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config.yml
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jaxlims_database:
name: rslims
user: dba
password: rsdba
host: rslims.jax.org
whereClause:
corepfs_database:
#baseURL: https://jacksonlabstest.platformforscience.com/PROD-COPY-2/odata/
baseURL: https://jacksonlabs.platformforscience.com/PROD/odata/
mouseEndpoint: KOMP_REQUEST?$expand=REV_MOUSESAMPLELOT_KOMPREQUEST($expand=SAMPLE/pfs.MOUSE_SAMPLE($filter=Active eq true))
experimentEndpointTemplate: KOMP_{exp}_EXPERIMENT?$filter=JAX_EXPERIMENT_STATUS eq 'Review Completed'&$expand=EXPERIMENT_SAMPLES($expand=ASSAY_DATA/pfs.KOMP_{exp}_ASSAY_DATA,ENTITY/pfs.MOUSE_SAMPLE_LOT($expand=SAMPLE/pfs.MOUSE_SAMPLE))
experimentOnlyEndpointTemplate: KOMP_{}_EXPERIMENT?$filter=JAX_EXPERIMENT_STATUS eq 'Data Sent to DCC'&$count=true
#experimentEndpointTemplate: KOMP_STARTLE_PPI_EXPERIMENT('KSPE3')?&$expand=EXPERIMENT_SAMPLES($expand=ASSAY_DATA/pfs.KOMP_STARTLE_PPI_ASSAY_DATA,ENTITY/pfs.MOUSE_SAMPLE_LOT($expand=SAMPLE/pfs.MOUSE_SAMPLE))
basicMouseInfoEndpoint: MOUSE_SAMPLE?$filter=Active eq true&$expand=MOUSE_SAMPLE_LOT($expand=SAMPLE)
#basicMouseInfoEndpoint: MOUSE_SAMPLE('{barcode}')
username: [email protected]
password: hRbP&6K&(Qvw
jax_study:
study: KOMP Phenotype
eap: KOMP Phenotype
lap: KOMP Aging
impc_pipeline:
pipeline: JAX_001
eap_pipeline: JAX_001
ip_pipeline: JAXIP_001
lap_pipeline: JAXLA_001
#BODY_WEIGHT
#AUDITORY_BRAINSTEM_RESPONSE
#BODY_COMPOSITION
#CLINICAL_BLOOD_CHEMISTRY
#ELECTROCARDIOGRAM
#ELECTRORETINOGRAPHY
#EYE_MORPHOLOGY
#FUNDUS_IMAGING
#GLUCOSE_TOLERANCE_TEST
#GRIP_STRENGTH
#HEART_WEIGHT
#HEMATOLOGY
#HOLEBOARD
#LIGHT_DARK_BOX
#OPEN_FIELD
#SHIRPA_DYSMORPHOLOGY
#STARTLE_PPI
impc_proc_codes:
impc_code_list: BODY_WEIGHT
impc_all_code_list: OPEN_FIELD,HOLEBOARD,SHIRPA_DYSMORPHOLOGY,STARTLE_PPI,GRIP_STRENGTH,HEMATOLOGY,CLINICAL_BLOOD_CHEMISTRY,HEART_WEIGHT,BODY_COMPOSITION,GLUCOSE_TOLERANCE_TEST,ELECTROCARDIOGRAM,ELECTRORETINOGRAPHY,FUNDUS_IMAGING,EYE_MORPHOLOGY,AUDITORY_BRAINSTEM_RESPONSE,LIGHT_DARK_BOX
impc_proc_status_codes:
impc_param_status_codes:
filenames:
dcc_xml_logfile_name: dcc_xml
directories:
dest: C:\Users\michaelm\Source\Workspaes\Teams\Lab Informatics\JAXLIMS\Main\DccReporter\data\
src: \\jax.org\jax\omero-drop\dropbox
xml_log_path: .\log\