API documentation for interacting with Galaxy¶
GalaxyInstance¶
-
class
bioblend.galaxy.
GalaxyInstance
(url, key=None, email=None, password=None)[source]¶ A base representation of an instance of Galaxy, identified by a URL and a user’s API key.
After you have created an
GalaxyInstance
object, access various modules via the class fields (see the source for the most up-to-date list):libraries
,histories
,workflows
,datasets
, andusers
are the minimum set supported. For example, to work with histories, and get a list of all the user’s histories, the following should be done:from bioblend import galaxy gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8000', key='your_api_key') hl = gi.histories.get_histories()
Parameters: - url (string) – A FQDN or IP for a given instance of Galaxy. For example: http://127.0.0.1:8080
- key (string) – User’s API key for the given instance of Galaxy, obtained from the user preferences. If a key is not supplied, an email address and password must be and key will automatically be created for the user.
- email (string) – Galaxy e-mail address corresponding to the user. Ignored if key is supplied directly.
- password (string) – Password of Galaxy account corresponding to the above e-mail address. Ignored if key is supplied directly.
-
__init__
(url, key=None, email=None, password=None)[source]¶ A base representation of an instance of Galaxy, identified by a URL and a user’s API key.
After you have created an
GalaxyInstance
object, access various modules via the class fields (see the source for the most up-to-date list):libraries
,histories
,workflows
,datasets
, andusers
are the minimum set supported. For example, to work with histories, and get a list of all the user’s histories, the following should be done:from bioblend import galaxy gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8000', key='your_api_key') hl = gi.histories.get_histories()
Parameters: - url (string) – A FQDN or IP for a given instance of Galaxy. For example: http://127.0.0.1:8080
- key (string) – User’s API key for the given instance of Galaxy, obtained from the user preferences. If a key is not supplied, an email address and password must be and key will automatically be created for the user.
- email (string) – Galaxy e-mail address corresponding to the user. Ignored if key is supplied directly.
- password (string) – Password of Galaxy account corresponding to the above e-mail address. Ignored if key is supplied directly.
-
get_retry_delay
¶
-
max_get_attempts
¶
Datasets¶
Contains possible interactions with the Galaxy Datasets
-
class
bioblend.galaxy.datasets.
DatasetClient
(galaxy_instance)[source]¶ -
download_dataset
(dataset_id, file_path=None, use_default_filename=True, wait_for_completion=False, maxwait=12000)[source]¶ Downloads the dataset identified by ‘id’.
Parameters: - dataset_id (str) – Encoded dataset ID
- file_path (str) – If the file_path argument is provided, the dataset will be streamed to disk at that path (Should not contain filename if use_default_name=True). If the file_path argument is not provided, the dataset content is loaded into memory and returned by the method (Memory consumption may be heavy as the entire file will be in memory).
- use_default_filename (bool) – If the use_default_name parameter is True, the exported file will be saved as file_path/%s, where %s is the dataset name. If use_default_name is False, file_path is assumed to contain the full file path including filename.
- wait_for_completion (bool) – If wait_for_completion is True, this call will block until the dataset is ready. If the dataset state becomes invalid, a DatasetStateException will be thrown.
- maxwait (float) – Time (in seconds) to wait for dataset to complete. If the dataset state is not complete within this time, a DatasetTimeoutException will be thrown.
Return type: dict
Returns: If a file_path argument is not provided, returns a dict containing the file_content. Otherwise returns nothing.
-
show_dataset
(dataset_id, deleted=False, hda_ldda='hda')[source]¶ Display information about and/or content of a dataset. This can be a history or a library dataset.
Parameters: - dataset_id (str) – Encoded dataset ID
- deleted (bool) – Whether to return results for a deleted dataset
- hda_ldda (str) – Whether to show a history dataset (‘hda’ - the default) or library dataset (‘ldda’).
-
Datatypes¶
Contains possible interactions with the Galaxy Datatype
-
class
bioblend.galaxy.datatypes.
DatatypesClient
(galaxy_instance)[source]¶ -
get_datatypes
(extension_only=False, upload_only=False)[source]¶ Displays a collection (list) of datatypes.
Return type: list Returns: A list of dicts with details on individual datatypes. For example: [ u'snpmatrix',
u’snptest’, u’tabular’, u’taxonomy’, u’twobit’, u’txt’, u’vcf’, u’wig’, u’xgmml’, u’xml’]
-
get_sniffers
()[source]¶ Displays a collection (list) of sniffers.
Return type: list Returns: A list of individual sniffers. For example: [u'galaxy.datatypes.tabular:Vcf',
u’galaxy.datatypes.binary:TwoBit’, u’galaxy.datatypes.binary:Bam’, u’galaxy.datatypes.binary:Sff’, u’galaxy.datatypes.xml:Phyloxml’, u’galaxy.datatypes.xml:GenericXml’, u’galaxy.datatypes.sequence:Maf’, u’galaxy.datatypes.sequence:Lav’, u’galaxy.datatypes.sequence:csFasta’]
-
Folders¶
Contains possible interactions with the Galaxy library folders
-
class
bioblend.galaxy.folders.
FoldersClient
(galaxy_instance)[source]¶ -
delete_folder
(folder_id, undelete=False)[source]¶ Marks the folder with the given
id
as deleted (or removes the deleted mark if the undelete param is True).Parameters: - folder_id (str) – the folder’s encoded id, prefixed by ‘F’
- undelete (bool) – If set to True, the folder will be undeleted (i.e. the deleted mark will be removed)
Returns: detailed folder information
Return type: dict
-
Forms¶
Contains possible interactions with the Galaxy Forms
-
class
bioblend.galaxy.forms.
FormsClient
(galaxy_instance)[source]¶ -
create_form
(form_xml_text)[source]¶ Create a new form
Parameters: form_xml_text (str) – Form xml to create a form on galaxy instance Return type: str Returns: Unique url of newly created form with encoded id
-
get_forms
()[source]¶ Get a list of forms
Return type: list Returns: Displays a collection (list) of forms. For example: [ { u'id': u'f2db41e1fa331b3e', u'model_class': u'FormDefinition', u'name': u'First form', u'url': u'/api/forms/f2db41e1fa331b3e'}, { u'id': u'ebfb8f50c6abde6d', u'model_class': u'FormDefinition', u'name': u'second form', u'url': u'/api/forms/ebfb8f50c6abde6d'}]
-
show_form
(form_id)[source]¶ Display information on a single form
Parameters: form_id (str) – Encoded form ID Return type: dict Returns: A description of single form For example: { u'desc': u'here it is ', u'fields': [], u'form_definition_current_id': u'f2db41e1fa331b3e', u'id': u'f2db41e1fa331b3e', u'layout': [], u'model_class': u'FormDefinition', u'name': u'First form', u'url': u'/api/forms/f2db41e1fa331b3e'}
-
FTP files¶
Contains possible interactions with the Galaxy FTP Files
Genomes¶
Contains possible interactions with the Galaxy Histories
-
class
bioblend.galaxy.genomes.
GenomeClient
(galaxy_instance)[source]¶ -
-
install_genome
(func='download', source=None, dbkey=None, ncbi_name=None, ensembl_dbkey=None, url_dbkey=None, indexers=None)[source]¶ Download and/or index a genome.
Parameters: - dbkey (str) – DB key of the build to download, ignored unless ‘UCSC’ is specified as the source
- ncbi_name (str) – NCBI’s genome identifier, ignored unless NCBI is specified as the source
- ensembl_dbkey (str) – Ensembl’s genome identifier, ignored unless Ensembl is specified as the source
- url_dbkey (str) – DB key to use for this build, ignored unless URL is specified as the source
- source (str) – Data source for this build. Can be: UCSC, Ensembl, NCBI, URL
- indexers (list) – POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...)
- func (str) – Allowed values: ‘download’, Download and index; ‘index’, Index only
Return type: dict
Returns: dict( status: ‘ok’, job: <job ID> ) If error: dict( status: ‘error’, error: <error message> )
-
Groups¶
Contains possible interactions with the Galaxy Groups
-
class
bioblend.galaxy.groups.
GroupsClient
(galaxy_instance)[source]¶ -
add_group_role
(group_id, role_id)[source]¶ Add a role to the given group.
Parameters: - group_id (str) – Encoded group ID
- role_id (str) – Encoded role ID to add to the group
Return type: dict
Returns: Added group role’s info
-
add_group_user
(group_id, user_id)[source]¶ Add a user to the given group.
Parameters: - group_id (str) – Encoded group ID
- user_id (str) – Encoded user ID to add to the group
Return type: dict
Returns: Added group user’s info
-
create_group
(group_name, user_ids=[], role_ids=[])[source]¶ Create a new group.
Parameters: Return type: Returns: A (size 1) list with newly created group details, like:
[{u'id': u'7c9636938c3e83bf', u'model_class': u'Group', u'name': u'My Group Name', u'url': u'/api/groups/7c9636938c3e83bf'}]
-
delete_group_role
(group_id, role_id)[source]¶ Remove a role from the given group.
Parameters: - group_id (str) – Encoded group ID
- role_id (str) – Encoded role ID to remove from the group
-
delete_group_user
(group_id, user_id)[source]¶ Remove a user from the given group.
Parameters: - group_id (str) – Encoded group ID
- user_id (str) – Encoded user ID to remove from the group
-
get_group_roles
(group_id)[source]¶ Get the list of roles associated to the given group.
Parameters: group_id (str) – Encoded group ID Return type: list of dicts Returns: List of group roles’ info
-
get_group_users
(group_id)[source]¶ Get the list of users associated to the given group.
Parameters: group_id (str) – Encoded group ID Return type: list of dicts Returns: List of group users’ info
-
get_groups
()[source]¶ Get all (not deleted) groups.
Return type: list Returns: A list of dicts with details on individual groups. For example: [ {"name": "Listeria", "url": "/api/groups/33abac023ff186c2", "model_class": "Group", "id": "33abac023ff186c2"}, {"name": "LPN", "url": "/api/groups/73187219cd372cf8", "model_class": "Group", "id": "73187219cd372cf8"} ]
-
show_group
(group_id)[source]¶ Get details of a given group.
Parameters: group_id (str) – Encoded group ID Return type: dict Returns: A description of group For example: {"roles_url": "/api/groups/33abac023ff186c2/roles", "name": "Listeria", "url": "/api/groups/33abac023ff186c2", "users_url": "/api/groups/33abac023ff186c2/users", "model_class": "Group", "id": "33abac023ff186c2"}
-
update_group
(group_id, group_name=None, user_ids=[], role_ids=[])[source]¶ Update a group.
Parameters: - group_id (str) – Encoded group ID
- group_name (str) – A new name for the group. If None, the group name is not changed.
- user_ids (list) – New list of encoded user IDs for the group. It will substitute the previous list of users (with [] if not specified)
- role_ids (list) – New list of encoded role IDs for the group. It will substitute the previous list of roles (with [] if not specified)
Return type: int
Returns: status code
-
Histories¶
Contains possible interactions with the Galaxy Histories
-
class
bioblend.galaxy.histories.
HistoryClient
(galaxy_instance)[source]¶ -
create_dataset_collection
(history_id, collection_description)[source]¶ Create a new dataset collection
Parameters: - history_id (str) – Encoded history ID
- collection_description (str) – a description of the dataset collection
-
create_history
(name=None)[source]¶ Create a new history, optionally setting the
name
.Parameters: name (str) – Optional name for new history Return type: dict Returns: Dictionary containing information about newly created history
-
create_history_tag
(history_id, tag)[source]¶ Create history tag
Parameters: - history_id (str) – Encoded history ID
- tag (str) – Add tag to history
Return type: dict
Returns: A dictionary with information regarding the tag. For example:
{'model_class':'HistoryTagAssociation', 'user_tname': 'NGS_PE_RUN', 'id': 'f792763bee8d277a', 'user_value': None}
-
delete_dataset
(history_id, dataset_id)[source]¶ Mark corresponding dataset as deleted.
Parameters: - history_id (str) – Encoded history ID
- dataset_id (str) – Encoded dataset ID
-
delete_dataset_collection
(history_id, dataset_collection_id)[source]¶ Mark corresponding dataset collection as deleted.
Parameters: - history_id (str) – Encoded history ID
- dataset_collection_id (str) – Encoded dataset collection ID
-
delete_history
(history_id, purge=False)[source]¶ Delete a history.
Parameters: - history_id (str) – Encoded history ID
- purge (bool) – if
True
, also purge (permanently delete) the history
Note
For the purge option to work, the Galaxy instance must have the
allow_user_dataset_purge
option set toTrue
in theconfig/galaxy.ini
configuration file.
-
download_dataset
(history_id, dataset_id, file_path, use_default_filename=True, to_ext=None)[source]¶ Download a
dataset_id
from history withhistory_id
to a file on the local file system, saving it tofile_path
.Parameters: to_ext (str) – this parameter is deprecated and ignored, it will be removed in BioBlend 0.6 Refer to
bioblend.galaxy.dataset.DatasetClient.download_dataset()
for the other available parameters.
-
download_history
(history_id, jeha_id, outf, chunk_size=4096)[source]¶ Download a history export archive. Use
export_history()
to create an export.Parameters: - history_id (str) – history ID
- jeha_id (str) – jeha ID (this should be obtained via
export_history()
) - outf (file) – output file object, open for writing in binary mode
- chunk_size (int) – how many bytes at a time should be read into memory
-
export_history
(history_id, gzip=True, include_hidden=False, include_deleted=False, wait=False)[source]¶ Start a job to create an export archive for the given history.
Parameters: - history_id (str) – history ID
- gzip (bool) – create .tar.gz archive if
True
, else .tar - include_hidden (bool) – whether to include hidden datasets in the export
- include_deleted (bool) – whether to include deleted datasets in the export
- wait (bool) – if
True
, block until the export is ready; else, return immediately
Return type: str
Returns: jeha_id
of the export, or empty ifwait
isFalse
and the export is not ready.
-
get_current_history
()[source]¶ Deprecated method.
Just an alias for get_most_recently_used_history().
-
get_histories
(history_id=None, name=None, deleted=False)[source]¶ Get all histories or filter the specific one(s) via the provided
name
orhistory_id
. Provide only one argument,name
orhistory_id
, but not both.If
deleted
is set toTrue
, return histories that have been deleted.Parameters: - history_id (str) – Encoded history ID to filter on
- name (str) – Name of history to filter on
Return type: dict
Returns: Return a list of history element dicts. If more than one history matches the given
name
, return the list of all the histories with the given name.
-
get_most_recently_used_history
()[source]¶ Returns the current user’s most recently used history (not deleted).
-
get_status
(history_id)[source]¶ Returns the state of this history
Parameters: history_id (str) – Encoded history ID Return type: dict Returns: A dict documenting the current state of the history. Has the following keys: ‘state’ = This is the current state of the history, such as ok, error, new etc. ‘state_details’ = Contains individual statistics for various dataset states. ‘percent_complete’ = The overall number of datasets processed to completion.
-
show_dataset
(history_id, dataset_id)[source]¶ Get details about a given history dataset.
Parameters: - history_id (str) – Encoded history ID
- dataset_id (str) – Encoded dataset ID
-
show_dataset_collection
(history_id, dataset_collection_id)[source]¶ Get details about a given history dataset collection.
Parameters: - history_id (str) – Encoded history ID
- dataset_collection_id (str) – Encoded dataset collection ID
-
show_dataset_provenance
(history_id, dataset_id, follow=False)[source]¶ Get details related to how dataset was created (
id
,job_id
,tool_id
,stdout
,stderr
,parameters
,inputs
, etc...).Parameters: - history_id (str) – Encoded history ID
- dataset_id (str) – Encoded dataset ID
- follow (bool) – If
follow
isTrue
, recursively fetch dataset provenance information for all inputs and their inputs, etc...
-
show_history
(history_id, contents=False, deleted=None, visible=None, details=None, types=None)[source]¶ Get details of a given history. By default, just get the history meta information.
Parameters: - history_id (str) – Encoded history ID to filter on
- contents (bool) – When
True
, the complete list of datasets in the given history. - deleted (str) – Used when contents=True, includes deleted datasets in history dataset list
- visible (str) – Used when contents=True, includes only visible datasets in history dataset list
- details (str) – Used when contents=True, includes dataset details. Set to ‘all’ for the most information
- types (str) –
???
-
show_matching_datasets
(history_id, name_filter=None)[source]¶ Get dataset details for matching datasets within a history.
Parameters: - history_id (str) – Encoded history ID
- name_filter (str) – Only datasets whose name matches the
name_filter
regular expression will be returned; use plain strings for exact matches and None to match all datasets in the history
-
undelete_history
(history_id)[source]¶ Undelete a history
Parameters: history_id (str) – Encoded history ID
-
update_dataset
(history_id, dataset_id, **kwds)[source]¶ Update history dataset metadata. Some of the attributes that can be modified are documented below.
Parameters: - history_id (str) – Encoded history ID
- dataset_id (str) – Id of the dataset
- name (str) – Replace history dataset name with the given string
- annotation (str) – Replace history dataset annotation with given string
- deleted (bool) – Mark or unmark history dataset as deleted
- visible (bool) – Mark or unmark history dataset as visible
Return type: int
Returns: status code
-
update_dataset_collection
(history_id, dataset_collection_id, **kwds)[source]¶ Update history dataset collection metadata. Some of the attributes that can be modified are documented below.
Parameters: - history_id (str) – Encoded history ID
- dataset_collection_id (str) – Encoded dataset_collection ID
- name (str) – Replace history dataset collection name with the given string
- deleted (bool) – Mark or unmark history dataset collection as deleted
- visible (bool) – Mark or unmark history dataset collection as visible
Return type: int
Returns: status code
-
update_history
(history_id, name=None, annotation=None, **kwds)[source]¶ Update history metadata information. Some of the attributes that can be modified are documented below.
Parameters: - history_id (str) – Encoded history ID
- name (str) – Replace history name with the given string
- annotation (str) – Replace history annotation with given string
- deleted (bool) – Mark or unmark history as deleted
- published (bool) – Mark or unmark history as published
- importable (bool) – Mark or unmark history as importable
- tags (list) – Replace history tags with the given list
Return type: int
Returns: status code
-
Jobs¶
Contains possible interactions with the Galaxy Jobs
-
class
bioblend.galaxy.jobs.
JobsClient
(galaxy_instance)[source]¶ -
get_jobs
()[source]¶ Get a list of jobs for current user
Parameters: state (str or list) – limit listing of jobs to those that match one of the included states. If none, all are returned. Valid Galaxy job states include: ‘new’, ‘upload’, ‘waiting’, ‘queued’, ‘running’, ‘ok’, ‘error’, ‘paused’, ‘deleted’, ‘deleted_new’
Parameters: - tool_id (str or list) – limit listing of jobs to those that match one of the included tool_ids. If none, all are returned.
- history_id (str) – limit listing of jobs to those that match the history_id. If none, all are returned.
Return type: Returns: list of dictionaries containing summary job information For example:
[{ u'create_time': u'2014-03-01T16:16:48.640550',
u’exit_code’: 0, u’id’: u’ebfb8f50c6abde6d’, u’model_class’: u’Job’, u’state’: u’ok’, u’tool_id’: u’fasta2tab’, u’update_time’: u‘2014-03-01T16:16:50.657399’}, {u’create_time’: u‘2014-03-01T16:05:34.851246’, u’exit_code’: 0, u’id’: u‘1cd8e2f6b131e891’, u’model_class’: u’Job’, u’state’: u’ok’, u’tool_id’: u’upload1’, u’update_time’: u‘2014-03-01T16:05:39.558458’}]
-
get_state
(job_id)[source]¶ Display the current state for a single job from current user.
Parameters: job_id (str) – Specific job ID Return type: str Returns: State of single job with the following being valid values: new, queued, running, waiting, ok. In case the state cannot be retrived, an empty string is returned. New in version 0.5.3.
-
search_jobs
(job_info)[source]¶ Return jobs for current user based payload content
Parameters: job_info (dict) – Dictionary containing description of requested job. This is in the same format as a request to POST /api/tools would take to initiate a job Return type: list Returns: list of dictionaries containing summary job information of the jobs that match the requested job run This method is designed to scan the list of previously run jobs and find records of jobs that had the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply recycle the old results.
-
show_job
(job_id)[source]¶ Display information on a single job from current user
Parameters: job_id (str) – Specific job ID Return type: dict Returns: A description of single job For example: { u'create_time': u'2014-03-01T16:17:29.828624',
u’exit_code’: 0, u’id’: u’a799d38679e985db’, u’inputs’: { u’input’: { u’id’: u’ebfb8f50c6abde6d’, u’src’: u’hda’}}, u’model_class’: u’Job’, u’outputs’: { u’output’: { u’id’: u’a799d38679e985db’, u’src’: u’hda’}}, u’params’: { u’chromInfo’: u’”/opt/galaxy-central/tool-data/shared/ucsc/chrom/?.len”’, u’dbkey’: u’”?”’, u’seq_col’: u‘“2”’, u’title_col’: u’[“1”]’}, u’state’: u’ok’, u’tool_id’: u’tab2fasta’, u’update_time’: u‘2014-03-01T16:17:31.930728’}
-
Libraries¶
Contains possible interactions with the Galaxy Data Libraries
-
class
bioblend.galaxy.libraries.
LibraryClient
(galaxy_instance)[source]¶ -
copy_from_dataset
(library_id, dataset_id, folder_id=None, message='')[source]¶ Copy a Galaxy dataset into a library.
Parameters: - library_id (str) – id of the library where to place the uploaded file
- dataset_id (str) – id of the dataset to copy from
- folder_id (str) – id of the folder where to place the uploaded files. If not provided, the root folder will be used
- message (str) – message for copying action
-
create_folder
(library_id, folder_name, description=None, base_folder_id=None)[source]¶ Create a folder in a library.
Parameters: - library_id (str) – library id to use
- folder_name (str) – name of the new folder in the data library
- description (str) – description of the new folder in the data library
- base_folder_id (str) – id of the folder where to create the new folder. If not provided, the root folder will be used
-
create_library
(name, description=None, synopsis=None)[source]¶ Create a data library with the properties defined in the arguments. Return a list of JSON dicts, looking like so:
:type name: str :param name: Name of the new data library
Parameters: - description (str) – Optional data library description
- synopsis (str) – Optional data library synopsis
Return type: Returns: List of dicts describing created library
- [{“id”: “f740ab636b360a70”,
“name”: “Library from bioblend”, “url”: “/api/libraries/f740ab636b360a70”}]
-
delete_library
(library_id)[source]¶ Delete a data library.
Parameters: library_id (str) – Encoded data library ID identifying the library to be deleted Warning
Deleting a data library is irreversible - all of the data from the library will be permanently deleted.
-
delete_library_dataset
(library_id, dataset_id, purged=False)[source]¶ Delete a library dataset in a data library.
Parameters: - library_id (str) – library id where dataset is found in
- dataset_id (str) – id of the dataset to be deleted
- purged (bool) – Indicate that the dataset should be purged (permanently deleted)
Return type: dict
Returns: A dictionary containing the dataset id and whether the dataset has been deleted For example:
{u'deleted': True, u'id': u'60e680a037f41974'}
-
get_folders
(library_id, folder_id=None, name=None, deleted=False)[source]¶ Get all the folders or filter specific one(s) via the provided
name
orfolder_id
in data library with idlibrary_id
. Provide only one argument:name
orfolder_id
, but not both.Parameters: - folder_id (str) – filter for folder by folder id
- name (str) – filter for folder by name. For
name
specify the full path of the folder starting from the library’s root folder, e.g./subfolder/subsubfolder
. - deleted (bool) – If set to
True
, return folders that have been deleted.
Return type: dict
Returns: list of dicts each containing basic information about a folder.
-
get_libraries
(library_id=None, name=None, deleted=False)[source]¶ Get all the libraries or filter for specific one(s) via the provided name or ID. Provide only one argument:
name
orlibrary_id
, but not both.Parameters: - library_id (str) – filter for library by library id
- name (str) – If
name
is set and multiple names match the given name, all the libraries matching the argument will be returned. - deleted (bool) – If set to
True
, return libraries that have been deleted.
Return type: dict
Returns: list of dicts each containing basic information about a library.
-
get_library_permissions
(library_id)[source]¶ Get the permessions for a library.
Parameters: library_id (str) – id of the library Return type: dict Returns: dictionary with all applicable permissions’ values
-
set_library_permissions
(library_id, access_in=None, modify_in=None, add_in=None, manage_in=None)[source]¶ Set the permissions for a library. Note: it will override all security for this library even if you leave out a permission type.
Parameters:
-
show_dataset
(library_id, dataset_id)[source]¶ Get details about a given library dataset. The required
library_id
can be obtained from the datasets’s library content details.Parameters: - library_id (str) – library id where dataset is found in
- dataset_id (str) – id of the dataset to be inspected
Return type: dict
Returns: A dictionary containing information about the dataset in the library
-
show_folder
(library_id, folder_id)[source]¶ Get details about a given folder. The required
folder_id
can be obtained from the folder’s library content details.Parameters: - library_id (str) – library id to inspect folders in
- folder_id (str) – id of the folder to be inspected
-
show_library
(library_id, contents=False)[source]¶ Get information about a library.
Parameters: - library_id (str) – filter for library by library id
- contents (bool) – True if want to get contents of the library (rather than just the library details).
Return type: Returns: a list of dicts containing library details.
-
upload_file_contents
(library_id, pasted_content, folder_id=None, file_type='auto', dbkey='?')[source]¶ Upload pasted_content to a data library as a new file.
Parameters: - library_id (str) – id of the library where to place the uploaded file
- pasted_content (str) – Content to upload into the library
- folder_id (str) – id of the folder where to place the uploaded file. If not provided, the root folder will be used
- file_type (str) – Galaxy file format name
- dbkey (str) – Dbkey
-
upload_file_from_local_path
(library_id, file_local_path, folder_id=None, file_type='auto', dbkey='?')[source]¶ Read local file contents from file_local_path and upload data to a library.
Parameters: - library_id (str) – id of the library where to place the uploaded file
- file_local_path (str) – path of local file to upload
- folder_id (str) – id of the folder where to place the uploaded file. If not provided, the root folder will be used
- file_type (str) – Galaxy file format name
- dbkey (str) – Dbkey
-
upload_file_from_server
(library_id, server_dir, folder_id=None, file_type='auto', dbkey='?', link_data_only=None, roles='')[source]¶ Upload all files in the specified subdirectory of the Galaxy library import directory to a library.
Note
For this method to work, the Galaxy instance must have the
library_import_dir
option configured in theconfig/galaxy.ini
configuration file.Parameters: - library_id (str) – id of the library where to place the uploaded file
- server_dir (str) – relative path of the subdirectory of
library_import_dir
to upload. All and only the files (i.e. no subdirectories) contained in the specified directory will be uploaded. - folder_id (str) – id of the folder where to place the uploaded files. If not provided, the root folder will be used
- file_type (str) – Galaxy file format name
- dbkey (str) – Dbkey
- link_data_only (str) – either ‘copy_files’ (default) or ‘link_to_files’. Setting to ‘link_to_files’ symlinks instead of copying the files
- roles (str) –
???
-
upload_file_from_url
(library_id, file_url, folder_id=None, file_type='auto', dbkey='?')[source]¶ Upload a file to a library from a URL.
Parameters: - library_id (str) – id of the library where to place the uploaded file
- file_url (str) – URL of the file to upload
- folder_id (str) – id of the folder where to place the uploaded file. If not provided, the root folder will be used
- file_type (str) – Galaxy file format name
- dbkey (str) – Dbkey
-
upload_from_galaxy_filesystem
(library_id, filesystem_paths, folder_id=None, file_type='auto', dbkey='?', link_data_only=None, roles='')[source]¶ Upload a set of files already present on the filesystem of the Galaxy server to a library.
Note
For this method to work, the Galaxy instance must have the
allow_library_path_paste
option set toTrue
in theconfig/galaxy.ini
configuration file.Parameters: - library_id (str) – id of the library where to place the uploaded file
- filesystem_paths (str) – file paths on the Galaxy server to upload to the library, one file per line
- folder_id (str) – id of the folder where to place the uploaded files. If not provided, the root folder will be used
- file_type (str) – Galaxy file format name
- dbkey (str) – Dbkey
- link_data_only (str) – either ‘copy_files’ (default) or ‘link_to_files’. Setting to ‘link_to_files’ symlinks instead of copying the files
- roles (str) –
???
-
Quotas¶
Contains possible interactions with the Galaxy Quota
-
class
bioblend.galaxy.quotas.
QuotaClient
(galaxy_instance)[source]¶ -
get_quotas
(deleted=False)[source]¶ Get a list of quotas
Parameters: deleted (bool) – Only return quota(s) that have been deleted Return type: list Returns: A list of dicts with details on individual quotas. For example: [{ u'id': u'0604c8a56abe9a50', u'model_class': u'Quota', u'name': u'test ', u'url': u'/api/quotas/0604c8a56abe9a50'}, { u'id': u'1ee267091d0190af', u'model_class': u'Quota', u'name': u'workshop', u'url': u'/api/quotas/1ee267091d0190af'}]
-
show_quota
(quota_id, deleted=False)[source]¶ Display information on a quota
Parameters: - quota_id (str) – Encoded quota ID
- deleted (bool) – Search for quota in list of ones already marked as deleted
Return type: dict
Returns: A description of quota For example:
{ u'bytes': 107374182400, u'default': [], u'description': u'just testing', u'display_amount': u'100.0 GB', u'groups': [], u'id': u'0604c8a56abe9a50', u'model_class': u'Quota', u'name': u'test ', u'operation': u'=', u'users': []}
-
Roles¶
Contains possible interactions with the Galaxy Roles
-
class
bioblend.galaxy.roles.
RolesClient
(galaxy_instance)[source]¶ -
get_roles
()[source]¶ Displays a collection (list) of roles.
Return type: list Returns: A list of dicts with details on individual roles. For example: [ {"id": "f2db41e1fa331b3e", "model_class": "Role", "name": "Foo", "url": "/api/roles/f2db41e1fa331b3e"}, {"id": "f597429621d6eb2b", "model_class": "Role", "name": "Bar", "url": "/api/roles/f597429621d6eb2b"} ]
-
show_role
(role_id)[source]¶ Display information on a single role
Parameters: role_id (str) – Encoded role ID Return type: dict Returns: A description of role For example: {"description": "Private Role for Foo", "id": "f2db41e1fa331b3e", "model_class": "Role", "name": "Foo", "type": "private", "url": "/api/roles/f2db41e1fa331b3e"}
-
Tools¶
Contains possible interaction dealing with Galaxy tools.
-
class
bioblend.galaxy.tools.
ToolClient
(galaxy_instance)[source]¶ -
get_tool_panel
()[source]¶ Get a list of available tool elements in Galaxy’s configured toolbox.
Return type: list Returns: List containing tools (if not in sections) or tool sections with nested tool descriptions.
-
get_tools
(tool_id=None, name=None, trackster=None)[source]¶ Get all tools or filter the specific one(s) via the provided
name
ortool_id
. Provide only one argument,name
ortool_id
, but not both.If
name
is set and multiple names match the given name, all the tools matching the argument will be returned.Parameters: - tool_id (str) – id of the requested tool
- name (str) – name of the requested tool(s)
- trackster (boolean) – if True, only tools that are compatible with Trackster are returned
Return type: Returns: List of tool descriptions.
-
paste_content
(content, history_id, **kwds)[source]¶ Upload a string to a new dataset in the history specified by
history_id
.Parameters: - content (str) – content of the new dataset to upload or a list of URLs (one per line) to upload
- history_id (str) – id of the history where to upload the content
See
upload_file()
for the optional parameters (except file_name).
-
put_url
(content, history_id, **kwds)¶ Upload a string to a new dataset in the history specified by
history_id
.Parameters: - content (str) – content of the new dataset to upload or a list of URLs (one per line) to upload
- history_id (str) – id of the history where to upload the content
See
upload_file()
for the optional parameters (except file_name).
-
run_tool
(history_id, tool_id, tool_inputs)[source]¶ Runs tool specified by
tool_id
in history indicated byhistory_id
with inputs fromdict
tool_inputs
.Parameters: - history_id (str) – encoded ID of the history in which to run the tool
- tool_id (str) – ID of the tool to be run
- tool_inputs (dict) – dictionary of input datasets and parameters for the tool (see below)
The
tool_inputs
dict should contain input datasets and parameters in the (largely undocumented) format used by the Galaxy API. Some examples can be found in https://bitbucket.org/galaxy/galaxy-central/src/tip/test/api/test_tools.py .
-
show_tool
(tool_id, io_details=False, link_details=False)[source]¶ Get details of a given tool.
Parameters: - tool_id (str) – id of the requested tool
- io_details (bool) – if True, get also input and output details
- link_details (bool) – if True, get also link details
-
upload_file
(path, history_id, **keywords)[source]¶ Upload file specified by
path
to the history specified byhistory_id
.Parameters: - path (str) – path of the file to upload
- history_id (str) – id of the history where to upload the file
- file_name (str) – (optional) name of the new history dataset
- file_type (str) – Galaxy datatype for the new dataset, default is auto
- dbkey (str) – (optional) genome dbkey
-
Tool data tables¶
Contains possible interactions with the Galaxy Tool data tables
-
class
bioblend.galaxy.tool_data.
ToolDataClient
(galaxy_instance)[source]¶ -
delete_data_table
(data_table_id, values)[source]¶ Delete an item from a data table.
Parameters: - data_table_id (str) – ID of the data table
- values (str) – a “|” separated list of column contents, there must be a value for all the columns of the data table
-
get_data_tables
()[source]¶ Displays a collection (list) of data tables.
Return type: list Returns: - A list of dicts with details on individual data tables.
- For example:
- [
- {
- “model_class”: “TabularToolDataTable”, “name”: “fasta_indexes”
}, {
“model_class”: “TabularToolDataTable”, “name”: “bwa_indexes”}
}
-
show_data_table
(data_table_id)[source]¶ Display information on a single data_table
Parameters: data_table_id (str) – ID of the data table Return type: dict Returns: - A description of data_table and its content
- For example:
- {
- “columns”: [“value”, “dbkey”, “name”, “path”],
“fields”: [
- [
- “test id”, “test”, “test name”, “/opt/galaxy-dist/tool-data/test/seq/test id.fa”
]
], “model_class”: “TabularToolDataTable”, “name”: “all_fasta”
}
-
ToolShed¶
Interaction with a Galaxy Tool Shed
-
class
bioblend.galaxy.toolshed.
ToolShedClient
(galaxy_instance)[source]¶ -
get_repositories
()[source]¶ Get a list of all repositories in the Tool Shed
Return type: list Returns: Returns a list of dictionaries containing information about repositories present in the Tool Shed. For example: [{u'changeset_revision': u'4afe13ac23b6', u'deleted': False, u'dist_to_shed': False, u'error_message': u'', u'name': u'velvet_toolsuite', u'owner': u'edward-kirton', u'status': u'Installed'}]
Changed in version 0.4.1: Changed method name from
get_tools
toget_repositories
to better align with the Tool Shed concepts
-
install_repository_revision
(tool_shed_url, name, owner, changeset_revision, install_tool_dependencies=False, install_repository_dependencies=False, tool_panel_section_id=None, new_tool_panel_section_label=None)[source]¶ Install a specified repository revision from a specified Tool Shed into this Galaxy instance. This example demonstrates installation of a repository that contains valid tools, loading them into a section of the Galaxy tool panel or creating a new tool panel section. You can choose if tool dependencies or repository dependencies should be installed, use
install_tool_dependencies
orinstall_repository_dependencies
.Installing the repository into an existing tool panel section requires the tool panel config file (e.g., tool_conf.xml, shed_tool_conf.xml, etc) to contain the given tool panel section:
<section id=”from_test_tool_shed” name=”From Test Tool Shed” version=”“> </section>Parameters: - tool_shed_url (str) – URL of the Tool Shed from which the repository should
be installed from (e.g.,
http://testtoolshed.g2.bx.psu.edu
) - name (str) – The name of the repository that should be installed
- owner (str) – The name of the repository owner
- changeset_revision (str) – The revision of the repository to be installed
- install_tool_dependencies (bool) – Whether or not to automatically handle tool dependencies (see http://wiki.galaxyproject.org/AToolOrASuitePerRepository for more details)
- install_repository_dependencies (bool) – Whether or not to automatically handle repository dependencies (see http://wiki.galaxyproject.org/DefiningRepositoryDependencies for more details)
- tool_panel_section_id (str) – The ID of the Galaxy tool panel section
where the tool should be insterted under.
Note that you should specify either this
parameter or the
new_tool_panel_section_label
. If both are specified, this one will take precedence. - new_tool_panel_section_label (str) – The name of a Galaxy tool panel section that should be created and the repository installed into.
- tool_shed_url (str) – URL of the Tool Shed from which the repository should
be installed from (e.g.,
-
show_repository
(toolShed_id)[source]¶ Display information of a repository from the Tool Shed
Parameters: toolShed_id (str) – Encoded toolShed ID Return type: dictionary Returns: Information about the tool For example: {u'changeset_revision': u'b17455fb6222', u'ctx_rev': u'8', u'owner': u'aaron', u'status': u'Installed', u'url': u'/api/tool_shed_repositories/82de4a4c7135b20a'}
Changed in version 0.4.1: Changed method name from
show_tool
toshow_repository
to better align with the Tool Shed concepts
-
Users¶
Contains possible interaction dealing with Galaxy users.
These methods must be executed by a registered Galaxy admin user.
-
class
bioblend.galaxy.users.
UserClient
(galaxy_instance)[source]¶ -
create_local_user
(username, user_email, password)[source]¶ Create a new Galaxy user.
Note
For this method to work, the Galaxy instance must have the
allow_user_creation
option set toTrue
anduse_remote_user
option set toFalse
in theconfig/galaxy.ini
configuration file.Parameters: - username (str) – Username of user to be created
- user_email (str) – Email of user to be created
- password (str) – password of user to be created
Return type: dict
Returns: dictionary containing information about the created user
-
create_remote_user
(user_email)[source]¶ Create a new Galaxy remote user.
Note
For this method to work, the Galaxy instance must have the
allow_user_creation
anduse_remote_user
options set toTrue
in theconfig/galaxy.ini
configuration file. Also note that settinguse_remote_user
will require an upstream authentication proxy server; however, if you do not have one, access to Galaxy via a browser will not be possible.Parameters: user_email (str) – Email of user to be created Return type: dict Returns: dictionary containing information about the created user
-
create_user_apikey
(user_id)[source]¶ Create a new api key for a user
Parameters: user_id (str) – Encoded user ID Return type: str Returns: The api key for the user
-
get_current_user
()[source]¶ Returns the user id associated with this Galaxy connection
Return type: dict Returns: dictionary containing information about the current user
-
get_users
(deleted=False)[source]¶ Get a list of all registered users. If
deleted
is set toTrue
, get a list of deleted users.Return type: list Returns: A list of dicts with user details. For example: [{u'email': u'a_user@example.com', u'id': u'dda47097d9189f15', u'url': u'/api/users/dda47097d9189f15'}]
-
show_user
(user_id, deleted=False)[source]¶ Display information about a user. If
deleted
is set toTrue
, display information about a deleted user.Parameters: - user_id (str) – User ID to inspect
- deleted (bool) – Whether to return results for a deleted user
Return type: dict
Returns: dictionary containing information about the user
-
Visual¶
Contains possible interactions with the Galaxy visualization
-
class
bioblend.galaxy.visual.
VisualClient
(galaxy_instance)[source]¶ -
get_visualizations
()[source]¶ Get a list of visualizations
Return type: list Returns: A list of dicts with details on individual visualizations. For example: [{ u'dbkey': u'eschColi_K12', u'id': u'df1c7c96fc427c2d', u'title': u'AVTest1', u'type': u'trackster', u'url': u'/api/visualizations/df1c7c96fc427c2d'}, { u'dbkey': u'mm9', u'id': u'a669f50f8bf55b02', u'title': u'Bam to Bigwig', u'type': u'trackster', u'url': u'/api/visualizations/a669f50f8bf55b02'}]
-
show_visualization
(visual_id)[source]¶ Display information on a visualization
Parameters: visual_id (str) – Encoded visualization ID Return type: dict Returns: A description of visualization For example: {u'annotation': None,u'dbkey': u'mm9', u'id': u'18df9134ea75e49c', u'latest_revision': { ... }, u'model_class': u'Visualization', u'revisions': [ u'aa90649bb3ec7dcb', u'20622bc6249c0c71'], u'slug': u'visualization-for-grant-1', u'title': u'Visualization For Grant', u'type': u'trackster', u'url': u'/u/azaron/v/visualization-for-grant-1', u'user_id': u'21e4aed91386ca8b'}
-
Workflows¶
Contains possible interactions with the Galaxy Workflows
-
class
bioblend.galaxy.workflows.
WorkflowClient
(galaxy_instance)[source]¶ -
delete_workflow
(workflow_id)[source]¶ Delete a workflow identified by workflow_id.
Parameters: workflow_id (str) – Encoded workflow ID Warning
Deleting a workflow is irreversible - all workflow data will be permanently deleted.
-
export_workflow_json
(workflow_id)[source]¶ Exports a workflow
Parameters: workflow_id (str) – Encoded workflow ID Return type: dict Returns: Dict representing the workflow requested
-
export_workflow_to_local_path
(workflow_id, file_local_path, use_default_filename=True)[source]¶ Exports a workflow in json format to a given local path.
Parameters: - workflow_id (str) – Encoded workflow ID
- file_local_path (str) – Local path to which the exported file will be saved. (Should not contain filename if use_default_name=True)
- use_default_filename (bool) – If the use_default_name parameter is True, the exported file will be saved as file_local_path/Galaxy-Workflow-%s.ga, where %s is the workflow name. If use_default_name is False, file_local_path is assumed to contain the full file path including filename.
-
get_workflow_inputs
(workflow_id, label)[source]¶ Get a list of workflow input IDs that match the given label. If no input matches the given label, an empty list is returned.
Parameters: - workflow_id (str) – Encoded workflow ID
- label (str) – label to filter workflow inputs on
Return type: Returns: list of workflow inputs matching the label query
-
get_workflows
(workflow_id=None, name=None, deleted=False, published=False)[source]¶ Get all workflows or filter the specific one(s) via the provided
name
orworkflow_id
. Provide only one argument,name
orworkflow_id
, but not both.Parameters: - workflow_id (str) – Encoded workflow ID (incompatible with
name
) - name (str) – Filter by name of workflow (incompatible with
workflow_id
). If multiple names match the given name, all the workflows matching the argument will be returned. - deleted (bool) – this parameter is deprecated and ignored, it will be removed in BioBlend 0.6
- published (bool) – if
True
, return also published workflows
Return type: Returns: A list of workflow dicts. For example:
[{u'id': u'92c56938c2f9b315', u'name': u'Simple', u'url': u'/api/workflows/92c56938c2f9b315'}]
- workflow_id (str) – Encoded workflow ID (incompatible with
Imports a new workflow from the shared published workflows
Parameters: workflow_id (str) – Encoded workflow ID Return type: dict Returns: A description of the workflow. For example: {u'id': u'ee0e2b4b696d9092', u'model_class': u'StoredWorkflow', u'name': u'Super workflow that solves everything!', u'published': False, u'tags': [], u'url': u'/api/workflows/ee0e2b4b696d9092'}
-
import_workflow_from_local_path
(file_local_path)[source]¶ Imports a new workflow given the path to a file containing a previously exported workflow.
Parameters: file_local_path (str) – File to upload to the server for new workflow
-
import_workflow_json
(workflow_json)[source]¶ Imports a new workflow given a json representation of a previously exported workflow.
Parameters: workflow_json (str) – JSON string representing the workflow to be imported
-
run_workflow
(workflow_id, dataset_map=None, params=None, history_id=None, history_name=None, import_inputs_to_history=False, replacement_params=None)[source]¶ Run the workflow identified by
workflow_id
Parameters: - workflow_id (str) – Encoded workflow ID
- dataset_map (str or dict) – A mapping of workflow inputs to datasets. The datasets
source can be a LibraryDatasetDatasetAssociation (
ldda
), LibraryDataset (ld
), or HistoryDatasetAssociation (hda
). The map must be in the following format:{'<input>': {'id': <encoded dataset ID>, 'src': '[ldda, ld, hda]'}}
(e.g.{'23': {'id': '29beef4fadeed09f', 'src': 'ld'}}
) - params (str or dict) – A mapping of tool parameters that are non-datasets parameters. The map must be in the
following format:
{'blastn': {'param': 'evalue', 'value': '1e-06'}}
- history_id (str) – The encoded history ID where to store the workflow
output. Alternatively,
history_name
may be specified to create a new history. - history_name (str) – Create a new history with the given name to store
the workflow output. If both
history_id
andhistory_name
are provided,history_name
is ignored. If neither is specified, a new ‘Unnamed history’ is created. - import_inputs_to_history (bool) – If
True
, used workflow inputs will be imported into the history. IfFalse
, only workflow outputs will be visible in the given history. - replacement_params (dict) – pattern-based replacements for post-job actions (see below)
Return type: dict
Returns: A dict containing the history ID where the outputs are placed as well as output dataset IDs. For example:
{u'history': u'64177123325c9cfd', u'outputs': [u'aa4d3084af404259']}
The
replacement_params
dict should map parameter names in post-job actions (PJAs) to their runtime values. For instance, if the final step has a PJA like the following:{u'RenameDatasetActionout_file1': { u'action_arguments': {u'newname': u'${output}'}, u'action_type': u'RenameDatasetAction', u'output_name': u'out_file1'}}
then the following renames the output dataset to ‘foo’:
replacement_params = {'output': 'foo'}
see also this thread
-
show_workflow
(workflow_id)[source]¶ Display information needed to run a workflow
Parameters: workflow_id (str) – Encoded workflow ID Return type: list Returns: A description of the workflow and its inputs as a JSON object. For example: {u'id': u'92c56938c2f9b315', u'inputs': {u'23': {u'label': u'Input Dataset', u'value': u''}}, u'name': u'Simple', u'url': u'/api/workflows/92c56938c2f9b315'}
-
Object-oriented Galaxy API¶
-
class
bioblend.galaxy.objects.galaxy_instance.
GalaxyInstance
(url, api_key=None, email=None, password=None)[source]¶ A representation of an instance of Galaxy, identified by a URL and a user’s API key.
Parameters: - url (str) – a FQDN or IP for a given instance of Galaxy. For example:
http://127.0.0.1:8080
- api_key (str) – user’s API key for the given instance of Galaxy, obtained from the Galaxy web UI.
This is actually a factory class which instantiates the entity-specific clients.
Example: get a list of all histories for a user with API key ‘foo’:
from bioblend.galaxy.objects import * gi = GalaxyInstance('http://127.0.0.1:8080', 'foo') histories = gi.histories.list()
-
histories
¶ Client module for Galaxy histories.
-
libraries
¶ Client module for Galaxy libraries.
-
tools
¶ Client module for Galaxy tools.
-
workflows
¶ Client module for Galaxy workflows.
- url (str) – a FQDN or IP for a given instance of Galaxy. For example:
Client¶
Clients for interacting with specific Galaxy entity types.
Classes in this module should not be instantiated directly, but used
via their handles in GalaxyInstance
.
-
class
bioblend.galaxy.objects.client.
ObjClient
(obj_gi)[source]¶ -
get_previews
(name=None, **kwargs)[source]¶ Get object previews (listings).
Previews model entity summaries provided by REST collection URIs, e.g.,
http://host:port/api/libraries
. Being the most lightweight objects associated to the various entities, these are the ones that should be used to retrieve basic info such as id and name.Parameters: name (str) – return only objects with this name Optional boolean kwargs for specific object types:
deleted
(libraries and histories)- if
True
, return only deleted objects published
(workflows)- if
True
, return published workflows
Return type: list of Preview
-
-
class
bioblend.galaxy.objects.client.
ObjHistoryClient
(obj_gi)[source]¶ Interacts with Galaxy histories.
-
create
(name=None)[source]¶ Create a new Galaxy history, optionally setting its name.
Return type: History
Returns: the history just created
-
delete
(id_=None, name=None, purge=False)[source]¶ Delete the history with the given id or name.
Note that the same name can map to multiple histories.
Parameters: purge (bool) – if True
, also purge (permanently delete) the historyNote
For the purge option to work, the Galaxy instance must have the
allow_user_dataset_purge
option set toTrue
in theconfig/galaxy.ini
configuration file.
-
-
class
bioblend.galaxy.objects.client.
ObjLibraryClient
(obj_gi)[source]¶ Interacts with Galaxy libraries.
-
create
(name, description=None, synopsis=None)[source]¶ Create a data library with the properties defined in the arguments.
Return type: Library
Returns: the library just created
-
delete
(id_=None, name=None)[source]¶ Delete the library with the given id or name.
Note that the same name can map to multiple libraries.
Warning
Deleting a data library is irreversible - all of the data from the library will be permanently deleted.
-
-
class
bioblend.galaxy.objects.client.
ObjToolClient
(obj_gi)[source]¶ Interacts with Galaxy tools.
-
get
(id_)[source]¶ Retrieve the tool corresponding to the given id.
Return type: Tool
Returns: the tool corresponding to id_
-
-
class
bioblend.galaxy.objects.client.
ObjWorkflowClient
(obj_gi)[source]¶ Interacts with Galaxy workflows.
-
delete
(id_=None, name=None)[source]¶ Delete the workflow with the given id or name.
Note that the same name can map to multiple workflows.
Warning
Deleting a workflow is irreversible - all of the data from the workflow will be permanently deleted.
-
get
(id_)[source]¶ Retrieve the workflow corresponding to the given id.
Return type: Workflow
Returns: the workflow corresponding to id_
-
import_new
(src)[source]¶ Imports a new workflow into Galaxy.
Parameters: src (dict or str) – deserialized (dictionary) or serialized (str) JSON dump of the workflow (this is normally obtained by exporting a workflow from Galaxy). Return type: Workflow
Returns: the workflow just imported
Imports a shared workflow to the user’s space.
Parameters: id (str) – workflow id Return type: Workflow
Returns: the workflow just imported
-
list
(name=None, deleted=False, published=False)[source]¶ Get workflows owned by the user of this Galaxy instance.
Parameters: - name (str) – return only workflows with this name
- deleted (bool) – this parameter is deprecated and ignored, it will be removed in BioBlend 0.6
- published (bool) – if
True
, return also published workflows
Return type: list of
Workflow
-
Wrappers¶
A basic object-oriented interface for Galaxy entities.
-
class
bioblend.galaxy.objects.wrappers.
Wrapper
(wrapped, parent=None, gi=None)[source]¶ Abstract base class for Galaxy entity wrappers.
Wrapper instances wrap deserialized JSON dictionaries such as the ones obtained by the Galaxy web API, converting key-based access to attribute-based access (e.g.,
library['name'] -> library.name
).Dict keys that are converted to attributes are listed in the
BASE_ATTRS
class variable: this is the ‘stable’ interface. Note that the wrapped dictionary is accessible via thewrapped
attribute.Parameters: - wrapped (dict) – JSON-serializable dictionary
- parent (
Wrapper
) – the parent of this wrapper - gi (
GalaxyInstance
) – the GalaxyInstance through which we can access this wrapper
-
BASE_ATTRS
= ('id', 'name')¶
-
gi_module
¶ The GalaxyInstance module that deals with objects of this type.
-
is_mapped
¶ True
if this wrapper is mapped to an actual Galaxy entity.
-
parent
¶ The parent of this wrapper.
-
class
bioblend.galaxy.objects.wrappers.
Step
(step_dict, parent)[source]¶ Abstract base class for workflow steps.
Steps are the main building blocks of a Galaxy workflow. A step can refer to either an input dataset (type ‘data_input`) or a computational tool (type ‘tool`).
-
BASE_ATTRS
= ('id', 'name', 'input_steps', 'tool_id', 'tool_inputs', 'tool_version', 'type')¶
-
gi_module
¶
-
-
class
bioblend.galaxy.objects.wrappers.
Workflow
(wf_dict, gi=None)[source]¶ Workflows represent ordered sequences of computations on Galaxy.
A workflow defines a sequence of steps that produce one or more results from an input dataset.
-
BASE_ATTRS
= ('id', 'name', 'deleted', 'inputs', 'published', 'steps', 'tags')¶
-
POLLING_INTERVAL
= 10¶
-
convert_input_map
(input_map)[source]¶ Convert
input_map
to the format required by the Galaxy web API.Parameters: input_map (dict) – a mapping from input labels to datasets Return type: dict Returns: a mapping from input slot ids to dataset ids in the format required by the Galaxy web API.
-
data_input_ids
¶ Return the list of data input steps for this workflow.
-
delete
()[source]¶ Delete this workflow.
Warning
Deleting a workflow is irreversible - all of the data from the workflow will be permanently deleted.
-
export
()[source]¶ Export a re-importable representation of the workflow.
Return type: dict Returns: a JSON-serializable dump of the workflow
-
gi_module
¶
-
input_labels
¶ Return the labels of this workflow’s input steps.
-
is_runnable
¶ Return True if the workflow can be run on Galaxy.
A workflow is considered runnable on a Galaxy instance if all of the tools it uses are installed in that instance.
-
run
(input_map=None, history='', params=None, import_inputs=False, replacement_params=None, wait=False, polling_interval=10, break_on_error=True)[source]¶ Run the workflow in the current Galaxy instance.
Parameters: - input_map (dict) – a mapping from workflow input labels to
datasets, e.g.:
dict(zip(workflow.input_labels, library.get_datasets()))
- history (
History
or str) – either a valid history object (results will be stored there) or a string (a new history will be created with the given name). - params (
Mapping
) – parameter settings for workflow steps (see below) - import_inputs (bool) – If
True
, workflow inputs will be imported into the history; ifFalse
, only workflow outputs will be visible in the history. - replacement_params (
Mapping
) – pattern-based replacements for post-job actions (see the docs forrun_workflow()
) - wait (boolean) – whether to wait while the returned datasets are in a pending state
- polling_interval (float) – polling interval in seconds
- break_on_error (boolean) – whether to break as soon as at least one of the returned datasets is in the ‘error’ state
Return type: tuple
Returns: list of output datasets, output history
The
params
dict should be structured as follows:PARAMS = {STEP_ID: PARAM_DICT, ...} PARAM_DICT = {NAME: VALUE, ...}
For backwards compatibility, the following (deprecated) format is also supported:
PARAMS = {TOOL_ID: PARAM_DICT, ...}
in which case PARAM_DICT affects all steps with the given tool id. If both by-tool-id and by-step-id specifications are used, the latter takes precedence.
Finally (again, for backwards compatibility), PARAM_DICT can also be specified as:
PARAM_DICT = {'param': NAME, 'value': VALUE}
Note that this format allows only one parameter to be set per step.
Example: set ‘a’ to 1 for the third workflow step:
params = {workflow.steps[2].id: {'a': 1}}
Warning
This is a blocking operation that can take a very long time. If
wait
is set toFalse
, the method will return as soon as the workflow has been scheduled, otherwise it will wait until the workflow has been run. With a large number of steps, however, the delay may not be negligible even in the former case (e.g. minutes for 100 steps).- input_map (dict) – a mapping from workflow input labels to
datasets, e.g.:
-
tool_ids
¶ Return the list of tool steps for this workflow.
-
-
class
bioblend.galaxy.objects.wrappers.
ContentInfo
(info_dict, gi=None)[source]¶ Instances of this class wrap dictionaries obtained by getting
/api/{histories,libraries}/<ID>/contents
from Galaxy.-
BASE_ATTRS
= ('id', 'name', 'type')¶
-
-
class
bioblend.galaxy.objects.wrappers.
LibraryContentInfo
(info_dict, gi=None)[source]¶ Instances of this class wrap dictionaries obtained by getting
/api/libraries/<ID>/contents
from Galaxy.-
gi_module
¶
-
-
class
bioblend.galaxy.objects.wrappers.
HistoryContentInfo
(info_dict, gi=None)[source]¶ Instances of this class wrap dictionaries obtained by getting
/api/histories/<ID>/contents
from Galaxy.-
BASE_ATTRS
= ('id', 'name', 'type', 'deleted', 'state', 'visible')¶
-
gi_module
¶
-
-
class
bioblend.galaxy.objects.wrappers.
DatasetContainer
(c_dict, content_infos=None, gi=None)[source]¶ Abstract base class for dataset containers (histories and libraries).
Parameters: content_infos (list of ContentInfo
) – info objects for the container’s contents-
BASE_ATTRS
= ('id', 'name', 'deleted')¶
-
dataset_ids
¶ Return the ids of the contained datasets.
-
get_dataset
(ds_id)[source]¶ Retrieve the dataset corresponding to the given id.
Parameters: ds_id (str) – dataset id Return type: HistoryDatasetAssociation
orLibraryDataset
Returns: the dataset corresponding to ds_id
-
get_datasets
(name=None)[source]¶ Get all datasets contained inside this dataset container.
Parameters: name (str) – return only datasets with this name Return type: list of HistoryDatasetAssociation
or list ofLibraryDataset
Returns: datasets with the given name contained inside this container Note
when filtering library datasets by name, specify their full paths starting from the library’s root folder, e.g.,
/seqdata/reads.fastq
. Full paths are available through thecontent_infos
attribute ofLibrary
objects.
-
-
class
bioblend.galaxy.objects.wrappers.
History
(hist_dict, content_infos=None, gi=None)[source]¶ Maps to a Galaxy history.
-
API_MODULE
= 'histories'¶
-
BASE_ATTRS
= ('id', 'name', 'deleted', 'annotation', 'state', 'state_ids', 'state_details', 'tags')¶
-
CONTENT_INFO_TYPE
¶ alias of
HistoryContentInfo
-
DS_TYPE
¶ alias of
HistoryDatasetAssociation
-
delete
(purge=False)[source]¶ Delete this history.
Parameters: purge (bool) – if True
, also purge (permanently delete) the historyNote
For the purge option to work, the Galaxy instance must have the
allow_user_dataset_purge
option set toTrue
in theconfig/galaxy.ini
configuration file.
-
download
(jeha_id, outf, chunk_size=4096)[source]¶ Download an export archive for this history. Use
export()
to create an export and get the requiredjeha_id
. Seedownload_history()
for parameter and return value info.
-
export
(gzip=True, include_hidden=False, include_deleted=False, wait=False)[source]¶ Start a job to create an export archive for this history. See
export_history()
for parameter and return value info.
-
gi_module
¶
-
import_dataset
(lds)[source]¶ Import a dataset into the history from a library.
Parameters: lds ( LibraryDataset
) – the library dataset to importReturn type: HistoryDatasetAssociation
Returns: the imported history dataset
-
paste_content
(content, **kwargs)[source]¶ Upload a string to a new dataset in this history.
Parameters: content (str) – content of the new dataset to upload See
upload_file()
for the optional parameters (except file_name).Return type: HistoryDatasetAssociation
Returns: the uploaded dataset
-
update
(name=None, annotation=None, **kwds)[source]¶ Update history metadata information. Some of the attributes that can be modified are documented below.
Parameters: - name (string) – Replace history name with the given string
- annotation (string) – Replace history annotation with given string
- deleted (boolean) – Mark or unmark history as deleted
- published (boolean) – Mark or unmark history as published
- importable (boolean) – Mark or unmark history as importable
- tags (list) – Replace history tags with the given list
-
upload_dataset
(path, **kwargs)¶ Upload the file specified by path to this history.
Parameters: path (str) – path of the file to upload See
upload_file()
for the optional parameters.Return type: HistoryDatasetAssociation
Returns: the uploaded dataset
-
upload_file
(path, **kwargs)[source]¶ Upload the file specified by path to this history.
Parameters: path (str) – path of the file to upload See
upload_file()
for the optional parameters.Return type: HistoryDatasetAssociation
Returns: the uploaded dataset
-
-
class
bioblend.galaxy.objects.wrappers.
Library
(lib_dict, content_infos=None, gi=None)[source]¶ Maps to a Galaxy library.
-
API_MODULE
= 'libraries'¶
-
BASE_ATTRS
= ('id', 'name', 'deleted', 'description', 'synopsis')¶
-
CONTENT_INFO_TYPE
¶ alias of
LibraryContentInfo
-
DS_TYPE
¶ alias of
LibraryDataset
-
copy_from_dataset
(hda, folder=None, message='')[source]¶ Copy a history dataset into this library.
Parameters: hda ( HistoryDatasetAssociation
) – history dataset to copy into the librarySee
upload_data()
for info on other params.
-
create_folder
(name, description=None, base_folder=None)[source]¶ Create a folder in this library.
Parameters: - name (str) – folder name
- description (str) – optional folder description
- base_folder (
Folder
) – parent folder, orNone
to create in the root folder
Return type: Returns: the folder just created
-
folder_ids
¶ Return the ids of the contained folders.
-
get_folder
(f_id)[source]¶ Retrieve the folder corresponding to the given id.
Return type: Folder
Returns: the folder corresponding to f_id
-
gi_module
¶
-
root_folder
¶ The root folder of this library.
Return type: Folder
Returns: the root folder of this library
-
upload_data
(data, folder=None, **kwargs)[source]¶ Upload data to this library.
Parameters: - data (str) – dataset contents
- folder (
Folder
) – a folder object, orNone
to upload to the root folder
Return type: Returns: the dataset object that represents the uploaded content
Optional keyword arguments:
file_type
,dbkey
.
-
upload_from_galaxy_fs
(paths, folder=None, link_data_only=None, **kwargs)[source]¶ Upload data to this library from filesystem paths on the server.
Note
For this method to work, the Galaxy instance must have the
allow_library_path_paste
option set toTrue
in theconfig/galaxy.ini
configuration file.Parameters: - paths (str or
Iterable
of str) – server-side file paths from which data should be read - link_data_only (str) – either ‘copy_files’ (default) or ‘link_to_files’. Setting to ‘link_to_files’ symlinks instead of copying the files
Return type: list of
LibraryDataset
Returns: the dataset objects that represent the uploaded content
See
upload_data()
for info on other params.- paths (str or
-
upload_from_local
(path, folder=None, **kwargs)[source]¶ Upload data to this library from a local file.
Parameters: path (str) – local file path from which data should be read See
upload_data()
for info on other params.
-
upload_from_url
(url, folder=None, **kwargs)[source]¶ Upload data to this library from the given URL.
Parameters: url (str) – URL from which data should be read See
upload_data()
for info on other params.
-
-
class
bioblend.galaxy.objects.wrappers.
Folder
(f_dict, container, gi=None)[source]¶ Maps to a folder in a Galaxy library.
-
BASE_ATTRS
= ('id', 'name', 'description', 'deleted', 'item_count')¶
-
container_id
¶ Deprecated property.
Id of the folder container. Use
container.id
instead.
-
gi_module
¶
-
-
class
bioblend.galaxy.objects.wrappers.
Dataset
(ds_dict, container, gi=None)[source]¶ Abstract base class for Galaxy datasets.
-
BASE_ATTRS
= ('id', 'name', 'data_type', 'file_name', 'file_size', 'state', 'deleted', 'file_ext')¶
-
POLLING_INTERVAL
= 1¶
-
container_id
¶ Deprecated property.
Id of the dataset container. Use
container.id
instead.
-
download
(file_object, chunk_size=4096)[source]¶ Open dataset for reading and save its contents to
file_object
.Parameters: file_object (file) – output file object See
get_stream()
for info on other params.
-
get_contents
(chunk_size=4096)[source]¶ Open dataset for reading and return its full contents.
See
get_stream()
for param info.
-
get_stream
(chunk_size=4096)[source]¶ Open dataset for reading and return an iterator over its contents.
Parameters: chunk_size (int) – read this amount of bytes at a time Warning
Due to a change in the Galaxy API endpoint, this method does not work on
LibraryDataset
instances with Galaxyrelease_2014.06.02
. Methods that delegate work to this one are also affected:peek()
,download()
andget_contents()
.
-
peek
(chunk_size=4096)[source]¶ Open dataset for reading and return the first chunk.
See
get_stream()
for param info.
-
wait
(polling_interval=1, break_on_error=True)[source]¶ Wait for this dataset to come out of the pending states.
Parameters: - polling_interval (float) – polling interval in seconds
- break_on_error (bool) – if
True
, raise a RuntimeError exception if the dataset ends in the ‘error’ state.
Warning
This is a blocking operation that can take a very long time. Also, note that this method does not return anything; however, this dataset is refreshed (possibly multiple times) during the execution.
-
-
class
bioblend.galaxy.objects.wrappers.
HistoryDatasetAssociation
(ds_dict, container, gi=None)[source]¶ Maps to a Galaxy
HistoryDatasetAssociation
.-
BASE_ATTRS
= ('id', 'name', 'data_type', 'file_name', 'file_size', 'state', 'deleted', 'file_ext', 'tags', 'visible')¶
-
SRC
= 'hda'¶
-
gi_module
¶
-
-
class
bioblend.galaxy.objects.wrappers.
LibraryDatasetDatasetAssociation
(ds_dict, container, gi=None)[source]¶ Maps to a Galaxy
LibraryDatasetDatasetAssociation
.-
SRC
= 'ldda'¶
-
-
class
bioblend.galaxy.objects.wrappers.
LibraryDataset
(ds_dict, container, gi=None)[source]¶ Maps to a Galaxy
LibraryDataset
.-
SRC
= 'ld'¶
-
-
class
bioblend.galaxy.objects.wrappers.
Tool
(t_dict, gi=None)[source]¶ Maps to a Galaxy tool.
-
BASE_ATTRS
= ('id', 'name', 'version')¶
-
POLLING_INTERVAL
= 10¶
-
gi_module
¶
-
run
(inputs, history, wait=False, polling_interval=10)[source]¶ Execute this tool in the given history with inputs from dict
inputs
.Parameters: - inputs (dict) – dictionary of input datasets and parameters for the tool (see below)
- history (
History
) – the history where to execute the tool - wait (boolean) – whether to wait while the returned datasets are in a pending state
- polling_interval (float) – polling interval in seconds
Return type: list of
HistoryDatasetAssociation
Returns: list of output datasets
The
inputs
dict should contain input datasets and parameters in the (largely undocumented) format used by the Galaxy API. Some examples can be found in Galaxy’s API test suite. The value of an input dataset can also be aDataset
object, which will be automatically converted to the needed format.
-
-
class
bioblend.galaxy.objects.wrappers.
Preview
(pw_dict, gi=None)[source]¶ Abstract base class for Galaxy entity ‘previews’.
Classes derived from this one model the short summaries returned by global getters such as
/api/libraries
.-
BASE_ATTRS
= ('id', 'name', 'deleted')¶
-
-
class
bioblend.galaxy.objects.wrappers.
LibraryPreview
(pw_dict, gi=None)[source]¶ Models Galaxy library ‘previews’.
Instances of this class wrap dictionaries obtained by getting
/api/libraries
from Galaxy.-
gi_module
¶
-