Usage¶
Commands¶
mind¶
Welcome to MSK MIND!
mind [OPTIONS] COMMAND [ARGS]...
Options
-
--host<host>¶ [default: http://localhost:8080]
download¶
download data.
QUERY - SQL select statement or Atlas DSL string.
- returns
link to download the data bundle.
mind download [OPTIONS] QUERY
Arguments
-
QUERY¶ Required argument
list-columns¶
show available columns given database and table.
DB - database name.
TABLE - table name in the database.
- returns
list of column names and comments
mind list-columns [OPTIONS] DB TABLE
Arguments
-
DB¶ Required argument
-
TABLE¶ Required argument
list-databases¶
show available databases.
- returns
list of available databases.
mind list-databases [OPTIONS]
Examples¶
A set of Zeppelin notebooks with CLI examples are provided. The notebooks can be found on the hdp sandbox at http://<staging_ip>:9995/#/
Get patient data where patients have clinical stage ‘3C’
$ mind query "SELECT * FROM patient WHERE diagnosis_clinical_stage_group = '3C'"
{'payload': [{'patient.age_at_diagnosis': 24525,
'patient.diagnosis_clinical_stage_group': '99',
'patient.diagnosis_pathology_stage_group': '3C',
'patient.gender': 'FEMALE',
'patient.icdo_histology_code': 'M8980/3',
'patient.icdo_site_code': 'C569',
'patient.patient_dmp_id': 'P-0039384',
'patient.patient_id': 'SPECTRUM-OV-001',
'patient.patient_last_known_alive_age': 25139,
'patient.project_id': 'OV',
'patient.race': 'WHITE',
'patient.vital_status': '1.0'},
...
'status': 'OK'}
Get url to patient data bundle
$ mind download "SELECT * FROM patient WHERE diagnosis_clinical_stage_group = '3C'" --download
{'payload': 'http://<vm_ip>:50070/data/tmp/1587571607403.gz',
'status': 'OK'}
Get operational metadata for files
$ mind query "from hive_table where name like '*clinical*' select name, owner"
{'payload': [{'name': 'clinical_patient', 'owner': 'raj_ops'},
{'name': 'clinical_diagnosis', 'owner': 'raj_ops'}],
'status': 'OK'}
$ mind query "from hdfs_path where name like '*genomic*' select name, qualifiedName, path"
{'payload': [{'name': '/user/hive/genomic_cna',
'path': 'hdfs://sandbox-hdp.hortonworks.com:8020/user/hive/genomic_cna',
'qualifiedName': 'hdfs://sandbox-hdp.hortonworks.com:8020/user/hive/genomic_cna@Sandbox'},
{'name': '/user/hive/genomic_maf',
'path': 'hdfs://sandbox-hdp.hortonworks.com:8020/user/hive/genomic_maf',
'qualifiedName': 'hdfs://sandbox-hdp.hortonworks.com:8020/user/hive/genomic_maf@Sandbox'},
{'name': '/user/hive/genomic_bam',
'path': 'hdfs://sandbox-hdp.hortonworks.com:8020/user/hive/genomic_bam',
'qualifiedName': 'hdfs://sandbox-hdp.hortonworks.com:8020/user/hive/genomic_bam@Sandbox'}],
'status': 'OK'}
Get url to the data bundle
$ mind download "hive_table where name like '*genomic*' and createTime >= '2020-04-20'"
{'payload': 'http://<vm_ip>:50070/data/tmp/1588078078927.gz',
'status': 'OK'}
List available databases.
$ mind list-databases
clinical
genomic
List available tables.
$ mind list-tables clinical
| name | description |
|------------+-------------------------------------------------------------------------------|
| medication | None |
| patient | (Patient level) de-identified patient IDs, demographics info, survival status |
| diagnosis | None |
List available columns.
$ mind list-columns clinical patient
| name | type | description |
|------------------------------+--------+---------------|
| dmp_patient_id | string | None |
| patient_last_known_alive_age | int | None |
| project_id | string | None |
| gender | string | None |
| race | string | None |
| patient_id | string | None |
| vital_status | string | None |