LMS-941 yeastx: config files

SVN: 11456

rtd_yeastx/sourceTest/bash/dss-config/datastore_server-service.properties

+# 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 = /misc/nas/openbis/store
+
+# Port
+port = 8444
+
+# Session timeout in minutes
+session-timeout = 720
+
+# Path to the keystore
+keystore.path = 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 = 20
+
+# 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 = 180
+
+# 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
+
+# The URL of the openBIS server
+server-url = https://imsb-us-openbis.ethz.ch:8443/openbis/openbis
+
+# The username to use when contacting the openBIS server
+username = etlserver_yeastx
+
+# The password to use when contacting the openBIS server
+password = Jd7;14A8Cka(
+
+# The base URL for Web client access.
+download-url = https://imsb-us-openbis.ethz.ch:8444
+
+# email settings 
+mail.smtp.host = smtp0.ethz.ch
+mail.from = openbis@imsb-us-openbis.ethz.ch
+mail.smtp.user = 
+mail.smtp.password = 
+
+# ---------------- 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 = 30
+
+# 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 any manual intervention.
+reprocess-faulty-datasets = true
+
+# 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=main-thread, eicml-uploader, fiaml-uploader
+
+# Globally used separator character which separates entities in a data set file name 
+data-set-file-name-entity-separator = .
+
+# ---------------------------------------------------------------------------
+# 'main-thread' thread configuration
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+main-thread.incoming-dir = /misc/nas/openbis/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'.
+main-thread.incoming-data-completeness-condition = auto-detection
+main-thread.incoming-dir.format = 
+
+sample-name-property-code = samplename
+experiment-name-property-code = name
+
+yeastx-databaseEngineCode = postgresql
+yeastx-basicDatabaseName = metabol
+yeastx-databaseKind = productive
+
+main-thread.dataset-handler = ch.systemsx.cisd.yeastx.etl.BatchDataSetHandler
+main-thread.dataset-handler.unique-sample-name-property-code = ${sample-name-property-code}
+main-thread.dataset-handler.unique-experiment-name-property-code = ${experiment-name-property-code}
+
+# The extractor class to use for code extraction
+main-thread.data-set-info-extractor = ch.systemsx.cisd.yeastx.etl.BatchDataSetInfoExtractor
+main-thread.data-set-info-extractor.unique-sample-name-property-code = ${sample-name-property-code}
+main-thread.data-set-info-extractor.unique-experiment-name-property-code = ${experiment-name-property-code}
+
+# The extractor class to use for type extraction
+main-thread.type-extractor = ch.systemsx.cisd.yeastx.etl.TypeExtractorYeastX
+
+# The storage processor (IStorageProcessor implementation)
+main-thread.storage-processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithDropboxes
+main-thread.storage-processor.eicml-dropbox-dir = /misc/dropbox/openbis/in-eicML
+main-thread.storage-processor.fiaml-dropbox-dir = /misc/dropbox/openbis/in-fiaML
+main-thread.storage-processor.entity-separator = .
+main-thread.storage-processor.processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithMLUploader
+main-thread.storage-processor.processor.unique-sample-name-property-code = ${sample-name-property-code}
+main-thread.storage-processor.processor.unique-experiment-name-property-code = ${experiment-name-property-code}
+main-thread.storage-processor.processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+main-thread.storage-processor.processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+main-thread.storage-processor.processor.database.databaseKind = ${yeastx-databaseKind}
+main-thread.storage-processor.processor.database.readOnlyGroup = metabol_readonly
+main-thread.storage-processor.processor.database.readWriteGroup = metabol_readwrite
+main-thread.storage-processor.processor.database.scriptFolder = sql
+main-thread.storage-processor.processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
+
+# ---------------------------------------------------------------------------
+# plugin properties for the thread which uploads eicML files
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+eicml-uploader.incoming-dir = /misc/nas/openbis/incoming-eicML
+eicml-uploader.incoming-data-completeness-condition = auto-detection
+eicml-uploader.incoming-dir.format = 
+
+# The extractor class to use for code extraction
+eicml-uploader.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+eicml-uploader.data-set-info-extractor.index-of-sample-code = 0
+eicml-uploader.data-set-info-extractor.index-of-group-code = 1
+eicml-uploader.data-set-info-extractor.index-of-parent-data-set-code = 2
+eicml-uploader.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
+
+# The extractor class to use for type extraction
+eicml-uploader.type-extractor = ch.systemsx.cisd.yeastx.etl.TypeExtractorYeastX
+eicml-uploader.type-extractor.file-format-type = XML
+eicml-uploader.type-extractor.locator-type = RELATIVE_LOCATION
+eicml-uploader.type-extractor.data-set-type = EICML
+eicml-uploader.type-extractor.is-measured = false
+
+# The storage processor which uploads the content of the files to the additional database
+eicml-uploader.storage-processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithMLUploader
+eicml-uploader.storage-processor.unique-sample-name-property-code = ${sample-name-property-code}
+eicml-uploader.storage-processor.unique-experiment-name-property-code = ${experiment-name-property-code}
+eicml-uploader.storage-processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+eicml-uploader.storage-processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+eicml-uploader.storage-processor.database.databaseKind = ${yeastx-databaseKind}
+eicml-uploader.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
+# ---------------- plugin properties for the thread which uploads fiaML files
+
+# The directory to watch for incoming data.
+fiaml-uploader.incoming-dir = /misc/nas/openbis/incoming-fiaML
+fiaml-uploader.incoming-data-completeness-condition = auto-detection
+fiaml-uploader.incoming-dir.format = 
+
+
+# The extractor class to use for code extraction
+fiaml-uploader.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+fiaml-uploader.data-set-info-extractor.index-of-sample-code = 0
+fiaml-uploader.data-set-info-extractor.index-of-group-code = 1
+fiaml-uploader.data-set-info-extractor.index-of-parent-data-set-code = 2
+fiaml-uploader.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
+
+# The extractor class to use for type extraction
+fiaml-uploader.type-extractor = ch.systemsx.cisd.yeastx.etl.TypeExtractorYeastX
+fiaml-uploader.type-extractor.file-format-type = XML
+fiaml-uploader.type-extractor.locator-type = RELATIVE_LOCATION
+fiaml-uploader.type-extractor.data-set-type = FIAML
+fiaml-uploader.type-extractor.is-measured = false
+
+# The storage processor which uploads the content of the files to the additional database
+fiaml-uploader.storage-processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithMLUploader
+fiaml-uploader.storage-processor.unique-sample-name-property-code = ${sample-name-property-code}
+fiaml-uploader.storage-processor.unique-experiment-name-property-code = ${experiment-name-property-code}
+fiaml-uploader.storage-processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+fiaml-uploader.storage-processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+fiaml-uploader.storage-processor.database.databaseKind = ${yeastx-databaseKind}
+fiaml-uploader.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
\ No newline at end of file

rtd_yeastx/sourceTest/bash/dss-config/service.properties

@@ -44,6 +44,14 @@ password = doesnotmatter
 # The base URL for Web client access.
 download-url = https://localhost:8889
 
+# email settings 
+#mail.smtp.host = smtp0.ethz.ch
+# TODO change this, just for tests !!!!!!!!
+mail.smtp.host = file:///Users/tpylak/main/tmp
+mail.from = openbis@imsb-us-openbis.ethz.ch
+mail.smtp.user = 
+mail.smtp.password = 
+
 # 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.
@@ -55,13 +63,6 @@ quiet-period = 3
 # Set this flag to true if the processing should be repeated after some time without any manual intervention.
 reprocess-faulty-datasets = true
 
-#mail.smtp.host = smtp0.ethz.ch
-# TODO change this, just for tests !!!!!!!!
-mail.smtp.host = file:///Users/tpylak/main/tmp
-mail.from = openbis@imsb-us-openbis.ethz.ch
-mail.smtp.user = 
-mail.smtp.password = 
-
 # 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=main-thread, eicml-uploader, fiaml-uploader