g3po 0.5.1

Assorted utility CLI to work with Gen3

g3po

Assorted utility CLI to work with Gen3

Required: Python 3.6, 3.7

pip install g3po

g3po --help
g3po version

General

Environment Variable

• You can override GEN3_URL environment variable to switch to different data commons

  GEN3_URL=https://caninedc.org/ g3po index list | jq
  

• Or, export GEN3_URL in your shell environment:

  export GEN3_URL=https://caninedc.org/
  g3po index get 0614e421-0cd6-4f93-ad1d-5f9354928bd2 | jq
  

• And unset the GEN3_URL env var:

  unset GEN3_URL
  

Credentials

• Some sub-commands are required privilege access e.g.

  g3po index delete --help
  Usage: g3po index delete [OPTIONS] GUID
  
  Options:
    --cred TEXT  Path to credentials.json i.e. API key from your profile
    --help       Show this message and exit.
  

• All sub-commands has optional --cred option. If this is not provided, it assumes to load from ~/.gen3/credentials.json directory.

• You can provide --cred path to credentials.json file

  g3po index delete --cred /path/credentials.json bd59f90a-286d-4688-96a6-777a6f1df79d
  

Output Format

• You can pipe jq with g3po output for pretty JSON format

  g3po index list | jq
  

• Get index by GUID/DID

  g3po index get 1543974f-93e7-4f67-85ac-802e19ec11e8 | jq
  

Generate UUID

g3po uuid
g3po uuid --help
g3po uuid --count 10 | jq

Data Dictionary Subcommand

You can convert/compile YAML schemas into a JSON as follows:

g3po dd convert local/yaml_schemas/ --out local/my_dd.json

e.g.

git clone https://github.com/umccr/umccr-dictionary.git
cd umccr-dictionary
g3po dd convert dictionary/umccr/ --out /tmp/umccr.json
g3po dd convert dictionary/gdc/ --out /tmp/gdc.json
g3po dd convert dictionary/anvil/ --out /tmp/anvil.json

Index Subcommand

g3po index --help
g3po index health
g3po index stats
g3po index list

Creating Blank Index

• Help

  g3po index blank create --help
  Usage: g3po index blank create [OPTIONS]
  
  Options:
    --uploader TEXT  Uploading user within system, e.g. [e-mail]
                     [required]
  
    --authz TEXT     Authz resources split by comma, e.g.
                     /programs/program1/projects/P1  [required]
  
    --filename TEXT  File name, e.g. test.bam
    --cred TEXT      Path to credentials.json downloaded from your profile
    --help           Show this message and exit.
  

• You can create a blank index record as follows:

  g3po index blank create --uploader [e-mail] --authz /programs/program1/projects/P1 | jq
  {
    "baseid": "93906e3e-6a1a-4e65-813b-dcec0763ae7b",
    "did": "835a367f-4f7d-4996-a562-e23f9d57cdeb",
    "rev": "6c75a7e8"
  }  
  

• Here, make sure --uploader option set to your login username for your Gen3 common site.

• And, also make sure --authz resource ACL has properly applied to your account in Fence user.yaml config.

• Blank index record has nothing yet. You can delete it back if you like so:

  g3po index delete 835a367f-4f7d-4996-a562-e23f9d57cdeb
  

Updating Blank Index

• Help

  g3po index blank update --help
  Usage: g3po index blank update [OPTIONS]
  
  Options:
    --guid TEXT        Blank GUID/DID to update e.g.
                       1543974f-93e7-4f67-85ac-802e19ec11e8  [required]
  
    --rev TEXT         Current revision e.g. 7bd043f3  [required]
    --hash_type TEXT   Hash type e.g. md5  [required]
    --hash_value TEXT  Hash value e.g. ab167e49d25b488939b1ede42752458b
                       [required]
  
    --size INTEGER     File size in bytes, e.g. 1024  [required]
    --authz TEXT       Authz resources split by comma, e.g.
                       /programs/program1/projects/P1  [required]
  
    --urls TEXT        Resource URLs split by comma, e.g.
                       s3://bucket/1543974f-93e7-4f67-85ac-802e19ec11e8/test.txt
  
    --cred TEXT        Path to credentials.json downloaded from your profile
    --help             Show this message and exit.
  

• You can update a blank index record with hashes, size, etc... as follows:

  g3po index blank update \
    --guid bd59f90a-286d-4688-96a6-777a6f1df79d \
    --rev 5f8e7f9d \
    --hash_type md5 \
    --hash_value d0df0d078def0a5d7eb8ed6eb1e06099 \
    --size 7149868 \
    --urls s3://g3po-gen3-dev/bd59f90a-286d-4688-96a6-777a6f1df79d/somatic-PASS.vcf.gz \
    --authz /programs/program1/projects/P1 \
    | jq
  
  {
    "baseid": "811a7786-16ff-46d4-b9a2-1d647bdebfb9",
    "did": "bd59f90a-286d-4688-96a6-777a6f1df79d",
    "rev": "c203ed4d"
  }
  

Manifest Indexing

• Help

  g3po index manifest --help
  Usage: g3po index manifest [OPTIONS]
  
  Options:
    --cred TEXT       Path to credentials.json downloaded from your profile
    --tsv TEXT        Path to manifest.tsv file
    --thread INTEGER  Number of thread, default 8
    --output TEXT     Output file
    --help            Show this message and exit.
  

Generate Manifest Template

g3po index template

tree .
.
└── manifest.tsv

Manifest Format:

• guid - leave blank if you like Gen3 to generate GUID/DID.
  • Otherwise, generate UUID like so: g3po uuid --count 10 | jq or uuid v4
• md5 - use md5sum to produce hashes for your file resource
• size - determine your file resource size in bytes.
• authz - comma separated list of associated DD and resource authz ACL path that configured in Fence user.yaml.
• file_name - File name
• urls - comma separated list of the file resource URLs

Validate Manifest Format

g3po index validate
validating "manifest.tsv" manifest
mapped manifest column "md5" to "MD5Validator" class instance
mapped manifest column "urls" to "URLValidator" class instance
mapped manifest column "size" to "SizeValidator" class instance
mapped manifest column "authz" to "AuthzValidator" class instance
finished validating "manifest.tsv" manifest, no errors were found
manifest.tsv is valid!

Run Indexing

g3po index manifest

tree .
.
├── manifest.tsv
└── manifest_output_1601392690.tsv

less manifest_output_1601392690.tsv

User Subcommand

g3po user --help

User YAML from LDAP

Before executing, the environment variable G3PO_LDAP_PASSWORD must be set to the password of the LDAP user (see full options below).

g3po user ldap --user-in-yaml sample/user.in.yaml

This will transform the given user.in.yaml using information retrieved from the corresponding LDAP server. The transformed YAML will be output to stdout.

Full options as follows:

export G3PO_LDAP_PASSWORD=<option_ldap-user_password_here>

g3po user ldap \
  --user-in-yaml sample/user.in.yaml \
  --ldap-server "ldaps://ldap-test.cilogon.org" \
  --ldap-user "uid=readonly_user,ou=system,o=UMCCR,o=CO,dc=biocommons,dc=org,dc=au" \
  --ldap-search-base "ou=people,o=UMCCR,o=CO,dc=biocommons,dc=org,dc=au" > user.yaml

Validate User YAML

g3po user validate --help
g3po user validate user.yaml
g3po user validate user1.yaml user2.yaml

NOTE: this is same-as or alias to gen3user validate user.yaml

Development

• Activate virtual environment
• And install pip dependencies

pip install -e '.[dev,tests]'
which g3po
g3po version