LMS-2818 improving core plugins and service.properties for proteomics

SVN: 24617

rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties

@@ -4,6 +4,9 @@
 # Variables:
 #   incoming-root-dir
 #     Path to the directory which contains incoming directories for drop boxes.
+#
+# This drop box assumes that data source 'proteomics-db' has been defined.
+#
 incoming-dir = ${incoming-root-dir}/incoming-ms-search
 
 incoming-data-completeness-condition = auto-detection
@@ -20,7 +23,7 @@ type-extractor.is-measured = false
 storage-processor = ch.systemsx.cisd.openbis.etlserver.proteomics.StorageProcessorWithResultDataSetUploader
 storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
 storage-processor.assuming-extended-prot-xml = false
-storage-processor.database.basic-name = ${data-source.basicDatabaseName}
-storage-processor.database.kind = ${data-source.databaseKind}
+storage-processor.database.basic-name = ${proteomics-db.basicDatabaseName}
+storage-processor.database.kind = ${proteomics-db.databaseKind}
 storage-processor.database.owner = 
 storage-processor.database.password = 
\ No newline at end of file

rtd_phosphonetx/etc/service.properties

 # Unique code of this Data Store Server. Not more than 40 characters.
 data-store-server-code = DSS1
 
+root-dir = targets/playground
+
 # The root directory of the data store
-storeroot-dir = targets/playground/data/store
+storeroot-dir = ${root-dir}/data/store
+
+incoming-root-dir = ${root-dir}/data
+
+proteomics-database-kind = dev
 
 # The directory where the command queue file is located; defaults to storeroot-dir 
 commandqueue-dir =
@@ -42,10 +48,14 @@ highwater-mark = -1
 # does not affect the mails which are sent, when the data set could not be registered.
 notify-successful-registration = false
 
+dss-temp-dir = ${root-dir}/dss-temp
+dss-registration-log-dir = ${root-dir}/dss-registration-logs
+
 use-ssl = false
 
 # The URL of the openBIS server
 server-url = http://localhost:8888/openbis
+server-timeout-in-minutes = 10
 
 # The username to use when contacting the openBIS server
 username = etlserver
@@ -76,157 +86,11 @@ failure-interval = 10
 # 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 = proteomics
-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 <plugin> include: 
-#   <plugin>.class - Fully qualified plugin class name
-#   <plugin>.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
+core-plugins-folder = dist/core-plugins
 
 # ---------------------------------------------------------------------------
 
 # 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.proteomics.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/proteomics/ 
-copy-data-sets.destination =  vesuvio:tmp/${user} 
-
-ms-inj-copy.label = MS INJECTION Data Set Copier
-ms-inj-copy.dataset-types = UNKNOWN, RAW_DATA,MZXML_DATA,PROT_RESULT
-ms-inj-copy.class = ch.systemsx.cisd.openbis.dss.proteomics.server.plugins.DataSetCopier
-ms-inj-copy.marker-file-prefix = .MARKER_finished_
-ms-inj-copy.send-detailed-email = true
-#ms-inj-copy.destination =  /Volumes/share-1-\$/user/cisd/felmer/proteomics/
-ms-inj-copy.destination =  vesuvio:tmp 
-
-protein-table-report-creation.label = Send me the APMS Report
-protein-table-report-creation.class = ch.systemsx.cisd.openbis.dss.proteomics.server.plugins.APMSReport
-protein-table-report-creation.dataset-types = PROT_RESULT
-
-data-set-validators = val1
-
-val1.data-set-type = HCS_IMAGE_ANALYSIS_DATA
-val1.path-patterns = **/*.tsv, **/*.txt
-val1.columns = id, col1, col2
-val1.id.header-pattern = ID|id
-val1.id.mandatory = true
-val1.id.order = 1
-# value-type is either unique, any, string, numeric
-val1.id.value-type = unique
-val1.id.value-pattern = ^(CHEBI:[0-9]{4}_)*(CHEBI:[0-9]{4})$
-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.proteomics.DataSetInfoExtractorForMSInjection
-ms-injection.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-ms-injection.type-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.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 = <change this>
-
-# ---------------- Plugin properties
-# The extractor class to use for code extraction
-prot-result.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.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.proteomics.StorageProcessorWithResultDataSetUploader
-prot-result.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-prot-result.storage-processor.database.basic-name = ${data-source.basicDatabaseName}
-prot-result.storage-processor.database.kind = ${data-source.databaseKind}
-prot-result.storage-processor.database.owner = 
-prot-result.storage-processor.database.password = 
-
-prot-result2. = prot-result.
-prot-result2.incoming-dir = targets/playground/data/incoming2
-prot-result2.data-set-info-extractor.experiment-type-code = MS_QUANTIFICATION
-prot-result2.data-set-info-extractor.experiment-properties-file-name = quantification.properties
-
-
-# ---------------------------------------------------------------------------
-# 'cifex' thread configuration
-# ---------------------------------------------------------------------------
-cifex.incoming-dir = targets/playground/data/incoming-cifex
-cifex.incoming-data-completeness-condition = auto-detection
-cifex.delete-unidentified = true
-cifex.data-set-info-extractor = ch.systemsx.cisd.etlserver.cifex.CifexDataSetInfoExtractor
-cifex.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor
-cifex.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor
-cifex.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-cifex.storage-processor.keep-file-regex = .*(?<!request\.properties)$