4.0.0 org.phenotips phenotips-components 1.3.6 patient-network 1.1.4 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-1.1.4 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-search communication ui matching-notification-resources matching-notification-ui matching-notification-api matching-notification-migrations 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. **/internal/** **/test/**