientIds(java.lang.String, java.lang.String) Added to search matches with provided paient IDs of matched patients. org/phenotips/matchingnotification/storage/MatchStorageManager 7012 boolean saveLocalMatches(java.util.List, java.lang.String) Added to save local matches. org/phenotips/matchingnotification/storage/MatchStorageManager 7012 boolean saveLocalMatchesViews(java.util.List, java.lang.String) Added to save local matches. org/phenotips/matchingnotification/storage/MatchStorageManager 7012 boolean saveRemoteMatches(java.util.List, java.lang.String, java.lang.String, boolean) Added to save outgoing or incoming remote matches. org/phenotips/matchingnotification/MatchingNotificationManager 7004 boolean saveIncomingMatches(java.util.List, java.lang.String) Added patient ID parameter to save incoming remote matches. org/phenotips/matchingnotification/storage/MatchStorageManager 7002 org.hibernate.Session beginNotificationMarkingTransaction() Cleaning API, decoupling implementation from API org/phenotips/matchingnotification/storage/MatchStorageManager 7002 boolean endNotificationMarkingTransaction(org.hibernate.Session) Cleaning API, decoupling implementation from API org/phenotips/matchingnotification/storage/MatchStorageManager 7012 boolean deleteMatchesForLocalPatient(java.lang.String) Cleaning API, decoupling implementation from API org/phenotips/matchingnotification/storage/MatchStorageManager 7012 boolean setStatus(java.util.List, java.lang.String) Cleaning API, decoupling implementation from API org/phenotips/matchingnotification/storage/MatchStorageManager 7004 boolean markNotified(org.hibernate.Session, java.util.List) Cleaning API, decoupling implementation from API org/phenotips/similarity/SimilarPatientsFinder 7012 java.util.List findSimilarPatients(org.phenotips.data.Patient, java.lang.String) Allows finding only matching patients which are consented to be found org/phenotips/matchingnotification/storage/MatchStorageManager 7004 java.util.List loadMatches(double, boolean) Added phenotypical and genotypical score parameters. org/phenotips/matchingnotification/MatchingNotificationManager 7004 java.util.List findAndSaveMatches(double) Removed score parameter. org/phenotips/matchingnotification/script/MatchingNotificationScriptService 7004 java.lang.String findAndSaveMatches(double) Removed score parameter. org/phenotips/matchingnotification/script/MatchingNotificationScriptService 7004 java.lang.String getMatches(double, boolean) Added phenotypical and genotypical score parameters. org/phenotips/matchingnotification/MatchingNotificationManager 7006 java.util.List findAndSaveMatches(double) void Removed unused return. org/phenotips/matchingnotification/script/MatchingNotificationScriptService 7006 java.lang.String findAndSaveMatches(double) void Removed unused return. org/phenotips/matchingnotification/finder/MatchFinder 7012 void recordStartMatchesSearch() Record the beginning time of matches search for each server org/phenotips/matchingnotification/finder/MatchFinder 7012 void recordEndMatchesSearch() Record the completion time of matches search for each server org/phenotips/matchingnotification/finder/MatchFinderManager 7012 void findMatchesForAllPatients() Record the completion time of matches search for each match finder org/phenotips/matchingnotification/finder/MatchFinder 7012 java.util.List findMatches(org.phenotips.data.Patient, boolean) Added an option to check matches for either all patients or only changed patients org/phenotips/matchingnotification/finder/MatchFinder 7012 java.lang.String getName() Ability to select matchers by name org/phenotips/matchingnotification/finder/MatchFinderManager 7012 void findMatchesForAllPatients(java.util.Set, boolean) A method with more control over which matches are searched for org/phenotips/matchingnotification/script/MatchingNotificationScriptService 7002 java.lang.String findAndSaveMatches(double) Updating API to match back-end changes and provide new functionality for better control over matchers org/phenotips/matchingnotification/MatchingNotificationManager 7002 java.util.List findAndSaveMatches(double) Updating API to match back-end changes and provide new functionality for better control over matchers org/phenotips/matchingnotification/finder/MatchFinderManager 7002 java.util.List findMatches(org.phenotips.data.Patient) Updating API to match back-end changes and provide new functionality for better control over matchers org/phenotips/matchingnotification/finder/MatchFinder 7004 java.util.List findMatches(org.phenotips.data.Patient) A method with more control over which matches are searched for org/phenotips/matchingnotification/finder/MatchFinder 7012 void recordStartMatchesSearch(java.lang.String) Record the completion time of matches search for each server org/phenotips/matchingnotification/finder/MatchFinder 7012 void recordEndMatchesSearch(java.lang.String) Record the completion time of matches search for each server org/phenotips/matchingnotification/match/PatientInMatch 7012 java.lang.String getGenesStatus() Record the completion time of matches search for each server org/phenotips/matchingnotification/script/MatchingNotificationScriptService 8001 Removing script service in favour of REST service. org/phenotips/matchingnotification/storage/MatchStorageManager 7012 java.util.List getMatchesToBePlacedIntoNotificationTable(java.util.List) New helper method org/phenotips/matchingnotification/MatchingNotificationManager 7012 org.json.JSONObject getEmailContent(java.lang.Long, java.lang.String) New helper method org/phenotips/matchingnotification/notification/PatientMatchEmail 7012 org.json.JSONObject getEmail() New helper method org/phenotips/matchingnotification/MatchingNotificationManager 7012 org.json.JSONObject getUserEmailContent(java.lang.Long, java.lang.String, java.lang.String) Added to enable preview for notification emails before sending. org/phenotips/matchingnotification/MatchingNotificationManager 7012 java.util.List sendAdminNotificationsToLocalUsers(java.util.Map) Added to enable preview for notification emails before sending. org/phenotips/matchingnotification/MatchingNotificationManager 7002 java.util.List sendNotifications(java.util.List) Removed in refactoring user notification. org/phenotips/matchingnotification/MatchingNotificationManager 7012 org.phenotips.matchingnotification.notification.PatientMatchNotificationResponse sendUserNotification(java.lang.Long, java.lang.String, java.lang.String, java.lang.String, java.lang.String) Added to implement preview for notification emails before sending. org/phenotips/matchingnotification/MatchingNotificationManager 7012 boolean setStatus(java.util.Set, java.lang.String) Added to implement preview for notification emails before sending. org/phenotips/matchingnotification/notification/PatientMatchNotifier 7012 java.util.List createAdminEmailsToLocalUsers(java.util.List, java.util.Map) Added to implement preview for notification emails before sending. org/phenotips/matchingnotification/notification/PatientMatchNotifier 7002 java.util.List createEmails(java.util.List) Removed in refactoring user notification. org/phenotips/matchingnotification/notification/PatientMatchNotifier 7012 org.phenotips.matchingnotification.notification.PatientMatchEmail createUserEmail(org.phenotips.matchingnotification.match.PatientMatch, java.lang.String, java.lang.String, java.lang.String, java.lang.String) Added to implement preview for notification emails before sending. org/phenotips/matchingnotification/storage/MatchStorageManager 7005 java.util.List loadMatchesByIds(java.util.List) java.util.List loadMatchesByIds(java.util.Set) Changed to implement preview for notification emails before sending. **/internal/** **/test/**