# ---------------------------------------------------------------------------
# BIOZENTRUM formats
# ---------------------------------------------------------------------------

bz-image-analysis-results.incoming-dir = ${incoming-root-dir}/incoming-analysis-bz
bz-image-analysis-results.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
bz-image-analysis-results.data-set-info-extractor = ch.systemsx.cisd.etlserver.DataSetInfoExtractorWithFileNameProperty 
bz-image-analysis-results.data-set-info-extractor.file-name-property-code = EXTERNAL_IDENTIFIER
bz-image-analysis-results.data-set-info-extractor.extractor = ch.systemsx.cisd.openbis.dss.etl.biozentrum.BZDataSetInfoExtractor
bz-image-analysis-results.data-set-info-extractor.extractor.space-code = ${import-space-code}
bz-image-analysis-results.data-set-info-extractor.extractor.project-code = DEFAULT
bz-image-analysis-results.data-set-info-extractor.extractor.plate-geometry = 384_WELLS_16X24

# The extractor class to use for type extraction
bz-image-analysis-results.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
bz-image-analysis-results.type-extractor.file-format-type = CSV
bz-image-analysis-results.type-extractor.locator-type = RELATIVE_LOCATION
bz-image-analysis-results.type-extractor.data-set-type = HCS_IMAGE_ANALYSIS_DATA
bz-image-analysis-results.type-extractor.is-measured = false

# The storage processor (IStorageProcessor implementation)
bz-image-analysis-results.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
bz-image-analysis-results.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
bz-image-analysis-results.storage-processor.data-source = imaging-db
# semi-colon (;) by default 
bz-image-analysis-results.storage-processor.separator = ,
bz-image-analysis-results.storage-processor.ignore-comments = true
bz-image-analysis-results.storage-processor.well-name-col-is-alphanum = true

# ---------------------------------------------------------------------------

matlab-analysis.incoming-dir = ${incoming-root-dir}/incoming-matlab

matlab-analysis.incoming-data-completeness-condition = auto-detection
matlab-analysis.entity-separator = .
# The extractor class to use for code extraction
matlab-analysis.data-set-info-extractor = ch.systemsx.cisd.openbis.dss.etl.biozentrum.BZDataSetInfoExtractor
matlab-analysis.data-set-info-extractor.space-code = ${import-space-code}
matlab-analysis.data-set-info-extractor.project-code = DEFAULT
matlab-analysis.data-set-info-extractor.plate-geometry = 384_WELLS_16X24

# The extractor class to use for type extraction
matlab-analysis.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
matlab-analysis.type-extractor.file-format-type = MAT
matlab-analysis.type-extractor.locator-type = RELATIVE_LOCATION
matlab-analysis.type-extractor.data-set-type = HCS_MATLAB_PER_CLUSTER_JOB
matlab-analysis.type-extractor.is-measured = false

# The storage processor (IStorageProcessor implementation)
matlab-analysis.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
matlab-analysis.storage-processor.unzip = true
#matlab-analysis.storage-processor.delete_unzipped = false


# ------------------------------------------------------------------------


# The directory to watch for incoming data.
thumbnail-dropbox.incoming-dir = ${incoming-root-dir}/incoming-bio/incoming-thumbnails
thumbnail-dropbox.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
thumbnail-dropbox.data-set-info-extractor = ch.systemsx.cisd.etlserver.DataSetInfoExtractorWithFileNameProperty
thumbnail-dropbox.data-set-info-extractor.file-name-property-code = EXTERNAL_IDENTIFIER
thumbnail-dropbox.data-set-info-extractor.extractor = ch.systemsx.cisd.openbis.dss.etl.biozentrum.BZDataSetInfoExtractor
thumbnail-dropbox.data-set-info-extractor.extractor.space-code = DEMO
thumbnail-dropbox.data-set-info-extractor.extractor.project-code = BIOZENTRUM

# The extractor class to use for type extraction
thumbnail-dropbox.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
thumbnail-dropbox.type-extractor.file-format-type = JPG
thumbnail-dropbox.type-extractor.locator-type = RELATIVE_LOCATION
thumbnail-dropbox.type-extractor.data-set-type = HCS_IMAGE
thumbnail-dropbox.type-extractor.is-measured = false

thumbnail-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.biozentrum.LinkingStorageProcessor
thumbnail-dropbox.storage-processor.target-dir = ${root-dir}/incoming-bio/openbis-out
thumbnail-dropbox.storage-processor.processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
thumbnail-dropbox.storage-processor.processor.generate-thumbnails = true
thumbnail-dropbox.storage-processor.processor.channel-names = DAPI, GFP, Cy3
thumbnail-dropbox.storage-processor.processor.well_geometry = 2x4
thumbnail-dropbox.storage-processor.processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.FlexibleHCSImageFileExtractor
thumbnail-dropbox.storage-processor.processor.data-source = imaging-db
thumbnail-dropbox.storage-processor.processor.tile_mapping = 1,2,3,4;5,6,7,8

# The directory to watch for incoming data.
image-analysis-results.incoming-dir = ${incoming-root-dir}/incoming-bio/incoming-analysis
image-analysis-results.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
image-analysis-results.data-set-info-extractor = ch.systemsx.cisd.etlserver.DataSetInfoExtractorWithFileNameProperty 
image-analysis-results.data-set-info-extractor.file-name-property-code = EXTERNAL_IDENTIFIER
image-analysis-results.data-set-info-extractor.extractor = ch.systemsx.cisd.openbis.dss.etl.biozentrum.BZDataSetInfoExtractor
# optional: text which appears directly after the identifier 
image-analysis-results.data-set-info-extractor.extractor.separator = .per-well
image-analysis-results.data-set-info-extractor.extractor.space-code = DEMO
image-analysis-results.data-set-info-extractor.extractor.project-code = BIOZENTRUM
image-analysis-results.data-set-info-extractor.extractor.plate-geometry = 384_WELLS_16X24

# The extractor class to use for type extraction
image-analysis-results.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
image-analysis-results.type-extractor.file-format-type = CSV
image-analysis-results.type-extractor.locator-type = RELATIVE_LOCATION
image-analysis-results.type-extractor.data-set-type = HCS_IMAGE_ANALYSIS_DATA
image-analysis-results.type-extractor.is-measured = false

# The storage processor (IStorageProcessor implementation)
image-analysis-results.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
image-analysis-results.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
image-analysis-results.storage-processor.data-source = imaging-db
# semi-colon (;) by default 
image-analysis-results.storage-processor.separator = ,
image-analysis-results.storage-processor.ignore-comments = true
image-analysis-results.storage-processor.well-name-col-is-alphanum = true
image-analysis-results.storage-processor.well-name-row = File_Name
image-analysis-results.storage-processor.well-name-col = File_Name

# ----------------------------

# The directory to watch for incoming data.
bz-split-channels-images.incoming-dir = ${incoming-root-dir}/incoming-images-bz
bz-split-channels-images.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
bz-split-channels-images.data-set-info-extractor = ch.systemsx.cisd.etlserver.DataSetInfoExtractorWithFileNameProperty
bz-split-channels-images.data-set-info-extractor.file-name-property-code = EXTERNAL_IDENTIFIER
bz-split-channels-images.data-set-info-extractor.extractor = ch.systemsx.cisd.openbis.dss.etl.biozentrum.BZDataSetInfoExtractor
bz-split-channels-images.data-set-info-extractor.extractor.space-code = ${import-space-code}
bz-split-channels-images.data-set-info-extractor.extractor.project-code = DEFAULT

# The extractor class to use for type extraction
bz-split-channels-images.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
bz-split-channels-images.type-extractor.file-format-type = TIFF
bz-split-channels-images.type-extractor.locator-type = RELATIVE_LOCATION
bz-split-channels-images.type-extractor.data-set-type = HCS_IMAGE
bz-split-channels-images.type-extractor.is-measured = true

bz-split-channels-images.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
bz-split-channels-images.storage-processor.generate-thumbnails = false
bz-split-channels-images.storage-processor.channel-names = DAPI, GFP, Cy3
bz-split-channels-images.storage-processor.well_geometry = 2x3
bz-split-channels-images.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.FlexibleImageFileExtractor
bz-split-channels-images.storage-processor.data-source = imaging-db
bz-split-channels-images.storage-processor.tile_mapping = 1,2,3;4,5,6

# ---------------------------------------------------------------------------
# END BIOZENTRUM formats
# ---------------------------------------------------------------------------