From jira at phenotips.atlassian.net Mon Feb 11 10:14:11 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Mon, 11 Feb 2019 15:14:11 +0000 (UTC) Subject: [JIRA] (PT-3855) Improve performance of getAccessLevel() In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 452 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Mon Feb 11 12:38:48 2019 From: jira at phenotips.atlassian.net (Sasha Andjic (JIRA)) Date: Mon, 11 Feb 2019 17:38:48 +0000 (UTC) Subject: [JIRA] (PT-3945) Variants are not properly counted as unique because of letter case differences and possibly trailing(?) spaces In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 613 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 633 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From noreply at github.com Mon Feb 11 12:39:00 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 09:39:00 -0800 Subject: [phenotips/remote-matching] 48ac01: RM-125: Support additional MME metrics: variants, ... Message-ID: Branch: refs/heads/master Home: https://github.com/phenotips/remote-matching Commit: 48ac0122d8ff1fcf1d91d9dfd51e8ca45d98598e https://github.com/phenotips/remote-matching/commit/48ac0122d8ff1fcf1d91d9dfd51e8ca45d98598e Author: veronikaslc Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfCasesWithFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfRequestsReceivedProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueVariantsProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java M core/metrics/src/main/resources/META-INF/components.txt Log Message: ----------- RM-125: Support additional MME metrics: variants, features, requests received Commit: 83ec2074f07a27697b57758115bd75cb09bc8283 https://github.com/phenotips/remote-matching/commit/83ec2074f07a27697b57758115bd75cb09bc8283 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfCasesWithFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfRequestsReceivedProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueVariantsProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java M core/metrics/src/main/resources/META-INF/components.txt Log Message: ----------- Merge pull request #89 from phenotips/RM-125 RM-125: Support additional MME metrics: variants, features, requests received Compare: https://github.com/phenotips/remote-matching/compare/d552101c13f3...83ec2074f07a From jira at phenotips.atlassian.net Mon Feb 11 12:39:12 2019 From: jira at phenotips.atlassian.net (Sasha Andjic (JIRA)) Date: Mon, 11 Feb 2019 17:39:12 +0000 (UTC) Subject: [JIRA] (PT-3945) Variants are not properly counted as unique because of letter case differences and possibly trailing spaces In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From noreply at github.com Mon Feb 11 12:42:24 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 09:42:24 -0800 Subject: [phenotips/remote-matching] 2f8e66: RM-125: Support additional MME metrics: variants, ... Message-ID: Branch: refs/heads/RM-125 Home: https://github.com/phenotips/remote-matching Commit: 2f8e6622b8e0c4ab8de584383a5082efb81dc82a https://github.com/phenotips/remote-matching/commit/2f8e6622b8e0c4ab8de584383a5082efb81dc82a Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java Log Message: ----------- RM-125: Support additional MME metrics: variants, features, requests received Corrected variants count From noreply at github.com Mon Feb 11 12:43:22 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Mon, 11 Feb 2019 17:43:22 +0000 (UTC) Subject: [phenotips/phenotips] 0c6d4f: [release] Set the phenotips.version to the right v... Message-ID: Branch: refs/tags/phenotips-1.3.10 Home: https://github.com/phenotips/phenotips Commit: 0c6d4ffe73630e7cd1d2a3d7c3b98e7a7fd8a108 https://github.com/phenotips/phenotips/commit/0c6d4ffe73630e7cd1d2a3d7c3b98e7a7fd8a108 Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [release] Set the phenotips.version to the right value Commit: 090e161cf2eff837d89ae903ba0039f3f9e5fac4 https://github.com/phenotips/phenotips/commit/090e161cf2eff837d89ae903ba0039f3f9e5fac4 Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M components/application-configuration/api/pom.xml M components/application-configuration/migrations/pom.xml M components/application-configuration/pom.xml M components/application-configuration/ui/pom.xml M components/base-war/pom.xml M components/constants/pom.xml M components/default-settings/pom.xml M components/diagnosis-suggestion/api/pom.xml M components/diagnosis-suggestion/pom.xml M components/diagnosis-suggestion/ui/pom.xml M components/entities/api/pom.xml M components/entities/pom.xml M components/entities/ui/pom.xml M components/export/api/pom.xml M components/export/pom.xml M components/export/ui/pom.xml M components/family-studies/api/pom.xml M components/family-studies/migrations/pom.xml M components/family-studies/pom.xml M components/family-studies/rest/pom.xml M components/family-studies/ui/pom.xml M components/gene-panels/api/pom.xml M components/gene-panels/pom.xml M components/gene-panels/rest/pom.xml M components/gene-panels/ui/pom.xml M components/navigation/api/pom.xml M components/navigation/pageobjects/pom.xml M components/navigation/pom.xml M components/navigation/tests/pom.xml M components/navigation/ui/pom.xml M components/obo2solr/pom.xml M components/patient-access-rules/api/pom.xml M components/patient-access-rules/migrations/pom.xml M components/patient-access-rules/pom.xml M components/patient-access-rules/rest/pom.xml M components/patient-access-rules/ui/pom.xml M components/patient-contacts/pom.xml M components/patient-data-extra/medication/api/pom.xml M components/patient-data-extra/medication/pom.xml M components/patient-data-extra/medication/ui/pom.xml M components/patient-data-extra/pom.xml M components/patient-data-sharing/pom.xml M components/patient-data-sharing/push-api/pom.xml M components/patient-data-sharing/push-ui/pom.xml M components/patient-data-sharing/receiver-api/pom.xml M components/patient-data-sharing/receiver-ui/pom.xml M components/patient-data-sharing/secure-storage/pom.xml M components/patient-data-sharing/share-protocol/pom.xml M components/patient-data/api/pom.xml M components/patient-data/impl/pom.xml M components/patient-data/indexing/pom.xml M components/patient-data/migrations/pom.xml M components/patient-data/pageobjects/pom.xml M components/patient-data/pom.xml M components/patient-data/rest/pom.xml M components/patient-data/tests/pom.xml M components/patient-data/ui/pom.xml M components/patient-measurements/api/pom.xml M components/patient-measurements/migrations/pom.xml M components/patient-measurements/pom.xml M components/patient-measurements/ui/pom.xml M components/patient-tools/pom.xml M components/pedigree/api/pom.xml M components/pedigree/pom.xml M components/pedigree/resources/pom.xml M components/pedigree/ui/pom.xml M components/pom.xml M components/record-locking/api/pom.xml M components/record-locking/pom.xml M components/record-locking/ui/pom.xml M components/rest-commons/pom.xml M components/security/authorization/pom.xml M components/security/bridge/pom.xml M components/security/crypto-api/pom.xml M components/security/crypto-xproperty/pom.xml M components/security/pom.xml M components/skin/api/pom.xml M components/skin/pom.xml M components/skin/ui/pom.xml M components/solr-access-service/api/pom.xml M components/solr-access-service/pom.xml M components/solr-access-service/ui/pom.xml M components/specificity-meter/api/pom.xml M components/specificity-meter/pom.xml M components/specificity-meter/ui/pom.xml M components/storage-migrators/api/pom.xml M components/storage-migrators/attachments/db/pom.xml M components/storage-migrators/attachments/fs/pom.xml M components/storage-migrators/attachments/migrator/pom.xml M components/storage-migrators/attachments/pom.xml M components/storage-migrators/pom.xml M components/studies/api/pom.xml M components/studies/migrations/pom.xml M components/studies/pom.xml M components/studies/ui/pom.xml M components/user-profile-ui/pom.xml M components/users/api/pom.xml M components/users/pom.xml M components/users/ui/pom.xml M components/utilities/component-registry/pom.xml M components/utilities/jodatime-service/pom.xml M components/utilities/ncbieutils-services/api/pom.xml M components/utilities/ncbieutils-services/pom.xml M components/utilities/ncbieutils-services/pubmed-suggestions-ui/pom.xml M components/utilities/pom.xml M components/utilities/proxy-authentication/pom.xml M components/utilities/xliff12/pom.xml M components/utilities/xwiki-platform-svg/pom.xml M components/utilities/xwiki-translation-manager/pom.xml M components/vocabularies/api/pom.xml M components/vocabularies/chebi/api/pom.xml M components/vocabularies/chebi/pom.xml M components/vocabularies/ethnicity/api/pom.xml M components/vocabularies/ethnicity/parser/pom.xml M components/vocabularies/ethnicity/pom.xml M components/vocabularies/hgnc-remote/api/pom.xml M components/vocabularies/hgnc-remote/pom.xml M components/vocabularies/hgnc/api/pom.xml M components/vocabularies/hgnc/pom.xml M components/vocabularies/hgnc/ui/pom.xml M components/vocabularies/hpo/annotations/pom.xml M components/vocabularies/hpo/api/pom.xml M components/vocabularies/hpo/pom.xml M components/vocabularies/hpo/translation-french/pom.xml M components/vocabularies/hpo/translation-italian/pom.xml M components/vocabularies/hpo/translation-spanish/pom.xml M components/vocabularies/hpo/ui/pom.xml M components/vocabularies/omim/api/pom.xml M components/vocabularies/omim/pom.xml M components/vocabularies/omim/ui/pom.xml M components/vocabularies/ordo/api/pom.xml M components/vocabularies/ordo/pom.xml M components/vocabularies/ordo/ui/pom.xml M components/vocabularies/pom.xml M components/vocabularies/rest/pom.xml M components/vocabularies/translations/pom.xml M components/vocabularies/translations/xliff/pom.xml M components/vocabularies/ui/pom.xml M components/widgets/api/pom.xml M components/widgets/pom.xml M components/widgets/resources/pom.xml M components/widgets/ui/pom.xml M components/xwiki-locks/pom.xml M components/xwiki-platform-users/pom.xml M components/xwiki-platform-users/xwiki-platform-users-api/pom.xml M components/xwiki-platform-users/xwiki-platform-users-wiki/pom.xml M distribution/dmg/pom.xml M distribution/hsqldb-database/pom.xml M distribution/pom.xml M distribution/rpm/pom.xml M distribution/standalone/pom.xml M distribution/war/pom.xml M pom.xml M resources/jetty/log-writer/pom.xml M resources/jetty/open-browser/pom.xml M resources/jetty/packaging/pom.xml M resources/jetty/pom.xml M resources/pom.xml M resources/solr-configuration/pom.xml M resources/ui/pom.xml Log Message: ----------- [maven-release-plugin] prepare release phenotips-1.3.10 Compare: https://github.com/phenotips/phenotips/compare/0c6d4ffe7363%5E...090e161cf2ef From noreply at github.com Mon Feb 11 12:49:05 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 09:49:05 -0800 Subject: [phenotips/remote-matching] 2f8e66: RM-125: Support additional MME metrics: variants, ... Message-ID: Branch: refs/heads/master Home: https://github.com/phenotips/remote-matching Commit: 2f8e6622b8e0c4ab8de584383a5082efb81dc82a https://github.com/phenotips/remote-matching/commit/2f8e6622b8e0c4ab8de584383a5082efb81dc82a Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java Log Message: ----------- RM-125: Support additional MME metrics: variants, features, requests received Corrected variants count Commit: 7aaf4ae45d97dc26cb9a57985433382682428a42 https://github.com/phenotips/remote-matching/commit/7aaf4ae45d97dc26cb9a57985433382682428a42 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java Log Message: ----------- Merge pull request #90 from phenotips/RM-125 RM-125: Support additional MME metrics: variants, features, requests received Compare: https://github.com/phenotips/remote-matching/compare/83ec2074f07a...7aaf4ae45d97 From ci at phenotype.ccm.sickkids.ca Mon Feb 11 13:10:34 2019 From: ci at phenotype.ccm.sickkids.ca (PhenoTips Jenkins) Date: Mon, 11 Feb 2019 13:10:34 -0500 (EST) Subject: Build failed in Jenkins: remote-matching-PR #19 Message-ID: <1422749226.66.1549908634706.JavaMail.jenkins@ci.local> See ------------------------------------------ GitHub pull request #90 of commit 2f8e6622b8e0c4ab8de584383a5082efb81dc82a, no merge conflicts. Setting status of 2f8e6622b8e0c4ab8de584383a5082efb81dc82a to PENDING with url https://ci.phenotips.org/job/remote-matching-PR/19/ and message: 'Build started for merge commit.' Using context: jenkins Building in workspace > git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/phenotips/remote-matching.git # timeout=10 Fetching upstream changes from https://github.com/phenotips/remote-matching.git > git --version # timeout=10 using GIT_SSH to set credentials Setting http proxy: 20.20.20.10:488 > git fetch --no-tags --progress https://github.com/phenotips/remote-matching.git +refs/pull/90/*:refs/remotes/origin/pr/90/* > git rev-parse refs/remotes/origin/pr/90/merge^{commit} # timeout=10 > git rev-parse refs/remotes/origin/origin/pr/90/merge^{commit} # timeout=10 > git rev-parse origin/pr/90/merge^{commit} # timeout=10 ERROR: Couldn't find any revision to build. Verify the repository and branch configuration for this job. ERROR: Build step failed with exception java.io.IOException: Cannot retrieve Git metadata for the build at org.jenkinsci.plugins.github.util.BuildDataHelper.getCommitSHA1(BuildDataHelper.java:87) at org.jenkinsci.plugins.github.status.sources.BuildDataRevisionShaSource.get(BuildDataRevisionShaSource.java:32) at org.jenkinsci.plugins.github.status.GitHubCommitStatusSetter.perform(GitHubCommitStatusSetter.java:135) Caused: org.jenkinsci.plugins.github.common.CombineErrorHandler$ErrorHandlingException at org.jenkinsci.plugins.github.common.CombineErrorHandler.handle(CombineErrorHandler.java:74) at org.jenkinsci.plugins.github.status.GitHubCommitStatusSetter.perform(GitHubCommitStatusSetter.java:164) at hudson.tasks.BuildStepCompatibilityLayer.perform(BuildStepCompatibilityLayer.java:81) at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20) at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:744) at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:690) at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.post2(MavenModuleSetBuild.java:1073) at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:635) at hudson.model.Run.execute(Run.java:1835) at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543) at hudson.model.ResourceController.execute(ResourceController.java:97) at hudson.model.Executor.run(Executor.java:429) Build step 'Set GitHub commit status (universal)' marked build as failure Setting status of 2f8e6622b8e0c4ab8de584383a5082efb81dc82a to FAILURE with url https://ci.phenotips.org/job/remote-matching-PR/19/ and message: 'Build finished. ' Using context: jenkins From noreply at github.com Mon Feb 11 12:52:12 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 09:52:12 -0800 Subject: [phenotips/remote-matching] 126df8: RM-125: Support additional MME metrics: variants, ... Message-ID: Branch: refs/heads/RM-125-stable Home: https://github.com/phenotips/remote-matching Commit: 126df83c5df6b0f7abe01b2e2fb856e38ac549c6 https://github.com/phenotips/remote-matching/commit/126df83c5df6b0f7abe01b2e2fb856e38ac549c6 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfCasesWithFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfRequestsReceivedProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueVariantsProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java M core/metrics/src/main/resources/META-INF/components.txt Log Message: ----------- RM-125: Support additional MME metrics: variants, features, requests received Commit: b91004080cc1860ad960356464a2792a826e9a23 https://github.com/phenotips/remote-matching/commit/b91004080cc1860ad960356464a2792a826e9a23 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java Log Message: ----------- RM-125: Support additional MME metrics: variants, features, requests received Corrected variants count Compare: https://github.com/phenotips/remote-matching/compare/126df83c5df6%5E...b91004080cc1 From noreply at github.com Mon Feb 11 12:52:59 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 09:52:59 -0800 Subject: [phenotips/remote-matching] 126df8: RM-125: Support additional MME metrics: variants, ... Message-ID: Branch: refs/heads/stable-1.1.x Home: https://github.com/phenotips/remote-matching Commit: 126df83c5df6b0f7abe01b2e2fb856e38ac549c6 https://github.com/phenotips/remote-matching/commit/126df83c5df6b0f7abe01b2e2fb856e38ac549c6 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfCasesWithFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfRequestsReceivedProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueVariantsProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java M core/metrics/src/main/resources/META-INF/components.txt Log Message: ----------- RM-125: Support additional MME metrics: variants, features, requests received Commit: b91004080cc1860ad960356464a2792a826e9a23 https://github.com/phenotips/remote-matching/commit/b91004080cc1860ad960356464a2792a826e9a23 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java Log Message: ----------- RM-125: Support additional MME metrics: variants, features, requests received Corrected variants count Commit: 2d7779a314d3542e85eb5f5af82ede13cba03b5f https://github.com/phenotips/remote-matching/commit/2d7779a314d3542e85eb5f5af82ede13cba03b5f Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfCasesWithFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfRequestsReceivedProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueFeaturesProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfUniqueVariantsProvider.java A core/metrics/src/main/java/org/phenotips/remote/metrics/internal/providers/NumberOfVariantsProvider.java M core/metrics/src/main/resources/META-INF/components.txt Log Message: ----------- Merge pull request #91 from phenotips/RM-125-stable RM-125: Support additional MME metrics: variants, features, requests received Compare: https://github.com/phenotips/remote-matching/compare/67c9354aeb76...2d7779a314d3 From noreply at github.com Mon Feb 11 12:53:37 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 17:53:37 +0000 (UTC) Subject: [phenotips/remote-matching] Message-ID: Branch: refs/heads/RM-125-stable Home: https://github.com/phenotips/remote-matching From noreply at github.com Mon Feb 11 12:53:39 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 09:53:39 -0800 Subject: [phenotips/remote-matching] Message-ID: Branch: refs/heads/RM-125 Home: https://github.com/phenotips/remote-matching From ci at phenotype.ccm.sickkids.ca Mon Feb 11 13:15:38 2019 From: ci at phenotype.ccm.sickkids.ca (PhenoTips Jenkins) Date: Mon, 11 Feb 2019 13:15:38 -0500 (EST) Subject: Jenkins build is back to normal : remote-matching-PR #20 In-Reply-To: <1422749226.66.1549908634706.JavaMail.jenkins@ci.local> References: <1422749226.66.1549908634706.JavaMail.jenkins@ci.local> Message-ID: <1613094448.68.1549908938942.JavaMail.jenkins@ci.local> See From noreply at github.com Mon Feb 11 13:30:39 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 18:30:39 +0000 (UTC) Subject: [phenotips/phenomecentral.org] 355e5f: PC-343: Generate PhenomeCentral/MME statistics Message-ID: Branch: refs/heads/PC-343 Home: https://github.com/phenotips/phenomecentral.org Commit: 355e5fdc12a58d29140cfaa33f903c0aed4d1bf4 https://github.com/phenotips/phenomecentral.org/commit/355e5fdc12a58d29140cfaa33f903c0aed4d1bf4 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: A ui/src/main/resources/PhenomeCentral/MMEStats.xml A ui/src/main/resources/PhenomeCentral/PCStats.xml Log Message: ----------- PC-343: Generate PhenomeCentral/MME statistics From jira at phenotips.atlassian.net Mon Feb 11 14:45:00 2019 From: jira at phenotips.atlassian.net (Andriy Misyura (JIRA)) Date: Mon, 11 Feb 2019 19:45:00 +0000 (UTC) Subject: [JIRA] (PT-3551) Separate "affected" status from final diagnosis In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From noreply at github.com Mon Feb 11 15:09:06 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 12:09:06 -0800 Subject: [phenotips/patient-network] 666942: PN-404: Add ability to record "My notes" to each m... Message-ID: Branch: refs/heads/PN-404 Home: https://github.com/phenotips/patient-network Commit: 66694283dbbb98691d3bdeddb5fd9e07fb6d2363 https://github.com/phenotips/patient-network/commit/66694283dbbb98691d3bdeddb5fd9e07fb6d2363 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/MatchingNotificationResource.java M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-404: Add ability to record "My notes" to each matching pair Done. Commit: c43f5ac383f26220d84d5bbc883d4c4bdc1256d8 https://github.com/phenotips/patient-network/commit/c43f5ac383f26220d84d5bbc883d4c4bdc1256d8 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/MatchingNotificationResource.java M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-404: Add ability to record My notes to each matching pair Addressed codereview comments Compare: https://github.com/phenotips/patient-network/compare/22574d956dc3...c43f5ac383f2 From noreply at github.com Mon Feb 11 15:42:40 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Mon, 11 Feb 2019 12:42:40 -0800 Subject: [phenotips/phenomecentral.org] 355e5f: PC-343: Generate PhenomeCentral/MME statistics Message-ID: Branch: refs/heads/stable-1.1.x Home: https://github.com/phenotips/phenomecentral.org Commit: 355e5fdc12a58d29140cfaa33f903c0aed4d1bf4 https://github.com/phenotips/phenomecentral.org/commit/355e5fdc12a58d29140cfaa33f903c0aed4d1bf4 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: A ui/src/main/resources/PhenomeCentral/MMEStats.xml A ui/src/main/resources/PhenomeCentral/PCStats.xml Log Message: ----------- PC-343: Generate PhenomeCentral/MME statistics Commit: fa9e00bcfe1e1d0795109fefbf441fb67e5ec17a https://github.com/phenotips/phenomecentral.org/commit/fa9e00bcfe1e1d0795109fefbf441fb67e5ec17a Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: A ui/src/main/resources/PhenomeCentral/MMEStats.xml A ui/src/main/resources/PhenomeCentral/PCStats.xml Log Message: ----------- Merge pull request #112 from phenotips/PC-343 PC-343: Generate PhenomeCentral/MME statistics Compare: https://github.com/phenotips/phenomecentral.org/compare/24fe30bb3509...fa9e00bcfe1e From noreply at github.com Mon Feb 11 15:42:44 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Mon, 11 Feb 2019 12:42:44 -0800 Subject: [phenotips/phenomecentral.org] Message-ID: Branch: refs/heads/PC-343 Home: https://github.com/phenotips/phenomecentral.org From noreply at github.com Mon Feb 11 16:04:07 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Mon, 11 Feb 2019 13:04:07 -0800 Subject: [phenotips/patient-network] 0cdc4b: [release] Set the parent version to the right value Message-ID: Branch: refs/tags/patient-network-1.1.16 Home: https://github.com/phenotips/patient-network Commit: 0cdc4b49013411353f4b66e241636b4a617e7bbc https://github.com/phenotips/patient-network/commit/0cdc4b49013411353f4b66e241636b4a617e7bbc Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [release] Set the parent version to the right value Commit: 7d9157c1dfb78a9ef20a71ecc5e09dc5185b249a https://github.com/phenotips/patient-network/commit/7d9157c1dfb78a9ef20a71ecc5e09dc5185b249a Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M access-rules/pom.xml M matching-notification-api/pom.xml M matching-notification-migrations/pom.xml M matching-notification-resources/pom.xml M matching-notification-rest/pom.xml M matching-notification-ui/pom.xml M pom.xml M similarity-data-api/pom.xml M similarity-data-impl/pom.xml M similarity-data-rest/pom.xml M similarity-genotype-view/pom.xml M similarity-phenotype-view/pom.xml M similarity-search/pom.xml M ui/pom.xml Log Message: ----------- [maven-release-plugin] prepare release patient-network-1.1.16 Compare: https://github.com/phenotips/patient-network/compare/0cdc4b490134%5E...7d9157c1dfb7 From noreply at github.com Mon Feb 11 16:07:17 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Mon, 11 Feb 2019 13:07:17 -0800 Subject: [phenotips/remote-matching] 51b3f4: [release] Set the parent version to the right value Message-ID: Branch: refs/tags/remote-matching-1.1.16 Home: https://github.com/phenotips/remote-matching Commit: 51b3f479afb15007b57371efc15164fca1c7a6eb https://github.com/phenotips/remote-matching/commit/51b3f479afb15007b57371efc15164fca1c7a6eb Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [release] Set the parent version to the right value Commit: 27fb919d1a863fb983c3746ef0d9d322c9b586dc https://github.com/phenotips/remote-matching/commit/27fb919d1a863fb983c3746ef0d9d322c9b586dc Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M core/api/pom.xml M core/client/pom.xml M core/common/pom.xml M core/hibernate/pom.xml M core/metrics/pom.xml M core/pom.xml M core/rest/pom.xml M core/server/pom.xml M pom.xml M ui/pom.xml Log Message: ----------- [maven-release-plugin] prepare release remote-matching-1.1.16 Compare: https://github.com/phenotips/remote-matching/compare/51b3f479afb1%5E...27fb919d1a86 From noreply at github.com Mon Feb 11 16:13:59 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Mon, 11 Feb 2019 13:13:59 -0800 Subject: [phenotips/phenomecentral.org] 965cf3: [release] Set the parent version to the right value Message-ID: Branch: refs/tags/phenomecentral-1.1.16 Home: https://github.com/phenotips/phenomecentral.org Commit: 965cf3f17297a0b596b72157d2de1987dc847203 https://github.com/phenotips/phenomecentral.org/commit/965cf3f17297a0b596b72157d2de1987dc847203 Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [release] Set the parent version to the right value Commit: f0d3e66c00c57ce2deecbf062200c70fc9c571e0 https://github.com/phenotips/phenomecentral.org/commit/f0d3e66c00c57ce2deecbf062200c70fc9c571e0 Author: Sergiu Dumitriu Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M hsqldb-database/pom.xml M pom.xml M rpm/pom.xml M standalone/pom.xml M ui/pom.xml M war/pom.xml Log Message: ----------- [maven-release-plugin] prepare release phenomecentral-1.1.16 Compare: https://github.com/phenotips/phenomecentral.org/compare/965cf3f17297%5E...f0d3e66c00c5 From noreply at github.com Mon Feb 11 17:04:19 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 14:04:19 -0800 Subject: [phenotips/patient-network] 742868: PN-404: Add ability to record My notes to each ma... Message-ID: Branch: refs/heads/PN-404 Home: https://github.com/phenotips/patient-network Commit: 7428684102abccb9229862db0e4ecc38d577ecc3 https://github.com/phenotips/patient-network/commit/7428684102abccb9229862db0e4ecc38d577ecc3 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-404: Add ability to record My notes to each matching pair Close all notes pop-ups before opening another From jira at phenotips.atlassian.net Mon Feb 11 17:08:41 2019 From: jira at phenotips.atlassian.net (Andriy Misyura (JIRA)) Date: Mon, 11 Feb 2019 22:08:41 +0000 (UTC) Subject: [JIRA] (PT-3927) Push code should handle usernames with extra leading and/or trailing spaces correctly In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From noreply at github.com Mon Feb 11 17:14:27 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 14:14:27 -0800 Subject: [phenotips/patient-network] 4ea917: PN-375: Support for notification history Message-ID: Branch: refs/heads/PN-375 Home: https://github.com/phenotips/patient-network Commit: 4ea91724df9e256fd01d5a1758e5e1a03686cd82 https://github.com/phenotips/patient-network/commit/4ea91724df9e256fd01d5a1758e5e1a03686cd82 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css Log Message: ----------- PN-375: Support for notification history Corrested CSS for notification history pop-up From noreply at github.com Mon Feb 11 19:21:46 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 16:21:46 -0800 Subject: [phenotips/patient-network] 2296e5: PN-345: Support for notification history Message-ID: Branch: refs/heads/PN-375 Home: https://github.com/phenotips/patient-network Commit: 2296e5ea6505318d7aa5682828356fb667119cdd https://github.com/phenotips/patient-network/commit/2296e5ea6505318d7aa5682828356fb667119cdd Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java Log Message: ----------- PN-345: Support for notification history Changed notificationHistory property getter/setter/updater to consume JSON instead of String Renamed some methods and keys Commit: f3d294995c0801de2db55cb90cf0126dc7aad159 https://github.com/phenotips/patient-network/commit/f3d294995c0801de2db55cb90cf0126dc7aad159 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history UI changes: * notification should be shown as PhenomeCentral in the notification table details for all notifications Commit: 31efbf068ef3299f795fef692f34cb16336e4c59 https://github.com/phenotips/patient-network/commit/31efbf068ef3299f795fef692f34cb16336e4c59 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java Log Message: ----------- PN-375: Support for notification history Catching NullPointerException for matching notification history JSON Commit: 04554e4be4230dfab488e37e073049c653ade41c https://github.com/phenotips/patient-network/commit/04554e4be4230dfab488e37e073049c653ade41c Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history UI changes: * before opening notification history close any notification history that is open * removed sender's link * changed tooltips contact to Email sent; notification to Notification sent * tooltips are shown when howering over column where the icon & date are shown only (not for the whole row) * undefined notification history should not be parsed to JSON * corrested CSS for notification history pop-up Compare: https://github.com/phenotips/patient-network/compare/4ea91724df9e...04554e4be423 From noreply at github.com Mon Feb 11 19:25:27 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 16:25:27 -0800 Subject: [phenotips/patient-network] 4f63cb: PN-345: Support for notification history Message-ID: Branch: refs/heads/PN-375 Home: https://github.com/phenotips/patient-network Commit: 4f63cb5191b2631fb42a73dee79791271f8037c8 https://github.com/phenotips/patient-network/commit/4f63cb5191b2631fb42a73dee79791271f8037c8 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java Log Message: ----------- PN-345: Support for notification history Changed notificationHistory property getter/setter/updater to consume JSON instead of String Renamed some methods and keys Catching NullPointerException for matching notification history JSON Commit: fee21002a5046c6e4c92ae7fc62e09099c28d5a1 https://github.com/phenotips/patient-network/commit/fee21002a5046c6e4c92ae7fc62e09099c28d5a1 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history UI changes: * notification should be shown as PhenomeCentral in the notification table details for all notifications * before opening notification history close any notification history that is open * removed sender's link * changed tooltips contact to Email sent; notification to Notification sent * tooltips are shown when howering over column where the icon & date are shown only (not for the whole row) * undefined notification history should not be parsed to JSON * corrested CSS for notification history pop-up Compare: https://github.com/phenotips/patient-network/compare/04554e4be423...fee21002a504 From noreply at github.com Mon Feb 11 19:37:01 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 16:37:01 -0800 Subject: [phenotips/patient-network] db8fcb: PN-399: Show Contact button wrt notification history Message-ID: Branch: refs/heads/PN-375 Home: https://github.com/phenotips/patient-network Commit: db8fcb33eaadfbecc882179083498c62a998ebc5 https://github.com/phenotips/patient-network/commit/db8fcb33eaadfbecc882179083498c62a998ebc5 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/MatchingNotificationResource.java M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-399: Show Contact button wrt notification history Show Contact button as secondary only if matched side has a 'contact' type record in the notification history or a match was contacted by the user outside the PhenomeCentral Removed last user column 'make contacted' button and shifted it to show in notification history pop-up on top Record user-contact outside Phenomecentral in the match notification history as a separate boolean JSON property Show 'mark user-contacted' button only if user did not contact through PhenomeCentral yet, in other words, if there is no 'contact' type records in the matched side of this match notification history Added 2 sets of filters for all users: Show/Hide contacted and notified Added information icons with hints for 2 sets of filters for all users: Show/Hide contacted and notified Commit: dece37bf1e01b72cbcdce170bdb99c8668637dcc https://github.com/phenotips/patient-network/commit/dece37bf1e01b72cbcdce170bdb99c8668637dcc Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java Log Message: ----------- PN-375: Support for notification history Preserve match notification history when match is re-descovered Commit: 7b507060374d4a5fd899c2d5b97ce282bd23d785 https://github.com/phenotips/patient-network/commit/7b507060374d4a5fd899c2d5b97ce282bd23d785 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history Save hours and minutes for notification record date Commit: a6da2d2c7396fb8d1cca5da1946453e8b9e99eaa https://github.com/phenotips/patient-network/commit/a6da2d2c7396fb8d1cca5da1946453e8b9e99eaa Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java Log Message: ----------- PN-345: Support for notification history Changed notificationHistory property getter/setter/updater to consume JSON instead of String Renamed some methods and keys Catching NullPointerException for matching notification history JSON Commit: 888df71ad1728646d4bc80436f7c2023a03cab79 https://github.com/phenotips/patient-network/commit/888df71ad1728646d4bc80436f7c2023a03cab79 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-375: Support for notification history UI changes: * show all notification history under Contact button * show Contact button as secondary if match was contacted outside PC or by any of match sides * highlighted communication popup * notification should be shown as PhenomeCentral in the notification table details for all notifications * before opening notification history close any notification history that is open * removed sender's link * changed tooltips contact to Email sent; notification to Notification sent * tooltips are shown when howering over column where the icon & date are shown only (not for the whole row) * undefined notification history should not be parsed to JSON * corrested CSS for notification history pop-up Compare: https://github.com/phenotips/patient-network/compare/fee21002a504...888df71ad172 From noreply at github.com Mon Feb 11 19:43:56 2019 From: noreply at github.com (veronikaslc) Date: Tue, 12 Feb 2019 00:43:56 +0000 (UTC) Subject: [phenotips/patient-network] 9cf7b3: PN-375: Support for notification history Message-ID: Branch: refs/heads/PN-375 Home: https://github.com/phenotips/patient-network Commit: 9cf7b3cd8972119a31c8f41e8d642ef08c59119c https://github.com/phenotips/patient-network/commit/9cf7b3cd8972119a31c8f41e8d642ef08c59119c Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java Log Message: ----------- PN-375: Support for notification history Changed notificationHistory property getter/setter/updater to consume JSON instead of String Renamed some methods and keys Catching NullPointerException for matching notification history JSON Commit: 616a30ed1d9130bee8033e04454a98dc7d59cc6d https://github.com/phenotips/patient-network/commit/616a30ed1d9130bee8033e04454a98dc7d59cc6d Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-375: Support for notification history UI changes: * show all notification history under Contact button * show Contact button as secondary if match was contacted outside PC or by any of match sides * highlighted communication popup * notification should be shown as PhenomeCentral in the notification table details for all notifications * before opening notification history close any notification history that is open * removed sender's link * changed tooltips contact to Email sent; notification to Notification sent * tooltips are shown when howering over column where the icon & date are shown only (not for the whole row) * undefined notification history should not be parsed to JSON * corrested CSS for notification history pop-up Compare: https://github.com/phenotips/patient-network/compare/888df71ad172...616a30ed1d91 From noreply at github.com Mon Feb 11 19:47:58 2019 From: noreply at github.com (veronikaslc) Date: Mon, 11 Feb 2019 16:47:58 -0800 Subject: [phenotips/patient-network] 59995e: PN-375: Support for notification history Message-ID: Branch: refs/heads/PN-375 Home: https://github.com/phenotips/patient-network Commit: 59995e47b9d887b8d421f4bf09dcd51423bdf7f7 https://github.com/phenotips/patient-network/commit/59995e47b9d887b8d421f4bf09dcd51423bdf7f7 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history Preserve match notification history when match is re-descovered Save hours and minutes for notification record date Changed notificationHistory property getter/setter/updater to consume JSON instead of String Renamed some methods and keys Catching NullPointerException for matching notification history JSON Commit: eee58576bfff0cec89ebc76a92043b2b14143659 https://github.com/phenotips/patient-network/commit/eee58576bfff0cec89ebc76a92043b2b14143659 Author: veronikaslc Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-375: Support for notification history UI changes: * show all notification history under Contact button * show Contact button as secondary if match was contacted outside PC or by any of match sides * highlighted communication popup * notification should be shown as PhenomeCentral in the notification table details for all notifications * before opening notification history close any notification history that is open * removed sender's link * changed tooltips contact to Email sent; notification to Notification sent * tooltips are shown when howering over column where the icon & date are shown only (not for the whole row) * undefined notification history should not be parsed to JSON * corrested CSS for notification history pop-up Compare: https://github.com/phenotips/patient-network/compare/616a30ed1d91...eee58576bfff From noreply at github.com Tue Feb 12 14:25:23 2019 From: noreply at github.com (veronikaslc) Date: Tue, 12 Feb 2019 19:25:23 +0000 (UTC) Subject: [phenotips/patient-network] 6423d2: PN-375: Support for notification history Message-ID: Branch: refs/heads/PN-375 Home: https://github.com/phenotips/patient-network Commit: 6423d2136b2e49a243b8930b9448006776eb0f9d https://github.com/phenotips/patient-network/commit/6423d2136b2e49a243b8930b9448006776eb0f9d Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history Show contacted outside PC button for admins From noreply at github.com Tue Feb 12 14:38:38 2019 From: noreply at github.com (veronikaslc) Date: Tue, 12 Feb 2019 19:38:38 +0000 (UTC) Subject: [phenotips/patient-network] e52ae7: PN-375: Support for notification history Message-ID: Branch: refs/heads/master Home: https://github.com/phenotips/patient-network Commit: e52ae7d7e4ea3544c26cc7b53890741614073236 https://github.com/phenotips/patient-network/commit/e52ae7d7e4ea3544c26cc7b53890741614073236 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientInMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/notification/PatientMatchNotifier.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/notification/internal/AbstractPatientMatchEmail.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/notification/internal/DefaultUserPatientMatchEmail.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/notification/internal/PatientMatchEmailNotifier.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history Commit: 253a5b509bb18dcc4946dbbf15b4dc894dbbfe23 https://github.com/phenotips/patient-network/commit/253a5b509bb18dcc4946dbbf15b4dc894dbbfe23 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-403: Display reference and matched patient in right places(columns) when we know Swap reference and matched if they are not in right place based on notMyCase if determined Commit: cdf44955f60d598b644336a58fa6555cbca73106 https://github.com/phenotips/patient-network/commit/cdf44955f60d598b644336a58fa6555cbca73106 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/MatchingNotificationResource.java M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-399: Show Contact button wrt notification history Show Contact button as secondary only if matched side has a 'contact' type record in the notification history or a match was contacted by the user outside the PhenomeCentral Removed last user column 'make contacted' button and shifted it to show in notification history pop-up on top Record user-contact outside Phenomecentral in the match notification history as a separate boolean JSON property Show 'mark user-contacted' button only if user did not contact through PhenomeCentral yet, in other words, if there is no 'contact' type records in the matched side of this match notification history Added 2 sets of filters for all users: Show/Hide contacted and notified Added information icons with hints for 2 sets of filters for all users: Show/Hide contacted and notified Commit: 30a65c7f3acc67cccb09fc57180d06bcab2f2ab7 https://github.com/phenotips/patient-network/commit/30a65c7f3acc67cccb09fc57180d06bcab2f2ab7 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history Preserve match notification history when match is re-descovered Save hours and minutes for notification record date Changed notificationHistory property getter/setter/updater to consume JSON instead of String Renamed some methods and keys Catching NullPointerException for matching notification history JSON Commit: 1bdd36160bf788370f39f4546c94be567f82c8f4 https://github.com/phenotips/patient-network/commit/1bdd36160bf788370f39f4546c94be567f82c8f4 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-375: Support for notification history UI changes: * show all notification history under Contact button * show Contact button as secondary if match was contacted outside PC or by any of match sides * highlighted communication popup * notification should be shown as PhenomeCentral in the notification table details for all notifications * before opening notification history close any notification history that is open * removed sender's link * changed tooltips contact to Email sent; notification to Notification sent * tooltips are shown when howering over column where the icon & date are shown only (not for the whole row) * undefined notification history should not be parsed to JSON * corrested CSS for notification history pop-up Commit: a4a052820221c1431a971cfb0c14d9d076adcfa3 https://github.com/phenotips/patient-network/commit/a4a052820221c1431a971cfb0c14d9d076adcfa3 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history Show contacted outside PC button for admins Compare: https://github.com/phenotips/patient-network/compare/c775d0a0b800...a4a052820221 From noreply at github.com Tue Feb 12 14:42:12 2019 From: noreply at github.com (veronikaslc) Date: Tue, 12 Feb 2019 11:42:12 -0800 Subject: [phenotips/patient-network] efd8ee: PN-404: Add ability to record "My notes" to each m... Message-ID: Branch: refs/heads/PN-404 Home: https://github.com/phenotips/patient-network Commit: efd8eee5be421067ebd2d44c770365169e65019a https://github.com/phenotips/patient-network/commit/efd8eee5be421067ebd2d44c770365169e65019a Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/MatchingNotificationResource.java M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-404: Add ability to record "My notes" to each matching pair Done. Commit: 8b0febe7bd7d456b488ae12ea64ac84ba46bb64a https://github.com/phenotips/patient-network/commit/8b0febe7bd7d456b488ae12ea64ac84ba46bb64a Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/MatchingNotificationResource.java M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-404: Add ability to record My notes to each matching pair Addressed codereview comments Commit: bf81b321ec6f024bd955417953fcb31afa3dcd49 https://github.com/phenotips/patient-network/commit/bf81b321ec6f024bd955417953fcb31afa3dcd49 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-404: Add ability to record My notes to each matching pair Close all notes pop-ups before opening another Compare: https://github.com/phenotips/patient-network/compare/7428684102ab...bf81b321ec6f From noreply at github.com Tue Feb 12 14:52:55 2019 From: noreply at github.com (veronikaslc) Date: Tue, 12 Feb 2019 11:52:55 -0800 Subject: [phenotips/patient-network] f6931a: PN-378: Change the stored format for the status co... Message-ID: Branch: refs/heads/PN-376 Home: https://github.com/phenotips/patient-network Commit: f6931a5bbfc1d7629e97491c0da37432262e501f https://github.com/phenotips/patient-network/commit/f6931a5bbfc1d7629e97491c0da37432262e501f Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-378: Change the stored format for the status comments Commit: b5edcf676cc4d58e3bc08ef2371f54bd74e3b740 https://github.com/phenotips/patient-network/commit/b5edcf676cc4d58e3bc08ef2371f54bd74e3b740 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: A matching-notification-migrations/src/main/java/org/phenotips/matchingnotification/internal/R74691PatientNetwork377DataMigration.java Log Message: ----------- PN-377: Migrate existing comments to the new format Done Commit: fc62632cee73a4879991abe681f514c06d150d3e https://github.com/phenotips/patient-network/commit/fc62632cee73a4879991abe681f514c06d150d3e Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-379: Change UI to display all comments, allow to edit new comment only Commit: 71f86c157bab846df22867293ab27f73122811eb https://github.com/phenotips/patient-network/commit/71f86c157bab846df22867293ab27f73122811eb Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- Pn-376: Preserve comment history per contributing user Addressed codereview comments: made comments uneditable Commit: e6eea22aa0bc68373744d12c891be3b205dc759d https://github.com/phenotips/patient-network/commit/e6eea22aa0bc68373744d12c891be3b205dc759d Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-migrations/src/main/java/org/phenotips/matchingnotification/internal/R74691PatientNetwork377DataMigration.java Log Message: ----------- PN-376: Preserve comment history per contributing user Fixed sql query Commit: 252cae7c0dbb26ca6d93492bc827a1a61a5df57f https://github.com/phenotips/patient-network/commit/252cae7c0dbb26ca6d93492bc827a1a61a5df57f Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-419: Improve the wording in the Matching table filters Commit: 2b3de7dbe834c1daa38709028f013b0c4faddd54 https://github.com/phenotips/patient-network/commit/2b3de7dbe834c1daa38709028f013b0c4faddd54 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-410: Highlight matching genes as bold font in patient details section Commit: a01e297f31471b77080485c7d8ba18d297c28b46 https://github.com/phenotips/patient-network/commit/a01e297f31471b77080485c7d8ba18d297c28b46 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-411: Highlight matching HPO terms as bold font in patient details section Commit: 5e756eee78487aa2e157f88a0e5406ee8f9355db https://github.com/phenotips/patient-network/commit/5e756eee78487aa2e157f88a0e5406ee8f9355db Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-410: Highlight matching genes as bold font in patient details section; PN-411: Highlight matching HPO terms as bold font in patient details section Addressed codereview comments Commit: e0432186c5ecbd83659343af6af675c58ee98838 https://github.com/phenotips/patient-network/commit/e0432186c5ecbd83659343af6af675c58ee98838 Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css Log Message: ----------- PN-419: Improve the wording in the Matching table filters; PN-410: Highlight matching genes as bold font in patient details section; PN-411: Highlight matching HPO terms as bold font in patient details section Addressed codereview comments Commit: ff78332dbc615a3f369eabaa948df1ea713b047d https://github.com/phenotips/patient-network/commit/ff78332dbc615a3f369eabaa948df1ea713b047d Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-410: Highlight matching genes as bold font in patient details section; PN-411: Highlight matching HPO terms as bold font in patient details section Addressed codereview comments Commit: ddbbcc3df7e44e37ea5ee264919d0c230c7a21cb https://github.com/phenotips/patient-network/commit/ddbbcc3df7e44e37ea5ee264919d0c230c7a21cb Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-419: Improve the flow of the Matching table filters Alligned Hide own solved cases filter label with othe labeles Compare: https://github.com/phenotips/patient-network/compare/03ed17d8461a...ddbbcc3df7e4 From noreply at github.com Tue Feb 12 15:26:55 2019 From: noreply at github.com (veronikaslc) Date: Tue, 12 Feb 2019 12:26:55 -0800 Subject: [phenotips/patient-network] 1c23bd: PN-404: Add ability to record My notes to each mat... Message-ID: Branch: refs/heads/PN-404 Home: https://github.com/phenotips/patient-network Commit: 1c23bdd0da9e998d2bd1889389b30094afa9bd7e https://github.com/phenotips/patient-network/commit/1c23bdd0da9e998d2bd1889389b30094afa9bd7e Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java Log Message: ----------- PN-404: Add ability to record My notes to each matching pair Corrected some getter/setter methods From noreply at github.com Tue Feb 12 15:41:51 2019 From: noreply at github.com (veronikaslc) Date: Tue, 12 Feb 2019 20:41:51 +0000 (UTC) Subject: [phenotips/patient-network] 206fab: PN-404: Add ability to record My notes to each mat... Message-ID: Branch: refs/heads/PN-404 Home: https://github.com/phenotips/patient-network Commit: 206fab2236deabdd94047571871df0ec86e043ab https://github.com/phenotips/patient-network/commit/206fab2236deabdd94047571871df0ec86e043ab Author: veronikaslc Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css Log Message: ----------- PN-404: Add ability to record My notes to each matching pair Corrected CSS notes pop-up width From jira at phenotips.atlassian.net Wed Feb 13 13:52:03 2019 From: jira at phenotips.atlassian.net (Sasha Andjic (JIRA)) Date: Wed, 13 Feb 2019 18:52:03 +0000 (UTC) Subject: [JIRA] (PT-3926) Reindexing HPO fails and leaves PhenoTips in a bad state In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From noreply at github.com Wed Feb 13 14:12:55 2019 From: noreply at github.com (veronikaslc) Date: Wed, 13 Feb 2019 11:12:55 -0800 Subject: [phenotips/patient-network] 0e2e9d: PN-404: Add ability to record My notes to each mat... Message-ID: Branch: refs/heads/PN-404 Home: https://github.com/phenotips/patient-network Commit: 0e2e9d79e616ac5a96d4d30598d991b86e369c12 https://github.com/phenotips/patient-network/commit/0e2e9d79e616ac5a96d4d30598d991b86e369c12 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-404: Add ability to record My notes to each matching pair Close all comments dialogs when open note dialog Close open note dialog by clicking on the note icon From noreply at github.com Wed Feb 13 17:41:02 2019 From: noreply at github.com (veronikaslc) Date: Wed, 13 Feb 2019 14:41:02 -0800 Subject: [phenotips/patient-network] 717073: PN-429: Update notification history table as soon ... Message-ID: Branch: refs/heads/PN-429 Home: https://github.com/phenotips/patient-network Commit: 71707337aea58659fa24060953e5b67dca2342e0 https://github.com/phenotips/patient-network/commit/71707337aea58659fa24060953e5b67dca2342e0 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-429: Update notification history table as soon as notification is successful From noreply at github.com Wed Feb 13 17:50:13 2019 From: noreply at github.com (veronikaslc) Date: Wed, 13 Feb 2019 22:50:13 +0000 (UTC) Subject: [phenotips/patient-network] 073df8: PN-378: Change the stored format for the status co... Message-ID: Branch: refs/heads/PN-376 Home: https://github.com/phenotips/patient-network Commit: 073df86e89597f6c4eabc85c329a881b80bd90ef https://github.com/phenotips/patient-network/commit/073df86e89597f6c4eabc85c329a881b80bd90ef Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/MatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/internal/DefaultMatchingNotificationManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/MatchStorageManager.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/storage/internal/DefaultMatchStorageManager.java M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-378: Change the stored format for the status comments Commit: 62513a2a0409f3291632a1e126708047de2aaaef https://github.com/phenotips/patient-network/commit/62513a2a0409f3291632a1e126708047de2aaaef Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: A matching-notification-migrations/src/main/java/org/phenotips/matchingnotification/internal/R74691PatientNetwork377DataMigration.java Log Message: ----------- PN-377: Migrate existing comments to the new format Done Commit: 3e1500b29591170f1a9343873e8f8e44d3600443 https://github.com/phenotips/patient-network/commit/3e1500b29591170f1a9343873e8f8e44d3600443 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-379: Change UI to display all comments, allow to edit new comment only Commit: d775e50e6f8dc1c1d1022c1c26e1abdfd50d6ebe https://github.com/phenotips/patient-network/commit/d775e50e6f8dc1c1d1022c1c26e1abdfd50d6ebe Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- Pn-376: Preserve comment history per contributing user Addressed codereview comments: made comments uneditable Commit: 5289f8d65f9cf9818b2fc01daa128e80094e42af https://github.com/phenotips/patient-network/commit/5289f8d65f9cf9818b2fc01daa128e80094e42af Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-migrations/src/main/java/org/phenotips/matchingnotification/internal/R74691PatientNetwork377DataMigration.java Log Message: ----------- PN-376: Preserve comment history per contributing user Fixed sql query Commit: 140e3ab8de07fa8506b705543703103795b8fca1 https://github.com/phenotips/patient-network/commit/140e3ab8de07fa8506b705543703103795b8fca1 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-419: Improve the wording in the Matching table filters Commit: b486fdfd35b5f3234ba022d6bd3e36d36d5fc8f7 https://github.com/phenotips/patient-network/commit/b486fdfd35b5f3234ba022d6bd3e36d36d5fc8f7 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-410: Highlight matching genes as bold font in patient details section Commit: 23a6cec876a8158cc159bcb839176c77288bbe18 https://github.com/phenotips/patient-network/commit/23a6cec876a8158cc159bcb839176c77288bbe18 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-411: Highlight matching HPO terms as bold font in patient details section Commit: 4eacdfa25b4ab16412850dda6e9ecdc35bd20527 https://github.com/phenotips/patient-network/commit/4eacdfa25b4ab16412850dda6e9ecdc35bd20527 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-410: Highlight matching genes as bold font in patient details section; PN-411: Highlight matching HPO terms as bold font in patient details section Addressed codereview comments Commit: 1de2b42433e4d238428fbe70450c96b038fe3298 https://github.com/phenotips/patient-network/commit/1de2b42433e4d238428fbe70450c96b038fe3298 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css Log Message: ----------- PN-419: Improve the wording in the Matching table filters; PN-410: Highlight matching genes as bold font in patient details section; PN-411: Highlight matching HPO terms as bold font in patient details section Addressed codereview comments Commit: a0f08f19494f4e39488e1d177e9d2f11e5b98343 https://github.com/phenotips/patient-network/commit/a0f08f19494f4e39488e1d177e9d2f11e5b98343 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.css M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-410: Highlight matching genes as bold font in patient details section; PN-411: Highlight matching HPO terms as bold font in patient details section Addressed codereview comments Commit: 7b3dfa5c54987304ea8e9786e5fe2febd4937327 https://github.com/phenotips/patient-network/commit/7b3dfa5c54987304ea8e9786e5fe2febd4937327 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-419: Improve the flow of the Matching table filters Alligned Hide own solved cases filter label with othe labeles Commit: a08e5934b1960ad02f6db95c7f15449c06ee11b5 https://github.com/phenotips/patient-network/commit/a08e5934b1960ad02f6db95c7f15449c06ee11b5 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-376: Preserve comment history per contributing user Little corrections in comment update methods documentation Compare: https://github.com/phenotips/patient-network/compare/ddbbcc3df7e4...a08e5934b196 From noreply at github.com Wed Feb 13 18:25:54 2019 From: noreply at github.com (veronikaslc) Date: Wed, 13 Feb 2019 15:25:54 -0800 Subject: [phenotips/patient-network] fbf964: PN-429: Update notification history table as soon ... Message-ID: Branch: refs/heads/PN-429 Home: https://github.com/phenotips/patient-network Commit: fbf964d836d434e4357c36b67ee7da92f59104eb https://github.com/phenotips/patient-network/commit/fbf964d836d434e4357c36b67ee7da92f59104eb Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-429: Update notification history table as soon as notification is successful From noreply at github.com Wed Feb 13 18:31:47 2019 From: noreply at github.com (veronikaslc) Date: Wed, 13 Feb 2019 15:31:47 -0800 Subject: [phenotips/patient-network] 50a1f3: PN-376: Preserve comment history per contributing ... Message-ID: Branch: refs/heads/PN-376 Home: https://github.com/phenotips/patient-network Commit: 50a1f319122ae164d799eab151829cb94efc35aa https://github.com/phenotips/patient-network/commit/50a1f319122ae164d799eab151829cb94efc35aa Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-376: Preserve comment history per contributing user Little corrections From noreply at github.com Wed Feb 13 19:46:07 2019 From: noreply at github.com (veronikaslc) Date: Wed, 13 Feb 2019 16:46:07 -0800 Subject: [phenotips/patient-network] 2ea542: PN-429: Update notification history table as soon ... Message-ID: Branch: refs/heads/PN-429 Home: https://github.com/phenotips/patient-network Commit: 2ea542a187c86836e6084bbd5f46ff65ff124667 https://github.com/phenotips/patient-network/commit/2ea542a187c86836e6084bbd5f46ff65ff124667 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-429: Update notification history table as soon as notification is successful From noreply at github.com Wed Feb 13 20:27:11 2019 From: noreply at github.com (veronikaslc) Date: Wed, 13 Feb 2019 17:27:11 -0800 Subject: [phenotips/patient-network] 360c63: PN-429: Update notification history table as soon ... Message-ID: Branch: refs/heads/PN-429 Home: https://github.com/phenotips/patient-network Commit: 360c63723068811fbf9cc40c40c46e95af4d3316 https://github.com/phenotips/patient-network/commit/360c63723068811fbf9cc40c40c46e95af4d3316 Author: veronikaslc Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matcherContactDialog.js M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-429: Update notification history table as soon as notification is successful From noreply at github.com Thu Feb 14 13:26:10 2019 From: noreply at github.com (veronikaslc) Date: Thu, 14 Feb 2019 10:26:10 -0800 Subject: [phenotips/patient-network] f8188a: PN-376: Preserve comment history per contributing ... Message-ID: Branch: refs/heads/PN-376 Home: https://github.com/phenotips/patient-network Commit: f8188afc686b298223fdbe9bb6ba31d264578b48 https://github.com/phenotips/patient-network/commit/f8188afc686b298223fdbe9bb6ba31d264578b48 Author: veronikaslc Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/PatientMatch.java M matching-notification-api/src/main/java/org/phenotips/matchingnotification/match/internal/DefaultPatientMatch.java M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-376: Preserve comment history per contributing user Little corrections From noreply at github.com Thu Feb 14 14:49:48 2019 From: noreply at github.com (veronikaslc) Date: Thu, 14 Feb 2019 19:49:48 +0000 (UTC) Subject: [phenotips/patient-network] 03d364: PN-429: Update notification history table as soon ... Message-ID: Branch: refs/heads/PN-429 Home: https://github.com/phenotips/patient-network Commit: 03d3643183277c0189873796b5a7b6a8ed7b9c64 https://github.com/phenotips/patient-network/commit/03d3643183277c0189873796b5a7b6a8ed7b9c64 Author: veronikaslc Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matcherContactDialog.js M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-429: Update notification history table as soon as notification is successful From jira at phenotips.atlassian.net Thu Feb 14 16:10:21 2019 From: jira at phenotips.atlassian.net (Andriy Misyura (JIRA)) Date: Thu, 14 Feb 2019 21:10:21 +0000 (UTC) Subject: [JIRA] (PT-3946) When a patient is imported via JSON an empty PubmedID is not discarded In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 633 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Thu Feb 14 16:11:42 2019 From: jira at phenotips.atlassian.net (Andriy Misyura (JIRA)) Date: Thu, 14 Feb 2019 21:11:42 +0000 (UTC) Subject: [JIRA] (PT-3946) When a patient is imported via JSON an empty PubmedID is not discarded In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Thu Feb 14 16:24:47 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Thu, 14 Feb 2019 21:24:47 +0000 (UTC) Subject: [JIRA] (PT-3946) When a patient is imported via JSON an empty PubmedID is not discarded In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Thu Feb 14 16:28:09 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Thu, 14 Feb 2019 21:28:09 +0000 (UTC) Subject: [JIRA] (PT-3946) When a patient is imported via JSON an empty PubmedID is not discarded In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 10:43:48 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 15:43:48 +0000 (UTC) Subject: [JIRA] (PT-3947) Write a migrator to clean up leading and trailing spaces from variants' cDNA field In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 452 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 633 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 10:44:32 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 15:44:32 +0000 (UTC) Subject: [JIRA] (PT-3948) Implement an event listener that cleans up leading and trailing spaces from variants' cDNA field when data is saved In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 452 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 633 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 10:45:10 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 15:45:10 +0000 (UTC) Subject: [JIRA] (PT-3945) Variants are not properly counted as unique because of letter case differences and possibly trailing spaces In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 10:54:29 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 15:54:29 +0000 (UTC) Subject: [JIRA] (PT-3945) The variant's cDNA is not standardized In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 10:54:37 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 15:54:37 +0000 (UTC) Subject: [JIRA] (PT-3945) The variant's cDNA is not standardized In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 10:55:09 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 15:55:09 +0000 (UTC) Subject: [JIRA] (PT-3945) The variant's cDNA field is not standardized In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 11:01:35 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 16:01:35 +0000 (UTC) Subject: [JIRA] (PT-3945) The variant's cDNA field is not standardized In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 11:12:14 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 16:12:14 +0000 (UTC) Subject: [JIRA] (PT-3945) The variant's cDNA field is not standardized In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 13:40:37 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 18:40:37 +0000 (UTC) Subject: [JIRA] (PT-3946) When a patient is imported via JSON an empty PubmedID is not discarded In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 14:24:35 2019 From: jira at phenotips.atlassian.net (VeronikaK (JIRA)) Date: Fri, 15 Feb 2019 19:24:35 +0000 (UTC) Subject: [JIRA] (PT-3930) Patient records entered in PhenoTips <1.4rc2 that has been upgraded to a version >= 1.4rc2 may have an empty PubMed ID In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From jira at phenotips.atlassian.net Fri Feb 15 14:54:41 2019 From: jira at phenotips.atlassian.net (Marta Girdea (JIRA)) Date: Fri, 15 Feb 2019 19:54:41 +0000 (UTC) Subject: [JIRA] (PT-3949) If the name of a "provider involved in care" contains an apostrophe, the entity code of the apostrophe is displayed in view mode In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From noreply at github.com Fri Feb 15 15:49:34 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Fri, 15 Feb 2019 12:49:34 -0800 Subject: [phenotips/phenotips] 5e5ec7: PT-3930: Do not migrate empty strings for pubmed ID Message-ID: Branch: refs/heads/stable-1.4.x Home: https://github.com/phenotips/phenotips Commit: 5e5ec75a7031c89fdab125647a9a5db4694185de https://github.com/phenotips/phenotips/commit/5e5ec75a7031c89fdab125647a9a5db4694185de Author: veronikaslc Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74690PhenoTips3663DataMigration.java Log Message: ----------- PT-3930: Do not migrate empty strings for pubmed ID Fixed Commit: b2b8e62e7a23ad8c41747220d292b4b3706d52ab https://github.com/phenotips/phenotips/commit/b2b8e62e7a23ad8c41747220d292b4b3706d52ab Author: veronikaslc Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: A components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74692PhenoTips3930DataMigration.java M components/patient-data/migrations/src/main/resources/META-INF/components.txt Log Message: ----------- PT-3930: Patient records entered in PhenoTips <1.4rc2 that has been upgraded to a version >= 1.4rc2 may have an empty PubMed ID Added additional migrator that removes all the empty string values added by the previous version of this one. Commit: 3435ba5fe2e5a352f6da6c2c9eefe2a89b565891 https://github.com/phenotips/phenotips/commit/3435ba5fe2e5a352f6da6c2c9eefe2a89b565891 Author: veronikaslc Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74692PhenoTips3930DataMigration.java Log Message: ----------- PT-3930: Patient records entered in PhenoTips <1.4rc2 that has been upgraded to a version >= 1.4rc2 may have an empty PubMed ID Corrected migrator description. Commit: 5891412a36254f466eb9477efff15635efa5fb0d https://github.com/phenotips/phenotips/commit/5891412a36254f466eb9477efff15635efa5fb0d Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74690PhenoTips3663DataMigration.java A components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74692PhenoTips3930DataMigration.java M components/patient-data/migrations/src/main/resources/META-INF/components.txt Log Message: ----------- Merge pull request #2807 from phenotips/PT-3930 PT-3930: Patient records entered in PhenoTips <1.4rc2 that has been upgraded to a version >= 1.4rc2 may have an empty PubMed ID Compare: https://github.com/phenotips/phenotips/compare/d9d75bef28db...5891412a3625 From noreply at github.com Fri Feb 15 15:49:36 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Fri, 15 Feb 2019 12:49:36 -0800 Subject: [phenotips/phenotips] Message-ID: Branch: refs/heads/PT-3930 Home: https://github.com/phenotips/phenotips From noreply at github.com Fri Feb 15 15:52:19 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Fri, 15 Feb 2019 12:52:19 -0800 Subject: [phenotips/phenotips] 8c5284: [misc] Upgrade POI to latest version Message-ID: Branch: refs/heads/master Home: https://github.com/phenotips/phenotips Commit: 8c52842d88cbd644f88b7172b956bbd386eeb529 https://github.com/phenotips/phenotips/commit/8c52842d88cbd644f88b7172b956bbd386eeb529 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/export/api/src/main/java/org/phenotips/export/internal/Styler.java M components/export/api/src/test/java/org/phenotips/export/internal/StylerTest.java M pom.xml Log Message: ----------- [misc] Upgrade POI to latest version Commit: daea5b48cf256791222e3b0c1fd0d055c20d37f7 https://github.com/phenotips/phenotips/commit/daea5b48cf256791222e3b0c1fd0d055c20d37f7 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/utilities/xliff12/pom.xml M components/vocabularies/api/src/main/java/org/phenotips/vocabulary/internal/solr/SolrVocabularyInputTerm.java M components/vocabularies/hpo/translation-french/src/test/java/org/phenotips/vocabulary/internal/solr/FrenchHPOTranslationTest.java M components/vocabularies/hpo/translation-german/src/test/java/org/phenotips/vocabulary/internal/solr/GermanHPOTranslationTest.java M components/vocabularies/hpo/translation-italian/src/test/java/org/phenotips/vocabulary/internal/solr/ItalianHPOTranslationTest.java M components/vocabularies/hpo/translation-russian/src/test/java/org/phenotips/vocabulary/internal/solr/RussianHPOTranslationTest.java M components/vocabularies/hpo/translation-spanish/src/test/java/org/phenotips/vocabulary/internal/solr/SpanishHPOTranslationTest.java M pom.xml Log Message: ----------- [misc] Upgraded Solr to 7.7.0 Commit: 3be3e0aa8c48b6373d5b0cadf0431daa11a675b0 https://github.com/phenotips/phenotips/commit/3be3e0aa8c48b6373d5b0cadf0431daa11a675b0 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [misc] Upgraded jackson Commit: bc5e598fdc55dfdf1ca6d209376750cfea0a3a88 https://github.com/phenotips/phenotips/commit/bc5e598fdc55dfdf1ca6d209376750cfea0a3a88 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [misc] Upgrade XWiki to 10.11.2 Commit: e16b12f070f751c961fd34946d7362b0e47c4fb7 https://github.com/phenotips/phenotips/commit/e16b12f070f751c961fd34946d7362b0e47c4fb7 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74690PhenoTips3663DataMigration.java A components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74692PhenoTips3930DataMigration.java M components/patient-data/migrations/src/main/resources/META-INF/components.txt Log Message: ----------- Merge pull request #2807 from phenotips/PT-3930 PT-3930: Patient records entered in PhenoTips <1.4rc2 that has been upgraded to a version >= 1.4rc2 may have an empty PubMed ID (cherry picked from commit 5891412a36254f466eb9477efff15635efa5fb0d) Compare: https://github.com/phenotips/phenotips/compare/a4b013de9aba...e16b12f070f7 From noreply at github.com Fri Feb 15 15:54:43 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Fri, 15 Feb 2019 12:54:43 -0800 Subject: [phenotips/phenotips] 93ceb7: Merge pull request #2807 from phenotips/PT-3930 Message-ID: Branch: refs/heads/master Home: https://github.com/phenotips/phenotips Commit: 93ceb7b7e2749bf7937c09688e298677cf70da7e https://github.com/phenotips/phenotips/commit/93ceb7b7e2749bf7937c09688e298677cf70da7e Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74690PhenoTips3663DataMigration.java A components/patient-data/migrations/src/main/java/org/phenotips/data/internal/R74692PhenoTips3930DataMigration.java M components/patient-data/migrations/src/main/resources/META-INF/components.txt Log Message: ----------- Merge pull request #2807 from phenotips/PT-3930 PT-3930: Patient records entered in PhenoTips <1.4rc2 that has been upgraded to a version >= 1.4rc2 may have an empty PubMed ID (cherry picked from commit 5891412a36254f466eb9477efff15635efa5fb0d) From jira at phenotips.atlassian.net Fri Feb 15 15:55:16 2019 From: jira at phenotips.atlassian.net (Sergiu Dumitriu (JIRA)) Date: Fri, 15 Feb 2019 20:55:16 +0000 (UTC) Subject: [JIRA] (PT-3930) Patient records entered in PhenoTips <1.4rc2 that has been upgraded to a version >= 1.4rc2 may have an empty PubMed ID In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 425 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 10805 bytes Desc: not available URL: From noreply at github.com Fri Feb 15 15:58:18 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Fri, 15 Feb 2019 12:58:18 -0800 Subject: [phenotips/phenotips] dd7b3f: [release] Set the phenotips.version to the right v... Message-ID: Branch: refs/heads/upgrades Home: https://github.com/phenotips/phenotips Commit: dd7b3f3deffdd4c26d108a183054829338286c2c https://github.com/phenotips/phenotips/commit/dd7b3f3deffdd4c26d108a183054829338286c2c Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [release] Set the phenotips.version to the right value From noreply at github.com Fri Feb 15 16:19:37 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Fri, 15 Feb 2019 13:19:37 -0800 Subject: [phenotips/phenotips] 24e412: [release] Set the phenotips.version to the right v... Message-ID: Branch: refs/tags/phenotips-1.4.4 Home: https://github.com/phenotips/phenotips Commit: 24e412b166183f825cbacff6c34ba8bd36b9e4ec https://github.com/phenotips/phenotips/commit/24e412b166183f825cbacff6c34ba8bd36b9e4ec Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [release] Set the phenotips.version to the right value Commit: cd5509ce3bdfe306de8499c90e166221c69d42dc https://github.com/phenotips/phenotips/commit/cd5509ce3bdfe306de8499c90e166221c69d42dc Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/application-configuration/api/pom.xml M components/application-configuration/migrations/pom.xml M components/application-configuration/pom.xml M components/application-configuration/ui/pom.xml M components/base-war/pom.xml M components/consents/api/pom.xml M components/consents/pom.xml M components/consents/rest/pom.xml M components/consents/ui/pom.xml M components/constants/pom.xml M components/default-settings/pom.xml M components/diagnosis-suggestion/api/pom.xml M components/diagnosis-suggestion/pom.xml M components/diagnosis-suggestion/ui/pom.xml M components/entities/api/pom.xml M components/entities/pom.xml M components/entities/ui/pom.xml M components/entity-access-rules/api/pom.xml M components/entity-access-rules/pom.xml M components/entity-access-rules/rest/pom.xml M components/export/api/pom.xml M components/export/pom.xml M components/export/ui/pom.xml M components/family-studies/api/pom.xml M components/family-studies/migrations/pom.xml M components/family-studies/pom.xml M components/family-studies/rest/pom.xml M components/family-studies/ui/pom.xml M components/gene-panels/api/pom.xml M components/gene-panels/pom.xml M components/gene-panels/rest/pom.xml M components/gene-panels/ui/pom.xml M components/navigation/api/pom.xml M components/navigation/pageobjects/pom.xml M components/navigation/pom.xml M components/navigation/tests/pom.xml M components/navigation/ui/pom.xml M components/obo2solr/pom.xml M components/patient-access-rules/api/pom.xml M components/patient-access-rules/migrations/pom.xml M components/patient-access-rules/pom.xml M components/patient-access-rules/ui/pom.xml M components/patient-contacts/pom.xml M components/patient-data-extra/medication/api/pom.xml M components/patient-data-extra/medication/pom.xml M components/patient-data-extra/medication/ui/pom.xml M components/patient-data-extra/pom.xml M components/patient-data-sharing/pom.xml M components/patient-data-sharing/push-api/pom.xml M components/patient-data-sharing/push-ui/pom.xml M components/patient-data-sharing/receiver-api/pom.xml M components/patient-data-sharing/receiver-ui/pom.xml M components/patient-data-sharing/secure-storage/pom.xml M components/patient-data-sharing/share-protocol/pom.xml M components/patient-data/api/pom.xml M components/patient-data/impl/pom.xml M components/patient-data/indexing/pom.xml M components/patient-data/migrations/pom.xml M components/patient-data/pageobjects/pom.xml M components/patient-data/pom.xml M components/patient-data/rest/pom.xml M components/patient-data/tests/pom.xml M components/patient-data/ui/pom.xml M components/patient-measurements/api/pom.xml M components/patient-measurements/migrations/pom.xml M components/patient-measurements/pom.xml M components/patient-measurements/ui/pom.xml M components/patient-tools/pom.xml M components/pedigree/api/pom.xml M components/pedigree/pom.xml M components/pedigree/resources/pom.xml M components/pedigree/ui/pom.xml M components/phenotype-suggest-service/api/pom.xml M components/phenotype-suggest-service/pom.xml M components/phenotype-suggest-service/ui/pom.xml M components/pom.xml M components/record-locking/api/pom.xml M components/record-locking/pom.xml M components/record-locking/ui/pom.xml M components/rest-commons/pom.xml M components/security/audit/backend/pom.xml M components/security/audit/frontend/pom.xml M components/security/audit/pom.xml M components/security/audit/rest/pom.xml M components/security/authorization/pom.xml M components/security/bridge/pom.xml M components/security/crypto-api/pom.xml M components/security/crypto-xproperty/pom.xml M components/security/pom.xml M components/skin/api/pom.xml M components/skin/pom.xml M components/skin/ui/pom.xml M components/specificity-meter/api/pom.xml M components/specificity-meter/pom.xml M components/specificity-meter/ui/pom.xml M components/storage-migrators/api/pom.xml M components/storage-migrators/attachments/db/pom.xml M components/storage-migrators/attachments/fs/pom.xml M components/storage-migrators/attachments/migrator/pom.xml M components/storage-migrators/attachments/pom.xml M components/storage-migrators/pom.xml M components/studies/api/pom.xml M components/studies/migrations/pom.xml M components/studies/pom.xml M components/studies/ui/pom.xml M components/user-profile-ui/pom.xml M components/users/api/pom.xml M components/users/pom.xml M components/users/rest/pom.xml M components/users/ui/pom.xml M components/utilities/component-registry/pom.xml M components/utilities/concurrency-locking/pom.xml M components/utilities/jodatime-service/pom.xml M components/utilities/ncbieutils-services/api/pom.xml M components/utilities/ncbieutils-services/pom.xml M components/utilities/ncbieutils-services/pubmed-suggestions-ui/pom.xml M components/utilities/pom.xml M components/utilities/proxy-authentication/pom.xml M components/utilities/xliff12/pom.xml M components/utilities/xwiki-platform-svg/pom.xml M components/utilities/xwiki-translation-manager/pom.xml M components/vocabularies/api/pom.xml M components/vocabularies/chebi/api/pom.xml M components/vocabularies/chebi/pom.xml M components/vocabularies/ethnicity/api/pom.xml M components/vocabularies/ethnicity/parser/pom.xml M components/vocabularies/ethnicity/pom.xml M components/vocabularies/hgnc-remote/api/pom.xml M components/vocabularies/hgnc-remote/pom.xml M components/vocabularies/hgnc/api/pom.xml M components/vocabularies/hgnc/pom.xml M components/vocabularies/hpo/annotations/pom.xml M components/vocabularies/hpo/api/pom.xml M components/vocabularies/hpo/pom.xml M components/vocabularies/hpo/translation-french/pom.xml M components/vocabularies/hpo/translation-german/pom.xml M components/vocabularies/hpo/translation-italian/pom.xml M components/vocabularies/hpo/translation-russian/pom.xml M components/vocabularies/hpo/translation-spanish/pom.xml M components/vocabularies/hpo/ui/pom.xml M components/vocabularies/omim/api/pom.xml M components/vocabularies/omim/pom.xml M components/vocabularies/oncotree/api/pom.xml M components/vocabularies/oncotree/pom.xml M components/vocabularies/ordo/api/pom.xml M components/vocabularies/ordo/pom.xml M components/vocabularies/pom.xml M components/vocabularies/rest/pom.xml M components/vocabularies/translations/pom.xml M components/vocabularies/translations/xliff/pom.xml M components/vocabularies/ui/pom.xml M components/widgets/api/pom.xml M components/widgets/pom.xml M components/widgets/resources/pom.xml M components/widgets/ui/pom.xml M components/xwiki-locks/pom.xml M components/xwiki-platform-users/pom.xml M components/xwiki-platform-users/xwiki-platform-users-api/pom.xml M components/xwiki-platform-users/xwiki-platform-users-wiki/pom.xml M distribution/dmg/pom.xml M distribution/hsqldb-database/pom.xml M distribution/pom.xml M distribution/rpm/pom.xml M distribution/standalone/pom.xml M distribution/war/pom.xml M pom.xml M resources/jetty/log-writer/pom.xml M resources/jetty/open-browser/pom.xml M resources/jetty/packaging/pom.xml M resources/jetty/pom.xml M resources/pom.xml M resources/solr-configuration/pom.xml M resources/ui/pom.xml Log Message: ----------- [maven-release-plugin] prepare release phenotips-1.4.4 Compare: https://github.com/phenotips/phenotips/compare/24e412b16618%5E...cd5509ce3bdf From noreply at github.com Fri Feb 15 20:21:00 2019 From: noreply at github.com (veronikaslc) Date: Fri, 15 Feb 2019 17:21:00 -0800 Subject: [phenotips/phenotips] 70a212: PT-3940: Add URL to contact providers Message-ID: Branch: refs/heads/PT-3940 Home: https://github.com/phenotips/phenotips Commit: 70a2121e374c0caf53e0dc3dad4a1c1e13a4abd5 https://github.com/phenotips/phenotips/commit/70a2121e374c0caf53e0dc3dad4a1c1e13a4abd5 Author: veronikaslc Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/patient-access-rules/api/src/test/java/org/phenotips/data/permissions/internal/OwnerContactProviderTest.java M components/patient-contacts/src/test/java/org/phenotips/data/internal/ReporterContactProviderTest.java Log Message: ----------- PT-3940: Add URL to contact providers Corrected tests From noreply at github.com Sat Feb 16 18:09:31 2019 From: noreply at github.com (veronikaslc) Date: Sat, 16 Feb 2019 15:09:31 -0800 Subject: [phenotips/patient-network] fc1d98: PN-429: Update notification history table as soon ... Message-ID: Branch: refs/heads/PN-429 Home: https://github.com/phenotips/patient-network Commit: fc1d98a578d96e044df2afce0a88ec72811fb810 https://github.com/phenotips/patient-network/commit/fc1d98a578d96e044df2afce0a88ec72811fb810 Author: veronikaslc Date: 2019-02-16 (Sat, 16 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matcherContactDialog.js M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-429: Update notification history table as soon as notification is successful Commit: 99f76d1ca117171b03bfac633b3131f3b1571132 https://github.com/phenotips/patient-network/commit/99f76d1ca117171b03bfac633b3131f3b1571132 Author: veronikaslc Date: 2019-02-16 (Sat, 16 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history UI changes: * Close/open history dialog by clicking on the history icon * Always show contacted outside PC button Compare: https://github.com/phenotips/patient-network/compare/03d364318327...99f76d1ca117 From noreply at github.com Sat Feb 16 19:09:09 2019 From: noreply at github.com (veronikaslc) Date: Sat, 16 Feb 2019 16:09:09 -0800 Subject: [phenotips/patient-network] a03111: PN-429: Update notification history table as soon ... Message-ID: Branch: refs/heads/PN-429 Home: https://github.com/phenotips/patient-network Commit: a03111b8664e5e87682a69c3f6816f9cbd182c3e https://github.com/phenotips/patient-network/commit/a03111b8664e5e87682a69c3f6816f9cbd182c3e Author: veronikaslc Date: 2019-02-16 (Sat, 16 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matcherContactDialog.js M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-rest/src/main/java/org/phenotips/matchingnotification/rest/internal/DefaultMatchingNotificationResource.java Log Message: ----------- PN-429: Update notification history table as soon as notification is successful Commit: 64abfa9adcc72c5cb9aeee4685be2878689d0e16 https://github.com/phenotips/patient-network/commit/64abfa9adcc72c5cb9aeee4685be2878689d0e16 Author: veronikaslc Date: 2019-02-16 (Sat, 16 Feb 2019) Changed paths: M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js Log Message: ----------- PN-375: Support for notification history UI changes: * Close/open history dialog by clicking on the history icon * Always show contacted outside PC button Compare: https://github.com/phenotips/patient-network/compare/99f76d1ca117...64abfa9adcc7 From noreply at github.com Sat Feb 16 19:22:37 2019 From: noreply at github.com (veronikaslc) Date: Sat, 16 Feb 2019 16:22:37 -0800 Subject: [phenotips/patient-network] 5cc7cf: PN-404: Add ability to record My notes to each mat... Message-ID: Branch: refs/heads/PN-404 Home: https://github.com/phenotips/patient-network Commit: 5cc7cfee1d0d860ee9c69387e585a7132aa80c1c https://github.com/phenotips/patient-network/commit/5cc7cfee1d0d860ee9c69387e585a7132aa80c1c Author: veronikaslc Date: 2019-02-16 (Sat, 16 Feb 2019) Changed paths: M matching-notification-api/src/main/resources/ApplicationResources.properties M matching-notification-resources/src/main/resources/resources/uicomponents/matchingNotification/matchesTable.js M matching-notification-ui/src/main/resources/MatchingNotification/MatchesTable.xml Log Message: ----------- PN-404: Add ability to record My notes to each matching pair Regular users can see notes in first column From noreply at github.com Sat Feb 16 21:50:40 2019 From: noreply at github.com (Sergiu Dumitriu) Date: Sat, 16 Feb 2019 18:50:40 -0800 Subject: [phenotips/phenotips] 8c5284: [misc] Upgrade POI to latest version Message-ID: Branch: refs/heads/upgrades Home: https://github.com/phenotips/phenotips Commit: 8c52842d88cbd644f88b7172b956bbd386eeb529 https://github.com/phenotips/phenotips/commit/8c52842d88cbd644f88b7172b956bbd386eeb529 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/export/api/src/main/java/org/phenotips/export/internal/Styler.java M components/export/api/src/test/java/org/phenotips/export/internal/StylerTest.java M pom.xml Log Message: ----------- [misc] Upgrade POI to latest version Commit: daea5b48cf256791222e3b0c1fd0d055c20d37f7 https://github.com/phenotips/phenotips/commit/daea5b48cf256791222e3b0c1fd0d055c20d37f7 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M components/utilities/xliff12/pom.xml M components/vocabularies/api/src/main/java/org/phenotips/vocabulary/internal/solr/SolrVocabularyInputTerm.java M components/vocabularies/hpo/translation-french/src/test/java/org/phenotips/vocabulary/internal/solr/FrenchHPOTranslationTest.java M components/vocabularies/hpo/translation-german/src/test/java/org/phenotips/vocabulary/internal/solr/GermanHPOTranslationTest.java M components/vocabularies/hpo/translation-italian/src/test/java/org/phenotips/vocabulary/internal/solr/ItalianHPOTranslationTest.java M components/vocabularies/hpo/translation-russian/src/test/java/org/phenotips/vocabulary/internal/solr/RussianHPOTranslationTest.java M components/vocabularies/hpo/translation-spanish/src/test/java/org/phenotips/vocabulary/internal/solr/SpanishHPOTranslationTest.java M pom.xml Log Message: ----------- [misc] Upgraded Solr to 7.7.0 Commit: 3be3e0aa8c48b6373d5b0cadf0431daa11a675b0 https://github.com/phenotips/phenotips/commit/3be3e0aa8c48b6373d5b0cadf0431daa11a675b0 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [misc] Upgraded jackson Commit: bc5e598fdc55dfdf1ca6d209376750cfea0a3a88 https://github.com/phenotips/phenotips/commit/bc5e598fdc55dfdf1ca6d209376750cfea0a3a88 Author: Sergiu Dumitriu Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M pom.xml Log Message: ----------- [misc] Upgrade XWiki to 10.11.2 Compare: https://github.com/phenotips/phenotips/compare/dd7b3f3deffd...bc5e598fdc55