python-tripal and tripaille¶

Contents:

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

Commands¶

Tripaille is a set of wrappers for accessing Tripal. Each utility is implemented as a subcommand of tripaille. This section of the documentation describes these commands.

analysis¶

This section is auto-generated from the help text for the tripaille command analysis.

`add_analysis` command¶

Usage:

tripaille analysis add_analysis [OPTIONS] NAME PROGRAM PROGRAMVERSION

Help

Create an analysis

Output

Analysis information

Options:

--algorithm TEXT      analysis algorithm
--sourceversion TEXT  analysis sourceversion
--sourceuri TEXT      analysis sourceuri
--description TEXT    analysis description
--date_executed TEXT  analysis date_executed (yyyy-mm-dd)
-h, --help            Show this message and exit.

`delete_orphans` command¶

Usage:

tripaille analysis delete_orphans [OPTIONS]

Help

Delete orphans Drupal analysis nodes

Output

status

Options:

--job_name TEXT  Name of the job
--no_wait        Return immediately without waiting for job completion
-h, --help       Show this message and exit.

`get_analyses` command¶

Usage:

tripaille analysis get_analyses [OPTIONS]

Help

Get analyses

Output

Analysis information

Options:

--analysis_id TEXT     An analysis ID
--name TEXT            analysis name
--program TEXT         analysis program
--programversion TEXT  analysis programversion
--algorithm TEXT       analysis algorithm
--sourcename TEXT      analysis sourcename
--sourceversion TEXT   analysis sourceversion
--sourceuri TEXT       analysis sourceuri
--date_executed TEXT   analysis date_executed (yyyy-mm-dd)
-h, --help             Show this message and exit.

`get_analyses_tripal` command¶

Usage:

tripaille analysis get_analyses_tripal [OPTIONS]

Help

Get analysis entities

Output

Analysis entity/node information

Options:

--analysis_id INTEGER  An analysis entity/node ID
-h, --help             Show this message and exit.

`load_blast` command¶

Usage:

tripaille analysis load_blast [OPTIONS] NAME PROGRAM PROGRAMVERSION

Help

Create a Blast analysis

Output

Loading information

Options:

--blast_ext TEXT         If looking for files in a directory, extension of the
                         blast result files
--blastdb TEXT           Name of the database blasted against (must be in the
                         Chado db table)
--blastdb_id TEXT        ID of the database blasted against (must be in the
                         Chado db table)
--blast_parameters TEXT  Blast parameters used to produce these results
--query_re TEXT          The regular expression that can uniquely identify the
                         query name. This parameters is required if the
                         feature name is not the first word in the blast query
                         name.
--query_type TEXT        The feature type (e.g. 'gene', 'mRNA', 'contig') of
                         the query. It must be a valid Sequence Ontology term.
--query_uniquename       Use this if the --query-re regular expression matches
                         unique names instead of names in the database.
--is_concat              If the blast result file is simply a list of
                         concatenated blast results.
--search_keywords        Extract keywords for Tripal search
--no_parsed TEXT         Maximum number of hits to parse per feature.
                         Default=all  [default: all]
--no_wait                Do not wait for job to complete
--algorithm TEXT         analysis algorithm
--sourceversion TEXT     analysis sourceversion
--sourceuri TEXT         analysis sourceuri
--description TEXT       analysis description
--date_executed TEXT     analysis date_executed (yyyy-mm-dd)
-h, --help               Show this message and exit.

`load_fasta` command¶

Usage:

tripaille analysis load_fasta [OPTIONS] FASTA

Help

Load fasta sequences

Output

Loading information

Options:

--organism TEXT          Organism common name or abbreviation
--organism_id INTEGER    Organism ID
--analysis TEXT          Analysis name
--analysis_id INTEGER    Analysis ID
--sequence_type TEXT     Sequence type  [default: contig]
--re_name TEXT           Regular expression for the name
--re_uniquename TEXT     Regular expression for the unique name
--db_ext_id TEXT         External DB ID
--re_accession TEXT      Regular expression for the accession from external DB
--rel_type TEXT          Relation type (part_of or derives_from)
--rel_subject_re TEXT    Relation subject regular expression (used to extract
                         id of related entity)
--rel_subject_type TEXT  Relation subject type (must match already loaded
                         data, e.g. mRNA)
--method TEXT            Insertion method (insert, update or insup,
                         default=insup (Insert and Update))  [default: insup]
--match_type TEXT        Match type for already loaded features (name or
                         uniquename; default=uniquename; used for "Update
                         only" or "Insert and update" methods)'  [default:
                         uniquename]
--job_name TEXT          Name of the job
--no_wait                Do not wait for job to complete
-h, --help               Show this message and exit.

`load_gff3` command¶

Usage:

tripaille analysis load_gff3 [OPTIONS] GFF

Help

Load GFF3 file

Output

Loading information

Options:

--organism TEXT               Organism common name or abbreviation
--organism_id INTEGER         Organism ID
--analysis TEXT               Analysis name
--analysis_id INTEGER         Analysis ID
--import_mode TEXT            Import mode (add_only=existing features won't be
                              touched, update=existing features will be
                              updated and obsolete attributes kept)')
                              [default: update]
--target_organism TEXT        In case of Target attribute in the GFF3, choose
                              the organism abbreviation or common name to
                              which target sequences belong. Select this only
                              if target sequences belong to a different
                              organism than the one specified with --organism-
                              id. And only choose an organism here if all of
                              the target sequences belong to the same species.
                              If the targets in the GFF file belong to
                              multiple different species then the organism
                              must be specified using the
                              'target_organism=genus:species' attribute in the
                              GFF file.')
--target_organism_id INTEGER  In case of Target attribute in the GFF3, choose
                              the organism ID to which target sequences
                              belong. Select this only if target sequences
                              belong to a different organism than the one
                              specified with --organism-id. And only choose an
                              organism here if all of the target sequences
                              belong to the same species. If the targets in
                              the GFF file belong to multiple different
                              species then the organism must be specified
                              using the 'target_organism=genus:species'
                              attribute in the GFF file.')
--target_type TEXT            In case of Target attribute in the GFF3, if the
                              unique name for a target sequence is not unique
                              (e.g. a protein and an mRNA have the same name)
                              then you must specify the type for all targets
                              in the GFF file. If the targets are of different
                              types then the type must be specified using the
                              'target_type=type' attribute in the GFF file.
                              This must be a valid Sequence Ontology (SO)
                              term.')
--target_create               In case of Target attribute in the GFF3, if the
                              target feature cannot be found, create one using
                              the organism and type specified above, or using
                              the 'target_organism' and 'target_type' fields
                              specified in the GFF file. Values specified in
                              the GFF file take precedence over those
                              specified above.')
--start_line INTEGER          The line in the GFF file where importing should
                              start
--landmark_type TEXT          A Sequence Ontology type for the landmark
                              sequences in the GFF fie (e.g. 'chromosome').
--alt_id_attr TEXT            When ID attribute is absent, specify which other
                              attribute can uniquely identify the feature.
--create_organism             Create organisms when encountering organism
                              attribute (these lines will be skip otherwise)
--re_mrna TEXT                Regular expression for the mRNA name
--re_protein TEXT             Replacement string for the protein name
--job_name TEXT               Name of the job
--no_wait                     Do not wait for job to complete
-h, --help                    Show this message and exit.

`load_go` command¶

Usage:

tripaille analysis load_go [OPTIONS] NAME PROGRAM PROGRAMVERSION

Help

Create a GO analysis

Output

Loading information

Options:

--organism TEXT        Organism common name or abbreviation
--organism_id INTEGER  Organism ID
--gaf_ext TEXT         If looking for files in a directory, extension of the
                       GAF files
--query_type TEXT      The feature type (e.g. 'gene', 'mRNA', 'contig') of the
                       query. It must be a valid Sequence Ontology term.
--query_matching TEXT  Method to match identifiers to features in the
                       database. ('name', 'uniquename' or 'dbxref')  [default:
                       uniquename]
--method TEXT          Import method ('add' or 'remove')  [default: add]
--name_column INTEGER  Column containing the feature identifiers (2, 3, 10 or
                       11; default=2).  [default: 2]
--re_name TEXT         Regular expression to extract the feature name from GAF
                       file.
--no_wait              Do not wait for job to complete
--algorithm TEXT       analysis algorithm
--sourceversion TEXT   analysis sourceversion
--sourceuri TEXT       analysis sourceuri
--description TEXT     analysis description
--date_executed TEXT   analysis date_executed (yyyy-mm-dd)
-h, --help             Show this message and exit.

`load_interpro` command¶

Usage:

tripaille analysis load_interpro [OPTIONS] NAME PROGRAM PROGRAMVERSION

Help

Create an Interpro analysis

Output

Loading information

Options:

--interpro_parameters TEXT  InterProScan parameters used to produce these
                            results
--query_re TEXT             The regular expression that can uniquely identify
                            the query name. This parameters is required if the
                            feature name is not the first word in the blast
                            query name.
--query_type TEXT           The feature type (e.g. 'gene', 'mRNA', 'contig')
                            of the query. It must be a valid Sequence Ontology
                            term.
--query_uniquename          Use this if the query_re regular expression
                            matches unique names instead of names in the
                            database.
--parse_go                  Load GO annotation to the database
--no_wait                   Do not wait for job to complete
--algorithm TEXT            analysis algorithm
--sourceversion TEXT        analysis sourceversion
--sourceuri TEXT            analysis sourceuri
--description TEXT          analysis description
--date_executed TEXT        analysis date_executed (yyyy-mm-dd)
-h, --help                  Show this message and exit.

`sync` command¶

Usage:

tripaille analysis sync [OPTIONS]

Help

Synchronize an analysis

Output

status

Options:

--analysis TEXT     Analysis name
--analysis_id TEXT  ID of the analysis to sync
--job_name TEXT     Name of the job
--no_wait           Return immediately without waiting for job completion
-h, --help          Show this message and exit.

db¶

This section is auto-generated from the help text for the tripaille command db.

`get_dbs` command¶

Usage:

tripaille db get_dbs [OPTIONS]

Help

Get all dbs

Output

Dbs information

Options:

--db_id TEXT  A db ID
--name TEXT   filter on db name
-h, --help    Show this message and exit.

`get_mviews` command¶

Usage:

tripaille db get_mviews [OPTIONS]

Help

Get all materialized views

Output

materialized views information

Options:

--name TEXT  filter on mview name
-h, --help   Show this message and exit.

`index` command¶

Usage:

tripaille db index [OPTIONS]

Help

Schedule database indexing using elasticsearch

Output

Indexing information

Options:

--mode TEXT        Indexing mode: 'website' to index everything, 'table' to
                   index a single table (default: website)  [default: website]
--table TEXT       Table to index (only in 'table' mode)
--index_name TEXT  Index name (only in 'table' mode)
--queues INTEGER   Number of indexing task queues  [default: 10]
--fields TEXT      Fields to index (only in 'table' mode), syntax:
                   <field_name>|<field_type>, field_type should be one of
                   'string', 'keyword', 'date', 'long', 'double', 'boolean',
                   'ip', 'object', 'nested', 'geo_point', 'geo_shape', or
                   'completion'
--links TEXT       List of links to show to users, syntax: <column-where-to-
                   show-the-link>|</your/url/[any-column-name]>
--tokenizer TEXT   Tokenizer to use (one of 'standard', 'letter', 'lowercase',
                   'whitespace', 'uax_url_email', 'classic', 'ngram',
                   'edge_ngram', 'keyword', 'pattern', or 'path_hierarchy';
                   default='standard')  [default: standard]
--job_name TEXT    Name of the job
--no_wait          Do not wait for job to complete
-h, --help         Show this message and exit.

`populate_mviews` command¶

Usage:

tripaille db populate_mviews [OPTIONS]

Help

Populate materialized views

Output

Loading information

Options:

--name TEXT  filter on mview name
--no_wait    Do not wait for job to complete
-h, --help   Show this message and exit.

entity¶

This section is auto-generated from the help text for the tripaille command entity.

`add_entity` command¶

Usage:

tripaille entity add_entity [OPTIONS] ENTITY

Help

Add a new entity to the database

Output

Entity information

Options:

--params TEXT  Values to populate the entity fields
-h, --help     Show this message and exit.

`get_bundles` command¶

Usage:

tripaille entity get_bundles [OPTIONS]

Help

Get the list of tripal bundles

Output

Bundles information

Options:

-h, --help  Show this message and exit.

`get_entities` command¶

Usage:

tripaille entity get_entities [OPTIONS]

Help

Get entities

Output

Entity information

Options:

--entity TEXT        Name of the entity type (e.g. Organism)
--entity_id INTEGER  ID of an entity
-h, --help           Show this message and exit.

`get_fields` command¶

Usage:

tripaille entity get_fields [OPTIONS] ENTITY

Help

Get the list of available fields for an entity

Output

Fields information

Options:

-h, --help  Show this message and exit.

`publish` command¶

Usage:

tripaille entity publish [OPTIONS]

Help

Publish entities (Tripal 3 only)

Output

status

Options:

--types TEXT     List of entity types to be published (e.g. Gene mRNA,
                 default: all)
--job_name TEXT  Name of the job
--no_wait        Return immediately without waiting for job completion
-h, --help       Show this message and exit.

expression¶

This section is auto-generated from the help text for the tripaille command expression.

`add_biomaterial` command¶

Usage:

tripaille expression add_biomaterial [OPTIONS] ORGANISM_ID FILE_PATH

Help

Add a new biomaterial to the database

Output

Job information

Options:

--no_wait   Do not wait for job to complete
-h, --help  Show this message and exit.

`add_expression` command¶

Usage:

tripaille expression add_expression [OPTIONS] ORGANISM_ID ANALYSIS_ID

Help

type organism_id:
	str :param organism_id: Organism Id

Output

Loading information

Options:

--match_type TEXT            Match to features using either name or
                             uniquename. Default to uniquename  [default:
                             uniquename]
--biomaterial_provider TEXT  The contact who provided the biomaterial.
                             (optional, non functional in Tripal2)
--array_design TEXT          The array design associated with this analysis.
                             This is not required if the experimental data was
                             gathered from next generation sequencing methods.
                             (optional, non functional in Tripal2)
--assay_id TEXT              The id of the assay associated with the
                             experiment. (optional, non functional in Tripal2)
--acquisition_id TEXT        The id of the acquisition associated with the
                             experiment (optional, non functional in Tripal2)
--quantification_id TEXT     The id of the quantification associated with the
                             experiment (optional, non functional in Tripal2)
--file_extension TEXT        File extension for the file(s) to be loaded into
                             Chado. Do not include the ".". Not required for
                             matrix files. (optional)
--start_regex TEXT           A regular expression to describe the line that
                             occurs before the start of the expression data.
                             If the file has no header, this is not needed.
                             (optional)
--stop_regex TEXT            A regular expression to describe the line that
                             occurs after the end of the expression data. If
                             the file has no footer text, this is not needed.
                             (optional)
--use_column                 Set if the expression file is a column file
--no_wait                    Do not wait for job to complete
-h, --help                   Show this message and exit.

`delete_biomaterials` command¶

Usage:

tripaille expression delete_biomaterials [OPTIONS]

Help

Delete some biomaterials

Output

status

Options:

--names TEXT        JSON list of biomaterial names to delete. (optional)
--organism_id TEXT  Organism id from which to delete biomaterials (optional)
--analysis_id TEXT  Analysis id from which to delete biomaterials (optional)
--job_name TEXT     Name of the job (optional)
--no_wait           Return immediately without waiting for job completion
-h, --help          Show this message and exit.

`get_biomaterials` command¶

Usage:

tripaille expression get_biomaterials [OPTIONS]

Help

List biomaterials in the database

Output

Job information

Options:

--provider_id TEXT     Limit query to the selected provider
--biomaterial_id TEXT  Limit query to the selected biomaterial
--organism_id TEXT     Limit query to the selected organism
--dbxref_id TEXT       Limit query to the selected ref
-h, --help             Show this message and exit.

`sync_biomaterials` command¶

Usage:

tripaille expression sync_biomaterials [OPTIONS]

Help

Synchronize some biomaterials

Output

status

Options:

--ids TEXT       JSON list of ids of biomaterials to be synced (default: all)
--max_sync TEXT  Maximum number of features to sync (default: all)
--job_name TEXT  Name of the job
--no_wait        Return immediately without waiting for job completion
-h, --help       Show this message and exit.

feature¶

This section is auto-generated from the help text for the tripaille command feature.

`delete_orphans` command¶

Usage:

tripaille feature delete_orphans [OPTIONS]

Help

Delete orphans Drupal feature nodes

Output

status

Options:

--job_name TEXT  Name of the job
--no_wait        Return immediately without waiting for job completion
-h, --help       Show this message and exit.

`get_features_tripal` command¶

Usage:

tripaille feature get_features_tripal [OPTIONS]

Help

Get features entities

Output

Feature entity/node information

Options:

--feature_id INTEGER  A feature entity/node ID
-h, --help            Show this message and exit.

`sync` command¶

Usage:

tripaille feature sync [OPTIONS]

Help

Synchronize some features (Tripal 2 only)

Output

status

Options:

--organism TEXT     Common name of the organism to sync
--organism_id TEXT  ID of the organism to sync
--max_sync TEXT     Maximum number of features to sync (default: all)
--types TEXT        List of types of records to be synced (e.g. gene mRNA,
                    default: all)
--ids TEXT          List of names of records to be synced (e.g. gene0001,
                    default: all)
--job_name TEXT     Name of the job
--no_wait           Return immediately without waiting for job completion
-h, --help          Show this message and exit.

job¶

This section is auto-generated from the help text for the tripaille command job.

`add_import_job` command¶

Usage:

tripaille job add_import_job [OPTIONS] NAME IMPORTER INPUT_FILE ARGUMENTS

Help

Schedule a new import job

Output

Job information

Options:

--priority INTEGER  An integer score to prioritize the job  [default: 10]
-h, --help          Show this message and exit.

`add_job` command¶

Usage:

tripaille job add_job [OPTIONS] NAME MODULE CALLBACK ARGUMENTS

Help

Schedule a new job

Output

Job information

Options:

--priority INTEGER  An integer score to prioritize the job  [default: 10]
-h, --help          Show this message and exit.

`get_jobs` command¶

Usage:

tripaille job get_jobs [OPTIONS]

Help

Get all jobs

Output

Jobs information

Options:

--job_id INTEGER  job id
-h, --help        Show this message and exit.

`get_logs` command¶

Usage:

tripaille job get_logs [OPTIONS] STDOUT STDERR

Help

Get job output

Output

Output information

Options:

-h, --help  Show this message and exit.

`run_jobs` command¶

Usage:

tripaille job run_jobs [OPTIONS]

Help

Run jobs in queue. There is no way to trigger a single job execution.

Output

Job information

Options:

--wait      Wait for job completion  [default: True]
-h, --help  Show this message and exit.

`wait` command¶

Usage:

tripaille job wait [OPTIONS] JOB_ID

Help

Wait for a job completion

Output

Job information

Options:

-h, --help  Show this message and exit.

organism¶

This section is auto-generated from the help text for the tripaille command organism.

`add_organism` command¶

Usage:

tripaille organism add_organism [OPTIONS] GENUS SPECIES

Help

Add a new organism to the database

Output

Organism information

Options:

--common TEXT              The common name of the organism
--abbr TEXT                The abbreviation of the organism
--comment TEXT             A comment / description
--infraspecific_rank TEXT  The type name of infraspecific name for any taxon
                           below the rank of species. Must be one of
                           ['subspecies', 'varietas', 'subvariety', 'forma',
                           'subforma']
--infraspecific_name TEXT  The infraspecific name for this organism.
-h, --help                 Show this message and exit.

`delete_orphans` command¶

Usage:

tripaille organism delete_orphans [OPTIONS]

Help

Delete orphans Drupal organism nodes

Output

status

Options:

--job_name TEXT  Name of the job
--no_wait        Return immediately without waiting for job completion
-h, --help       Show this message and exit.

`get_organisms` command¶

Usage:

tripaille organism get_organisms [OPTIONS]

Help

Get organisms from chado table

Output

Organism information

Options:

--organism_id TEXT  An organism ID
--genus TEXT        The genus of the organism
--species TEXT      The species of the organism
--common TEXT       The common name of the organism
--abbr TEXT         The abbreviation of the organism
--comment TEXT      A comment / description
-h, --help          Show this message and exit.

`get_organisms_tripal` command¶

Usage:

tripaille organism get_organisms_tripal [OPTIONS]

Help

Get organism entities

Output

Organism entity information

Options:

--organism_id INTEGER  An organism entity ID
-h, --help             Show this message and exit.

`get_taxonomic_ranks` command¶

Usage:

tripaille organism get_taxonomic_ranks [OPTIONS]

Help

Get taxonomic ranks

Output

Taxonomic ranks

Options:

-h, --help  Show this message and exit.

`sync` command¶

Usage:

tripaille organism sync [OPTIONS]

Help

Synchronize an organism

Output

status

Options:

--organism TEXT     Common name of the organism to sync
--organism_id TEXT  ID of the organism to sync
--job_name TEXT     Name of the job
--no_wait           Return immediately without waiting for job completion
-h, --help          Show this message and exit.

phylogeny¶

This section is auto-generated from the help text for the tripaille command phylogeny.

`sync` command¶

Usage:

tripaille phylogeny sync [OPTIONS]

Help

Synchronize some phylotree

Output

status

Options:

--max_sync TEXT  Maximum number of features to sync (default: all)
--job_name TEXT  Name of the job
--no_wait        Return immediately without waiting for job completion
-h, --help       Show this message and exit.

tripal package¶

Subpackages¶

tripal.analysis package¶

Module contents¶

class tripal.analysis.AnalysisClient(tripalinstance, **requestArgs)¶

Bases: tripal.client.Client

Manage Tripal analyses

add_analysis(name, program, programversion, sourcename, algorithm=None, sourceversion=None, sourceuri=None, description=None, date_executed=None)¶

Create an analysis

Parameters:	name (str) – analysis name program (str) – analysis program programversion (str) – analysis programversion algorithm (str) – analysis algorithm sourcename (str) – analysis sourcename sourceversion (str) – analysis sourceversion sourceuri (str) – analysis sourceuri description (str) – analysis description date_executed (str) – analysis date_executed (yyyy-mm-dd)
Return type:	dict
Returns:	Analysis information

delete_orphans(job_name=None, no_wait=None)¶

Delete orphans Drupal analysis nodes

Parameters:	job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

get_analyses(analysis_id=None, name=None, program=None, programversion=None, algorithm=None, sourcename=None, sourceversion=None, sourceuri=None, date_executed=None)¶

Get analyses

Parameters:	analysis_id (str) – An analysis ID name (str) – analysis name program (str) – analysis program programversion (str) – analysis programversion algorithm (str) – analysis algorithm sourcename (str) – analysis sourcename sourceversion (str) – analysis sourceversion sourceuri (str) – analysis sourceuri date_executed (str) – analysis date_executed (yyyy-mm-dd)
Return type:	list of dict
Returns:	Analysis information

get_analyses_tripal(analysis_id=None)¶

Get analysis entities

Parameters:	analysis_id (int) – An analysis entity/node ID
Return type:	list of dict
Returns:	Analysis entity/node information

load_blast(name, program, programversion, sourcename, blast_output, blast_ext=None, blastdb=None, blastdb_id=None, blast_parameters=None, query_re=None, query_type=None, query_uniquename=False, is_concat=False, search_keywords=False, no_parsed=u'all', no_wait=False, algorithm=None, sourceversion=None, sourceuri=None, description=u'', date_executed=None)¶

Create a Blast analysis

Parameters:	name (str) – analysis name program (str) – analysis program programversion (str) – analysis programversion sourcename (str) – analysis sourcename blast_output (str) – Path to the Blast file to load (single XML file, or directory containing multiple XML files) blast_ext (str) – If looking for files in a directory, extension of the blast result files blastdb (str) – Name of the database blasted against (must be in the Chado db table) blastdb_id (str) – ID of the database blasted against (must be in the Chado db table) blast_parameters (str) – Blast parameters used to produce these results query_re (str) – The regular expression that can uniquely identify the query name. This parameters is required if the feature name is not the first word in the blast query name. query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘contig’) of the query. It must be a valid Sequence Ontology term. query_uniquename (bool) – Use this if the –query-re regular expression matches unique names instead of names in the database. is_concat (bool) – If the blast result file is simply a list of concatenated blast results. search_keywords (bool) – Extract keywords for Tripal search no_parsed (str) – Maximum number of hits to parse per feature. Default=all no_wait (bool) – Do not wait for job to complete algorithm (str) – analysis algorithm sourceversion (str) – analysis sourceversion sourceuri (str) – analysis sourceuri description (str) – analysis description date_executed (str) – analysis date_executed (yyyy-mm-dd)
Return type:	str
Returns:	Loading information

load_fasta(fasta, organism=None, organism_id=None, analysis=None, analysis_id=None, sequence_type=u'contig', re_name=None, re_uniquename=None, db_ext_id=None, re_accession=None, rel_type=None, rel_subject_re=None, rel_subject_type=None, method=u'insup', match_type=u'uniquename', job_name=None, no_wait=False)¶

Load fasta sequences

Parameters:	fasta (str) – Path to the Fasta file to load organism (str) – Organism common name or abbreviation organism_id (int) – Organism ID analysis (str) – Analysis name analysis_id (int) – Analysis ID sequence_type (str) – Sequence type re_name (str) – Regular expression for the name re_uniquename (str) – Regular expression for the unique name db_ext_id (str) – External DB ID re_accession (str) – Regular expression for the accession from external DB rel_type (str) – Relation type (part_of or derives_from) rel_subject_re (str) – Relation subject regular expression (used to extract id of related entity) rel_subject_type (str) – Relation subject type (must match already loaded data, e.g. mRNA) method (str) – Insertion method (insert, update or insup, default=insup (Insert and Update)) match_type (str) – Match type for already loaded features (name or uniquename; default=uniquename; used for “Update only” or “Insert and update” methods)’ job_name (str) – Name of the job no_wait (bool) – Do not wait for job to complete
Return type:	str
Returns:	Loading information

load_gff3(gff, organism=None, organism_id=None, analysis=None, analysis_id=None, import_mode=u'update', target_organism=None, target_organism_id=None, target_type=None, target_create=False, start_line=None, landmark_type=None, alt_id_attr=None, create_organism=False, re_mrna=None, re_protein=None, job_name=None, no_wait=False)¶

Load GFF3 file

Parameters:	gff (str) – Path to the GFF file to load organism (str) – Organism common name or abbreviation organism_id (int) – Organism ID analysis (str) – Analysis name analysis_id (int) – Analysis ID import_mode (str) – Import mode (add_only=existing features won’t be touched, update=existing features will be updated and obsolete attributes kept)’) target_organism (str) – In case of Target attribute in the GFF3, choose the organism abbreviation or common name to which target sequences belong. Select this only if target sequences belong to a different organism than the one specified with –organism-id. And only choose an organism here if all of the target sequences belong to the same species. If the targets in the GFF file belong to multiple different species then the organism must be specified using the ‘target_organism=genus:species’ attribute in the GFF file.’) target_organism_id (int) – In case of Target attribute in the GFF3, choose the organism ID to which target sequences belong. Select this only if target sequences belong to a different organism than the one specified with –organism-id. And only choose an organism here if all of the target sequences belong to the same species. If the targets in the GFF file belong to multiple different species then the organism must be specified using the ‘target_organism=genus:species’ attribute in the GFF file.’) target_type (str) – In case of Target attribute in the GFF3, if the unique name for a target sequence is not unique (e.g. a protein and an mRNA have the same name) then you must specify the type for all targets in the GFF file. If the targets are of different types then the type must be specified using the ‘target_type=type’ attribute in the GFF file. This must be a valid Sequence Ontology (SO) term.’) target_create (bool) – In case of Target attribute in the GFF3, if the target feature cannot be found, create one using the organism and type specified above, or using the ‘target_organism’ and ‘target_type’ fields specified in the GFF file. Values specified in the GFF file take precedence over those specified above.’) start_line (int) – The line in the GFF file where importing should start landmark_type (str) – A Sequence Ontology type for the landmark sequences in the GFF fie (e.g. ‘chromosome’). alt_id_attr (str) – When ID attribute is absent, specify which other attribute can uniquely identify the feature. create_organism (bool) – Create organisms when encountering organism attribute (these lines will be skip otherwise) re_mrna (str) – Regular expression for the mRNA name re_protein (str) – Replacement string for the protein name job_name (str) – Name of the job no_wait (bool) – Do not wait for job to complete
Return type:	str
Returns:	Loading information

load_go(name, program, programversion, sourcename, gaf_output, organism=None, organism_id=None, gaf_ext=None, query_type=None, query_matching=u'uniquename', method=u'add', name_column=2, re_name=None, no_wait=False, algorithm=None, sourceversion=None, sourceuri=None, description=None, date_executed=None)¶

Create a GO analysis

Parameters:	organism (str) – Organism common name or abbreviation organism_id (int) – Organism ID name (str) – analysis name program (str) – analysis program programversion (str) – analysis programversion sourcename (str) – analysis sourcename gaf_output (str) – Path to the GAF file to load (single file, or directory containing multiple GAF files) gaf_ext (str) – If looking for files in a directory, extension of the GAF files query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘contig’) of the query. It must be a valid Sequence Ontology term. query_matching (str) – Method to match identifiers to features in the database. (‘name’, ‘uniquename’ or ‘dbxref’) method (str) – Import method (‘add’ or ‘remove’) name_column (int) – Column containing the feature identifiers (2, 3, 10 or 11; default=2). re_name (str) – Regular expression to extract the feature name from GAF file. no_wait (bool) – Do not wait for job to complete algorithm (str) – analysis algorithm sourceversion (str) – analysis sourceversion sourceuri (str) – analysis sourceuri description (str) – analysis description date_executed (str) – analysis date_executed (yyyy-mm-dd)
Return type:	str
Returns:	Loading information

load_interpro(name, program, programversion, sourcename, interpro_output, interpro_parameters=None, query_re=None, query_type=None, query_uniquename=False, parse_go=False, no_wait=False, algorithm=None, sourceversion=None, sourceuri=None, description=u'', date_executed=None)¶

Create an Interpro analysis

Parameters:	name (str) – analysis name program (str) – analysis program programversion (str) – analysis programversion sourcename (str) – analysis sourcename interpro_output (str) – Path to the InterProScan file to load (single XML file, or directory containing multiple XML files) interpro_parameters (str) – InterProScan parameters used to produce these results query_re (str) – The regular expression that can uniquely identify the query name. This parameters is required if the feature name is not the first word in the blast query name. query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘contig’) of the query. It must be a valid Sequence Ontology term. query_uniquename (bool) – Use this if the query_re regular expression matches unique names instead of names in the database. parse_go (bool) – Load GO annotation to the database no_wait (bool) – Do not wait for job to complete algorithm (str) – analysis algorithm sourceversion (str) – analysis sourceversion sourceuri (str) – analysis sourceuri description (str) – analysis description date_executed (str) – analysis date_executed (yyyy-mm-dd)
Return type:	str
Returns:	Loading information

sync(analysis=None, analysis_id=None, job_name=None, no_wait=None)¶

Synchronize an analysis

Parameters:	analysis (str) – Analysis name analysis_id (str) – ID of the analysis to sync job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

tripal.db package¶

Module contents¶

class tripal.db.DbClient(tripalinstance, **requestArgs)¶

Bases: tripal.client.Client

Access Tripal/Chado database

get_dbs(db_id=None, name=None)¶

Get all dbs

Parameters:	db_id (str) – A db ID name (str) – filter on db name
Return type:	list of dict
Returns:	Dbs information

get_mviews(name=None)¶

Get all materialized views

Parameters:	name (str) – filter on mview name
Return type:	list of dict
Returns:	materialized views information

index(mode=u'website', table=None, index_name=None, queues=10, fields=[], links={}, tokenizer=u'standard', token_filters=[], exposed=False, index_url=None, job_name=None, no_wait=False)¶

Schedule database indexing using elasticsearch

Parameters:	mode (str) – Indexing mode: ‘website’ to index the website , ‘nodes’ for the website nodes, ‘entities’ for the website entities (Tripal 3), ‘table’ to index a single table, ‘gene’ to build a Gene search index (Tripal 3 only) (default: website) (‘website’ default to ‘nodes’ for Tripal 2, ‘entities’ for Tripal 3) table (str) – Table to index (only in ‘table’ mode) index_name (str) – Index name (only in ‘table’ mode) queues (int) – Number of indexing task queues (Tripal 2 only) fields (list of str) – Fields to index (only in ‘table’ mode), syntax: <field_name>\|<field_type>, field_type should be one of ‘string’ (Tripal2), ‘text’ (Tripal3), ‘keyword’, ‘date’, ‘long’, ‘double’, ‘boolean’, ‘ip’, ‘object’, ‘nested’, ‘geo_point’, ‘geo_shape’, or ‘completion’ links (list of str) – List of links to show to users, syntax: <column-where-to-show-the-link>\|</your/url/[any-column-name]> (Tripal 2 only) tokenizer (str) – Tokenizer to use (only in ‘table’ mode) (one of ‘standard’, ‘letter’, ‘lowercase’, ‘whitespace’, ‘uax_url_email’, ‘classic’, ‘ngram’, ‘edge_ngram’, ‘keywordx’, ‘pattern’, or ‘path_hierarchy’; default=’standard’) token_filters (list of str) – Token filters (Tripal 3 only) (only in ‘table’ mode) (available filters are ‘standard’, ‘asciifolding’, ‘length’, ‘lowercase’, ‘uppercase’) (Default to [‘standard’, ‘lowercase’]) exposed (bool) – “Expose the index (read-only) to other websites index_url (str) – In order for other sites to link back to your results page, you must specify a path where the form for this index can be reached job_name (str) – Name of the job no_wait (bool) – Do not wait for job to complete
Return type:	str
Returns:	Indexing information

populate_mviews(name=None, no_wait=None)¶

Populate materialized views

Parameters:	name (str) – filter on mview name no_wait (bool) – Do not wait for job to complete
Return type:	str
Returns:	Loading information

tune()¶

Setup default entity index priority for whole website indexing

Return type:	dict
Returns:	“Status”

tripal.entity package¶

Module contents¶

class tripal.entity.EntityClient(tripalinstance, **requestArgs)¶

Bases: tripal.client.Client

Manage any type of Tripal entities

add_entity(entity, params={})¶

Add a new entity to the database

Parameters:	entity (str) – Name of the entity params (dict) – Values to populate the entity fields
Return type:	dict
Returns:	Entity information

get_bundles()¶

Get the list of tripal bundles

Return type:	list of dict
Returns:	Bundles information

get_entities(entity=None, entity_id=None)¶

Get entities

Parameters:	entity (str) – Name of the entity type (e.g. Organism) entity_id (int) – ID of an entity
Return type:	list of dict
Returns:	Entity information

get_fields(entity)¶

Get the list of available fields for an entity

Parameters:	entity (str) – Name of the entity
Return type:	dict
Returns:	Fields information

publish(types=[], job_name=None, no_wait=None)¶

Publish entities (Tripal 3 only)

Parameters:	types (list of str) – List of entity types to be published (e.g. Gene mRNA, default: all) job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

tripal.expression package¶

Module contents¶

class tripal.expression.ExpressionClient(tripalinstance, **requestArgs)¶

Bases: tripal.client.Client

Manage Tripal expressions

add_biomaterial(organism_id, file_path, file_type, analysis_id=None, no_wait=False)¶

Add a new biomaterial file to the database

Parameters:	organism_id (str) – The id of the associated organism analysis_id (str) – The id of the associated analysis. Required for TripalV3 file_path (str) – The path to the biomaterial file file_type (str) – The type of the biomaterial file (xml, tsv or csv) no_wait (bool) – Do not wait for job to complete
Return type:	dict
Returns:	Job information

add_expression(organism_id, analysis_id, file_path, match_type=u'uniquename', array_design_id=None, quantification_units=None, file_extension=None, start_regex=None, stop_regex=None, seq_type=None, use_column=False, no_wait=False)¶

Add an expression file to tripal

Parameters:	organism_id (str) – Organism Id analysis_id (str) – Id of the analysis match_type (str) – Match to features using either name or uniquename. Default to uniquename file_path (str) – Path to the expression file, or directory containing multiple expression files array_design_id (str) – The array design ID associated with this analysis. (Non functional in Tripal2) quantification_units (str) – The units associated with the loaded values (ie, FPKM, RPKM, raw counts). file_extension (str) – File extension for the file(s) to be loaded into Chado. Do not include the “.”. Not required for matrix files. start_regex (str) – A regular expression to describe the line that occurs before the start of the expression data. If the file has no header, this is not needed. seq_type (str) – Specify the feature type to associate the data with. (Tripal3 only) stop_regex (str) – A regular expression to describe the line that occurs after the end of the expression data. If the file has no footer text, this is not needed. use_column (bool) – Set if the expression file is a column file no_wait (bool) – Do not wait for job to complete
Return type:	str
Returns:	Loading information

delete_biomaterials(names=[], organism_id=u'', analysis_id=u'', job_name=u'', no_wait=False)¶

Delete some biomaterials

Parameters:	names (str) – JSON list of biomaterial names to delete. (optional) organism_id (str) – Organism id from which to delete biomaterials (optional) analysis_id (str) – Analysis id from which to delete biomaterials (optional) no_wait (bool) – Return immediately without waiting for job completion job_name (str) – Name of the job (optional)
Return type:	str
Returns:	status

get_biomaterials(biomaterial_name=u'', provider_id=u'', biomaterial_id=u'', organism_id=u'', dbxref_id=u'')¶

List biomaterials in the database

Parameters:	organism_id (str) – Limit query to the selected organism biomaterial_id (str) – Limit query to the selected biomaterial biomaterial_name (str) – Limit query to the selected biomaterial provider_id (str) – Limit query to the selected provider dbxref_id (str) – Limit query to the selected ref
Return type:	dict
Returns:	Biomaterial list

get_biomaterials_tripal(biomaterial_id=None)¶

Get Biomaterial entities

Parameters:	biomaterial_id (int) – A biomaterial entity ID
Return type:	list of dict
Returns:	Organism entity information

sync_biomaterials(ids=u'[]', max_sync=u'', job_name=None, no_wait=False)¶

Synchronize some biomaterials

Parameters:	ids (str) – JSON list of ids of biomaterials to be synced (default: all) max_sync (str) – Maximum number of features to sync (default: all) job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

tripal.feature package¶

Module contents¶

class tripal.feature.FeatureClient(tripalinstance, **requestArgs)¶

Bases: tripal.client.Client

Manage Tripal features

delete_orphans(job_name=None, no_wait=None)¶

Delete orphans Drupal feature nodes

Parameters:	job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

get_features(feature_id=None)¶

Get features entities

Parameters:	feature_id (int) – A feature entity/node ID
Return type:	list of dict
Returns:	Feature entity/node information

get_features_tripal(feature_id=None)¶

Get features entities

Parameters:	feature_id (int) – A feature entity/node ID
Return type:	list of dict
Returns:	Feature entity/node information

sync(organism=None, organism_id=None, max_sync=u'', types=[], ids=[], job_name=None, no_wait=None)¶

Synchronize some features (Tripal 2 only)

Parameters:	organism (str) – Common name of the organism to sync organism_id (str) – ID of the organism to sync max_sync (str) – Maximum number of features to sync (default: all) types (list of str) – List of types of records to be synced (e.g. gene mRNA, default: all) ids (list of str) – List of names of records to be synced (e.g. gene0001, default: all) job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

tripal.job package¶

Module contents¶

class tripal.job.JobClient(tripalinstance, **requestArgs)¶

Bases: tripal.client.Client

Manage Tripal jobs

add_import_job(name, importer, input_file, arguments, priority=10)¶

Schedule a new import job

Parameters:	name (str) – The name of the job importer (str) – The Tripal importer to use (e.g. FASTAImporter) input_file (str) – Local path to the file to import arguments (str) – A JSON string representing an array of arguments (e.g. “[‘some’, ‘arg’, 42, ‘foo’]”) priority (int) – An integer score to prioritize the job
Return type:	dict
Returns:	Job information

add_job(name, module, callback, arguments, priority=10)¶

Schedule a new job

Parameters:	name (str) – The name of the job module (str) – The Tripal module name to invoke callback (str) – The Tripal module callback function to invoke arguments (str) – A JSON string representing an array of arguments (e.g. “[‘some’, ‘arg’, 42, ‘foo’]”) priority (int) – An integer score to prioritize the job
Return type:	dict
Returns:	Job information

get_jobs(job_id=None)¶

Get all jobs

Parameters:	job_id (int) – job id
Return type:	list of dict
Returns:	Jobs information

get_logs(stdout, stderr)¶

Get job output

Parameters:	stdout (str) – Path to stdout file, as returned by run_jobs stderr (str) – Path to stderr file, as returned by run_jobs
Return type:	dict
Returns:	Output information

run_jobs(wait=True)¶

Run jobs in queue. There is no way to trigger a single job execution.

Parameters:	wait (bool) – Wait for job completion
Return type:	dict
Returns:	Job information

wait(job_id)¶

Wait for a job completion

Parameters:	job_id (int) – job id
Return type:	dict
Returns:	Job information

tripal.organism package¶

Module contents¶

class tripal.organism.OrganismClient(tripalinstance, **requestArgs)¶

Bases: tripal.client.Client

Manage Tripal organisms

add_organism(genus, species, common=None, abbr=None, comment=None, infraspecific_rank=None, infraspecific_name=None)¶

Add a new organism to the database

Parameters:	genus (str) – The genus of the organism species (str) – The species of the organism common (str) – The common name of the organism abbr (str) – The abbreviation of the organism comment (str) – A comment / description infraspecific_rank (str) – The type name of infraspecific name for any taxon below the rank of species. Must be one of [‘subspecies’, ‘varietas’, ‘subvariety’, ‘forma’, ‘subforma’] infraspecific_name (str) – The infraspecific name for this organism.
Return type:	dict
Returns:	Organism information

delete_orphans(job_name=None, no_wait=None)¶

Delete orphans Drupal organism nodes

Parameters:	job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

get_organisms(organism_id=None, genus=None, species=None, common=None, abbr=None, comment=None)¶

Get organisms from chado table

Parameters:	organism_id (str) – An organism ID genus (str) – The genus of the organism common (str) – The common name of the organism abbr (str) – The abbreviation of the organism species (str) – The species of the organism comment (str) – A comment / description
Return type:	list of dict
Returns:	Organism information

get_organisms_tripal(organism_id=None)¶

Get organism entities

Parameters:	organism_id (int) – An organism entity ID
Return type:	list of dict
Returns:	Organism entity information

get_taxonomic_ranks()¶

Get taxonomic ranks

Return type:	list of dict
Returns:	Taxonomic ranks

sync(organism=None, organism_id=None, job_name=None, no_wait=None)¶

Synchronize an organism

Parameters:	organism (str) – Common name of the organism to sync organism_id (str) – ID of the organism to sync job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

tripal.phylogeny package¶

Module contents¶

class tripal.phylogeny.PhylogenyClient(tripalinstance, **requestArgs)¶

Bases: tripal.client.Client

Manage Tripal phylogeny

sync(max_sync=u'', job_name=None, no_wait=None)¶

Synchronize some phylotree

Parameters:	max_sync (str) – Maximum number of features to sync (default: all) job_name (str) – Name of the job no_wait (bool) – Return immediately without waiting for job completion
Return type:	str
Returns:	status

Submodules¶

tripal.client module¶

Base tripal client

class tripal.client.Client(tripalinstance, **requestArgs)¶

Bases: object

Base client class implementing methods to make queries to the server

CLIENT_BASE = u'/tripal_api/'¶

Module contents¶

class tripal.TripalInstance(tripal_url=u'http://localhost/tripal/', username=u'admin', password=u'changeme', auth_login=None, auth_password=None, **kwargs)¶: Bases: object

python-tripal and tripaille¶

Tripal Library¶

Requirements¶

Installation¶

Examples¶

History¶

License¶

Commands¶

analysis¶

add_analysis command¶

delete_orphans command¶

get_analyses command¶

get_analyses_tripal command¶

load_blast command¶

load_fasta command¶

load_gff3 command¶

load_go command¶

load_interpro command¶

sync command¶

db¶

get_dbs command¶

get_mviews command¶

index command¶

populate_mviews command¶

entity¶

add_entity command¶

get_bundles command¶

get_entities command¶

get_fields command¶

publish command¶

expression¶

add_biomaterial command¶

add_expression command¶

delete_biomaterials command¶

get_biomaterials command¶

sync_biomaterials command¶

feature¶

delete_orphans command¶

get_features_tripal command¶

sync command¶

job¶

add_import_job command¶

add_job command¶

get_jobs command¶

get_logs command¶

run_jobs command¶

wait command¶

organism¶

add_organism command¶

delete_orphans command¶

get_organisms command¶

get_organisms_tripal command¶

get_taxonomic_ranks command¶

sync command¶

phylogeny¶

sync command¶

tripal package¶

Subpackages¶

tripal.analysis package¶

Module contents¶

tripal.db package¶

Module contents¶

tripal.entity package¶

Module contents¶

tripal.expression package¶

Module contents¶

tripal.feature package¶

Module contents¶

tripal.job package¶

Module contents¶

tripal.organism package¶

Module contents¶

tripal.phylogeny package¶

Module contents¶

Submodules¶

tripal.client module¶

Module contents¶

`add_analysis` command¶

`delete_orphans` command¶

`get_analyses` command¶

`get_analyses_tripal` command¶

`load_blast` command¶

`load_fasta` command¶

`load_gff3` command¶

`load_go` command¶

`load_interpro` command¶

`sync` command¶

`get_dbs` command¶

`get_mviews` command¶

`index` command¶

`populate_mviews` command¶

`add_entity` command¶

`get_bundles` command¶

`get_entities` command¶

`get_fields` command¶

`publish` command¶

`add_biomaterial` command¶

`add_expression` command¶

`delete_biomaterials` command¶

`get_biomaterials` command¶

`sync_biomaterials` command¶

`delete_orphans` command¶

`get_features_tripal` command¶

`sync` command¶

`add_import_job` command¶

`add_job` command¶

`get_jobs` command¶

`get_logs` command¶

`run_jobs` command¶

`wait` command¶

`add_organism` command¶

`delete_orphans` command¶

`get_organisms` command¶

`get_organisms_tripal` command¶

`get_taxonomic_ranks` command¶

`sync` command¶

`sync` command¶