Tripal Library

A Python library for interacting with Tripal.

It allows to load data into a remote Tripal instance, and explore its content, directly from Python code, or using a CLI (Command Line Interface).

See below for examples of what you can do using the tripal python module, and the tripaille CLI.

(in case you wonder: Tripaille's name comes from a bad french word play)

Requirements

The tripal_rest_api module needs to be installed on your Tripal instance (choose the master branch for Tripal 2, or the branch 7.x-3.x for Tripal 3).

Installation

$ pip install tripal

# On first use you'll need to create a config file to connect to the tripal server, just run:

$ tripaille init
Welcome to Tripal's Tripaille!
TRIPAL_URL: http://localhost/
TRIPAL_USER: admin
TRIPAL_PASS: changeme

This will create a tripaille config file in ~/.tripaille.yml

Examples

    from tripal import TripalInstance
    ti = TripalInstance(tripal_url='http://localhost:8500/', username='admin', password='changeme')

    # Create human species
    org = ti.organism.add_organism(genus="Homo", species="sapiens", common="Human", abbr="H.sapiens")

    # Then display the list of organisms
    orgs = ti.organism.get_organisms()

    for org in orgs:
        print('{} {}'.format(org['genus'], org['species']))

    # Create an analysis
    an = ti.analysis.add_analysis(name="My cool analysis",
                                       program="Something",
                                       programversion="1.0",
                                       algorithm="Google",
                                       sourcename="src",
                                       sourceversion="2.1beta",
                                       sourceuri="http://example.org/",
                                       date_executed="2018-02-03")

    # Then display the list of organisms
    ans = ti.analysis.get_analyses()

    # And load some data
    ti.analysis.load_fasta(fasta="./test-data/Citrus_sinensis-scaffold00001.fasta", analysis_id=ans[0]['analysis_id'], organism_id=orgs[0]['organism_id'])
    ti.analysis.load_gff3(gff="./test-data/Citrus_sinensis-orange1.1g015632m.g.gff3", analysis_id=ans[0]['analysis_id'], organism_id=orgs[0]['organism_id'])

Or with the Tripaille client:

    $ tripaille organism add_organism --abbr H.sapiens --common Human Homo sapiens

    $ tripaille organism get_organisms
    [
        {
            "organism_id": "17",
            "abbreviation": "H.sapiens",
            "genus": "Homo",
            "species": "sapiens",
            "common_name": "Human",
            "infraspecific_name": null,
            "type_id": null,
            "comment": ""
        }
    ]

    # Then load some data
    $ tripaille analysis add_analysis \
        "My cool analysis" \
        "Something" \
        "v1.0" \
        "src"

    $ tripaille analysis get_analyses
    [
        {
            "analysis_id": "68",
            "name": "My cool analysis",
            "description": "",
            "program": "Something",
            "programversion": "1.0",
            "timeexecuted": "2018-02-03 00:00:00"
        },
    ]

    $ tripaille analysis load_fasta \
        --analysis_id 68 \
        --sequence_type contig \
        --organism_id 17 \
        ./test-data/Citrus_sinensis-scaffold00001.fasta

History

• 3.2.1

  • Fix error when loading blast or interpro with empty description

• 3.2

  • Fix support for elasticsearch indexing with Tripal 3

• 3.1.1

  • Minor release to fix broken package at pypi, no code change

• 3.1

  • Add expression module to manage biomaterials and expression data (with tripal_expression module)
  • Add entity.get_bundles() and entity.publish() methods for Tripal 3

• 3.0

  • Added some support for Tripal 3
    • Add job add_import_job for generic Tripal 3 importer
    • Add preliminary code for entity management (waiting for https://github.com/tripal/tripal/issues/202)
    • sync and delete_orphans are not yet implemented (https://github.com/tripal/tripal/issues/337)
  • GFF3: removed bugged 'refresh' and 'remove' loading mode (no more available in Tripal3)
  • Renamed organism get_organism_nodes to organism get_organisms_tripal and analysis get_analysis_nodes to analysis get_analyses_tripal. Both now return Drupal Nodes for Tripal 2 or Entities for Tripal 3.
  • Added delete_orphans methods for organisms and analyses
  • Added tests

• 2.0.4

  • Small bug fixes

• 2.0.3

  • More reliable detection of job failures

• 2.0.2

  • Fix broken pip install tripal

• 2.0.1

  • Fix missing requirements

• 2.0

  • Rewritten most of the code, now working in a similar way as parsec or chakin
  • New cli tool named 'tripaille'
  • Tripal jobs can now be run directly by python-tripal and stdout and stderr are retrieved at the end of jobs.
  • Updated indexing code to latest tripal_elasticsearch module

• 1.9

  • Wait for job completion and get logs

License

Available under the MIT License