# Unique code of this Data Store Server. Not more than 40 characters. data-store-server-code = DSS1 # The root directory of the data store storeroot-dir = targets/playground/data/store # The directory where the command queue file is located; defaults to storeroot-dir commandqueue-dir = # Port port = 8889 # Session timeout in minutes session-timeout = 720 # Path to the keystore keystore.path = ../datastore_server/dist/etc/openBIS.keystore # Password of the keystore keystore.password = changeit # Key password of the keystore keystore.key-password = changeit # The check interval (in seconds) check-interval = 5 # The time-out for clean up work in the shutdown sequence (in seconds). # Note that that the maximal time for the shutdown sequence to complete can be as large # as twice this time. # Remark: On a network file system, it is not recommended to turn this value to something # lower than 180. shutdown-timeout = 2 # If free disk space goes below value defined here, a notification email will be sent. # Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is # specified or if value is negative, the system will not be watching. highwater-mark = -1 # If a data set is successfully registered it sends out an email to the registrator. # If this property is not specified, no email is sent to the registrator. This property # does not affect the mails which are sent, when the data set could not be registered. notify-successful-registration = false use-ssl = false # The URL of the openBIS server server-url = http://localhost:8888/openbis # The username to use when contacting the openBIS server username = etlserver # The password to use when contacting the openBIS server password = etlserver # The base URL for Web client access. download-url = http://localhost:8889 # SMTP properties (must start with 'mail' to be considered). mail.smtp.host = file://targets/email mail.from = datastore_server@localhost # ---------------- Timing parameters for file system operations on remote shares. # Time (in seconds) to wait for any file system operation to finish. Operations exceeding this # timeout will be terminated. timeout = 60 # Number of times that a timed out operation will be tried again (0 means: every file system # operation will only ever be performed once). max-retries = 11 # Time (in seconds) to wait after an operation has been timed out before re-trying. failure-interval = 10 # The period of no write access that needs to pass before an incoming data item is considered # complete and ready to be processed (in seconds) [default: 300]. # Valid only when auto-detection method is used to determine if an incoming data are ready to be processed. quiet-period = 10 # Define names of data sources data-sources = data-source data-source.databaseEngineCode = postgresql data-source.basicDatabaseName = phosphonetx data-source.databaseKind = dev # --------------------------------------------------------------------------- # maintenance plugins configuration # --------------------------------------------------------------------------- # Comma separated names of maintenance plugins. # Each plugin should have configuration properties prefixed with its name. # Mandatory properties for each include: # .class - Fully qualified plugin class name # .interval - The time between plugin executions (in seconds) maintenance-plugins = data-set-clean-up data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask data-set-clean-up.interval = 300 data-set-clean-up.data-source = data-source # --------------------------------------------------------------------------- # Globally used separator character which separates entities in a data set file name data-set-file-name-entity-separator = _ # Specifies what should happen if an error occurs during dataset processing. # By default this flag is set to false and user has to modify the 'faulty paths file' # each time the faulty dataset should be processed again. # Set this flag to true if the processing should be repeated after some time without manual intervention. # Note that this can increase the server load. # reprocess-faulty-datasets = false reporting-plugins = demo-reporter, protein-table-report # Label of the plugin which will be shown for the users. demo-reporter.label = Show Dataset Size # Comma separated list of dataset type codes which can be handled by this plugin. demo-reporter.dataset-types = PROT_RESULT # Plugin class specification (together with the list of packages this class belongs to). demo-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoReportingPlugin # The property file. Its content will be passed as a parameter to the plugin. demo-reporter.properties-file = protein-table-report.label = APMS Report protein-table-report.class = ch.systemsx.cisd.openbis.dss.phosphonetx.server.plugins.APMSReport protein-table-report.dataset-types = PROT_RESULT # Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name. processing-plugins = copy-data-sets, ms-inj-copy, protein-table-report-creation # The configuration of the processing plugin is the same as the reporting plugins configuration. copy-data-sets.label = Data Set Copier to User Location copy-data-sets.dataset-types = UNKNOWN, PROT_RESULT copy-data-sets.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopierForUsers copy-data-sets.send-detailed-email = true #copy-data-sets.destination = /Volumes/share-1-\$/user/cisd/felmer/phosphonetx/ copy-data-sets.destination = vesuvio:tmp/${user} ms-inj-copy.label = MS INJECTION Data Set Copier ms-inj-copy.dataset-types = UNKNOWN, RAW_DATA,MZXML_DATA,PROT_RESULT ms-inj-copy.class = ch.systemsx.cisd.openbis.dss.phosphonetx.server.plugins.DataSetCopier ms-inj-copy.marker-file-prefix = .MARKER_finished_ ms-inj-copy.send-detailed-email = true #ms-inj-copy.destination = /Volumes/share-1-\$/user/cisd/felmer/phosphonetx/ ms-inj-copy.destination = vesuvio:tmp protein-table-report-creation.label = Send me the APMS Report protein-table-report-creation.class = ch.systemsx.cisd.openbis.dss.phosphonetx.server.plugins.APMSReport protein-table-report-creation.dataset-types = PROT_RESULT data-set-validators = val1 val1.data-set-type = HCS_IMAGE_ANALYSIS_DATA val1.path-patterns = **/*.tsv, **/*.txt val1.columns = id, col1, col2 val1.id.header-pattern = ID|id val1.id.mandatory = true val1.id.order = 1 # value-type is either unique, any, string, numeric val1.id.value-type = unique val1.id.value-pattern = ^(CHEBI:[0-9]{4}_)*(CHEBI:[0-9]{4})$ val1.col1.header-pattern = Description val1.col1.mandatory = true val1.col2.header-pattern = .* val1.col2.value-type = numeric val1.col2.value-range = [0,Infinity) # Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name. # E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor' inputs=ms-injection,prot-result,prot-result2,cifex # --------------------------------------------------------------------------- # MS Injection thread configuration # --------------------------------------------------------------------------- ms-injection.incoming-dir = targets/playground/data/incoming-ms ms-injection.incoming-data-completeness-condition = auto-detection ms-injection.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection ms-injection.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor ms-injection.type-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.TypeExtractorForMSInjection # --------------------------------------------------------------------------- # 'prot-result' thread configuration # --------------------------------------------------------------------------- # The directory to watch for incoming data. prot-result.incoming-dir = targets/playground/data/incoming # Determines when the incoming data should be considered complete and ready to be processed. # Allowed values: # - auto-detection - when no write access will be detected for a specified 'quite-period' # - marker-file - when an appropriate marker file for the data exists. # The default value is 'marker-file'. prot-result.incoming-data-completeness-condition = auto-detection # The group the samples extracted by this thread belong to. If commented out or empty, then samples # are considered associated to a database instance (not group private). # prot-result.group-code = # ---------------- Plugin properties # The extractor class to use for code extraction prot-result.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults prot-result.data-set-info-extractor.separator = + # The extractor class to use for type extraction prot-result.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor prot-result.type-extractor.file-format-type = XML prot-result.type-extractor.locator-type = RELATIVE_LOCATION prot-result.type-extractor.data-set-type = PROT_RESULT prot-result.type-extractor.is-measured = true # The storage processor (IStorageProcessor implementation) prot-result.storage-processor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.StorageProcessorWithResultDataSetUploader prot-result.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor prot-result.storage-processor.database.kind = dev prot-result.storage-processor.database.owner = prot-result.storage-processor.database.password = prot-result2. = prot-result. prot-result2.incoming-dir = targets/playground/data/incoming2 prot-result2.data-set-info-extractor.experiment-type-code = MS_QUANTIFICATION prot-result2.data-set-info-extractor.experiment-properties-file-name = quantification.properties # --------------------------------------------------------------------------- # 'cifex' thread configuration # --------------------------------------------------------------------------- cifex.incoming-dir = targets/playground/data/incoming-cifex cifex.incoming-data-completeness-condition = auto-detection cifex.delete-unidentified = true cifex.data-set-info-extractor = ch.systemsx.cisd.etlserver.cifex.CifexDataSetInfoExtractor cifex.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor cifex.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor cifex.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor cifex.storage-processor.keep-file-regex = .*(?