diff --git a/dockstore_launcher_config/compose.config b/dockstore_launcher_config/compose.config index f284df5..c999b33 100644 --- a/dockstore_launcher_config/compose.config +++ b/dockstore_launcher_config/compose.config @@ -17,6 +17,8 @@ "DISCOURSE_URL":"foobar", "DOCKSTORE_DBPASSWORD":"replaceme", "DOCKSTORE_VERSION":"develop", +"DOCKSTORE_ZENODO_ACCESS_TOKEN":"", +"DOCKSTORE_ZENODO_COMMUNITY_ID":"", "DOCUMENTATION_URL":"foobar", "DOMAIN_NAME":"foobar", "ELASTICSEARCH_DOMAIN":"replaceme", @@ -52,6 +54,7 @@ "PRODUCTION":false, "QUAY_CLIENT_ID":"foobared", "QUAY_CLIENT_SECRET":"foobared", +"READONLY_DBPASSWORD":"replaceme", "SAM_PATH":"replaceme", "SLACK_URL":"replaeceme", "TAG_MANAGER_ID":"foobar", diff --git a/templates/init_migration.sh.template b/templates/init_migration.sh.template index 07a488d..08e7894 100755 --- a/templates/init_migration.sh.template +++ b/templates/init_migration.sh.template @@ -12,4 +12,4 @@ java -Ddw.database.user=postgres -Ddw.database.password="{{{ POSTGRES_DBPASSWORD # this particular migration needs to run as postgres because only postgres can surrender ownership java -Ddw.database.user=postgres -Ddw.database.password="{{{ POSTGRES_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.7.0.relinquish # future migrations will start here and should be run as dockstore -java -Ddw.database.user=dockstore -Ddw.database.password="{{{ DOCKSTORE_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.8.0,1.9.0,1.10.0,1.11.0,1.12.0,1.13.0,1.14.0,1.15.0 +java -Ddw.database.user=dockstore -Ddw.database.password="{{{ DOCKSTORE_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.8.0,1.9.0,1.10.0,1.11.0,1.12.0,1.13.0,1.14.0,1.15.0,1.16.0 diff --git a/templates/web.yml.template b/templates/web.yml.template index e20427d..d3ea375 100644 --- a/templates/web.yml.template +++ b/templates/web.yml.template @@ -25,6 +25,8 @@ zenodoClientID: {{ ZENODO_CLIENT_ID }} zenodoClientSecret: {{ ZENODO_CLIENT_SECRET }} zenodoRedirectURI: https://{{ DOMAIN_NAME }}/auth/zenodo.org zenodoUrl: {{ ZENODO_URL }} +dockstoreZenodoAccessToken: {{ DOCKSTORE_ZENODO_ACCESS_TOKEN }} +dockstoreZenodoCommunityId: {{ DOCKSTORE_ZENODO_COMMUNITY_ID }} orcidClientID: {{ ORCID_CLIENT_ID }} orcidClientSecret: {{ ORCID_CLIENT_SECRET }} @@ -58,6 +60,10 @@ samconfiguration: metricsConfig: s3BucketName: {{ METRICS_BUCKET_NAME }} +diagnosticsConfig: + logRequests: true + logPeriodic: true + # the following values describe where the webservice is being run (and on what port and using what scheme) to configure swagger externalConfig: basePath: /api/ @@ -86,14 +92,14 @@ logging: appenders: - type: console logFormat: "%-5p [%d{ISO8601,UTC}] %c\t %replace(%replace(%msg){'[\\n{};]',''}){'([A-Za-z]) ([A-Za-z])','$1_$2'}%n%rEx" + "io.dockstore.webservice.helpers.DiagnosticsHelper": DEBUG #logging for other dropwizard things appenders: - type: console # this the default dropwizard (logstash) logFormat for reference #logFormat: "%-5p [%d{ISO8601,UTC}] %c: %m%n%rEx" -# this is a logFormat that replaces new lines in messages with a → -# TODO: should do the same with exceptions, but I couldn't figure it out - logFormat: "%-5p [%d{ISO8601,UTC}] %c: %replace(%msg){'[\\n]','→'}%n%rEx" +# this is a logFormat that replaces new lines with carriage returns + logFormat: "%-5p [%d{ISO8601,UTC}] %c: %replace(%m){'\n','\r'}%n%replace(%rEx){'\n','\r'}" database: