Resolve conflicts for master #81
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…ero (#71) The ETL script and related modules can now properly register metadata properties in the OMERO server as key-value pairs. The ETL script now reads the TSV and creates a property map for each file, it then uses the backend module to register the property pairs. I verified that the metadata properties are properly registered in the OMERO server. this is a sample of the ETL output for test dataset 3: New incoming image file for OMERO registration: /home/qeana10/dss/store/1/pre-staging/2021-02-25_12-46-46-408_register-omero-metadata_QIMGT654A2/QIMGT654A2/sub_tomo_1.mrc Created OMERO image identifiers: ['11035'] Metadata properties: KEY : VALUE --> SAMPLE_BARCODE : QIMGT649A1 --> IMAGING_MODALITY : Cryo-ET --> IMAGE_BINNING : 2 --> IMAGED_TISSUE : cell --> CAMERA_ACQUISITION_TIME : 0.15 --> INSTRUMENT_MANUFACTURER : FEI New incoming image file for OMERO registration: /home/qeana10/dss/store/1/pre-staging/2021-02-25_12-46-46-408_register-omero-metadata_QIMGT654A2/QIMGT654A2/rubisco_avg.mrc Created OMERO image identifiers: ['11036'] Metadata properties: KEY : VALUE --> SAMPLE_BARCODE : QIMGT649A1 --> IMAGING_MODALITY : Cryo-ET --> IMAGE_BINNING : 2 --> IMAGED_TISSUE : cell --> CAMERA_ACQUISITION_TIME : 0.15 --> INSTRUMENT_MANUFACTURER : FEI New incoming image file for OMERO registration: /home/qeana10/dss/store/1/pre-staging/2021-02-25_12-46-46-408_register-omero-metadata_QIMGT654A2/QIMGT654A2/Image7246.tif Created OMERO image identifiers: ['11037'] Metadata properties: KEY : VALUE --> SAMPLE_BARCODE : QIMGT649A1 --> IMAGING_MODALITY : TEM --> IMAGE_BINNING : 2 --> IMAGED_TISSUE : leaf --> CAMERA_ACQUISITION_TIME : 0.15 --> INSTRUMENT_MANUFACTURER : Zeiss New incoming image file for OMERO registration: /home/qeana10/dss/store/1/pre-staging/2021-02-25_12-46-46-408_register-omero-metadata_QIMGT654A2/QIMGT654A2/Est-B1a.lif Created OMERO image identifiers: ['11038', '11039', '11040', '11041'] Metadata properties: KEY : VALUE --> SAMPLE_BARCODE : QIMGT649A1 --> IMAGING_MODALITY : confocal_microscopy --> IMAGE_BINNING : 2 --> IMAGED_TISSUE : root --> CAMERA_ACQUISITION_TIME : 0.15 --> INSTRUMENT_MANUFACTURER : Zeiss New incoming image file for OMERO registration: /home/qeana10/dss/store/1/pre-staging/2021-02-25_12-46-46-408_register-omero-metadata_QIMGT654A2/QIMGT654A2/Image_1.czi Created OMERO image identifiers: ['11042'] Metadata properties: KEY : VALUE --> SAMPLE_BARCODE : QIMGT649A1 --> IMAGING_MODALITY : confocal_microscopy --> IMAGE_BINNING : 2 --> IMAGED_TISSUE : leaf --> CAMERA_ACQUISITION_TIME : 0.15 --> INSTRUMENT_MANUFACTURER : Zeiss New incoming image file for OMERO registration: /home/qeana10/dss/store/1/pre-staging/2021-02-25_12-46-46-408_register-omero-metadata_QIMGT654A2/QIMGT654A2/Image_2.czi Created OMERO image identifiers: ['11043'] Metadata properties: KEY : VALUE --> SAMPLE_BARCODE : QIMGT649A1 --> IMAGING_MODALITY : confocal_microscopy --> IMAGE_BINNING : 2 --> IMAGED_TISSUE : leaf --> CAMERA_ACQUISITION_TIME : 0.15 --> INSTRUMENT_MANUFACTURER : Zeiss
Feature/omero openbis metadata
* Handle registration of imaging data and metadata (OMERO and openBIS) * Update drop-boxes/register-omero-metadata/register-omero.py * format omero ids correctly for openbis * handle datamover folders correctly Co-authored-by: wow-such-code <andreas.friedrich@uni-tuebingen.de>
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