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Extract quickstart, reorg GX/TS Doc index
This commit is contained in:
Eric Rasche
@@ -0,0 +1,186 @@
|
||||
Quickstart
|
||||
==========
|
||||
|
||||
Log in as your user, navigate to the API Keys page in the User menu, and
|
||||
generate a new API key. Make a note of the API key, and then pull up a
|
||||
terminal. Now we'll use the display.py script in your galaxy/scripts/api
|
||||
directory for a short example::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories
|
||||
Collection Members
|
||||
------------------
|
||||
#1: /api/histories/8c49be448cfe29bc
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||||
name: Unnamed history
|
||||
id: 8c49be448cfe29bc
|
||||
#2: /api/histories/33b43b4e7093c91f
|
||||
name: output test
|
||||
id: 33b43b4e7093c91f
|
||||
|
||||
The result is a Collection of the histories of the user specified by the API
|
||||
key (you). To look at the details of a particular history, say #1 above, do
|
||||
the following::
|
||||
|
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% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc
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Member Information
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||||
------------------
|
||||
state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
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||||
state: ok
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||||
contents_url: /api/histories/8c49be448cfe29bc/contents
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||||
id: 8c49be448cfe29bc
|
||||
name: Unnamed history
|
||||
|
||||
This gives detailed information about the specific member in question, in this
|
||||
case the History. To view history contents, do the following::
|
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|
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|
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% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents
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Collection Members
|
||||
------------------
|
||||
#1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
|
||||
name: Pasted Entry
|
||||
type: file
|
||||
id: 6f91353f3eb0fa4a
|
||||
|
||||
What we have here is another Collection of items containing all of the datasets
|
||||
in this particular history. Finally, to view details of a particular dataset
|
||||
in this collection, execute the following::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
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||||
Member Information
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||||
------------------
|
||||
misc_blurb: 1 line
|
||||
name: Pasted Entry
|
||||
data_type: txt
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||||
deleted: False
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||||
file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
|
||||
state: ok
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||||
download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
|
||||
visible: True
|
||||
genome_build: ?
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model_class: HistoryDatasetAssociation
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file_size: 17
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||||
metadata_data_lines: 1
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||||
id: 6f91353f3eb0fa4a
|
||||
misc_info: uploaded txt file
|
||||
metadata_dbkey: ?
|
||||
|
||||
And now you've successfully used the API to request and select a history,
|
||||
browse the contents of that history, and then look at detailed information
|
||||
about a particular dataset.
|
||||
|
||||
For a more comprehensive Data Library example, set the following option in your
|
||||
galaxy.ini as well, and restart galaxy again::
|
||||
|
||||
admin_users = you@example.org
|
||||
library_import_dir = /path/to/some/directory
|
||||
|
||||
In the directory you specified for 'library_import_dir', create some
|
||||
subdirectories, and put (or symlink) files to import into Galaxy into those
|
||||
subdirectories.
|
||||
|
||||
In Galaxy, create an account that matches the address you put in 'admin_users',
|
||||
then browse to that user's preferences and generate a new API Key. Copy the
|
||||
key to your clipboard and then use these scripts::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries
|
||||
Collection Members
|
||||
------------------
|
||||
|
||||
0 elements in collection
|
||||
|
||||
% ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006
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name: api_test
|
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id: f3f73e481f432006
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006
|
||||
name: api_test
|
||||
id: f3f73e481f432006
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
|
||||
Member Information
|
||||
------------------
|
||||
synopsis: None
|
||||
contents_url: /api/libraries/f3f73e481f432006/contents
|
||||
description: API Test Library
|
||||
name: api_test
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
|
||||
name: /
|
||||
type: folder
|
||||
id: 28202595c0d2591f61ddda595d2c3670
|
||||
|
||||
% ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
|
||||
name: api_test_folder1
|
||||
id: 28202595c0d2591fa4f9089d2303fd89
|
||||
|
||||
% ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
name: 2.bed
|
||||
id: e9ef7fdb2db87d7b
|
||||
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
|
||||
name: 3.bed
|
||||
id: 3b7f6a31f80a5018
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
|
||||
name: /
|
||||
type: folder
|
||||
id: 28202595c0d2591f61ddda595d2c3670
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
|
||||
name: /api_test_folder1
|
||||
type: folder
|
||||
id: 28202595c0d2591fa4f9089d2303fd89
|
||||
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
name: /api_test_folder1/2.bed
|
||||
type: file
|
||||
id: e9ef7fdb2db87d7b
|
||||
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
|
||||
name: /api_test_folder1/3.bed
|
||||
type: file
|
||||
id: 3b7f6a31f80a5018
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
Member Information
|
||||
------------------
|
||||
misc_blurb: 68 regions
|
||||
metadata_endCol: 3
|
||||
data_type: bed
|
||||
metadata_columns: 6
|
||||
metadata_nameCol: 4
|
||||
uploaded_by: nate@...
|
||||
metadata_strandCol: 6
|
||||
name: 2.bed
|
||||
genome_build: hg19
|
||||
metadata_comment_lines: None
|
||||
metadata_startCol: 2
|
||||
metadata_chromCol: 1
|
||||
file_size: 4272
|
||||
metadata_data_lines: 68
|
||||
message:
|
||||
metadata_dbkey: hg19
|
||||
misc_info: uploaded bed file
|
||||
date_uploaded: 2010-06-22T17:01:51.266119
|
||||
metadata_column_types: str, int, int, str, int, str
|
||||
|
||||
Other parameters are valid when uploading, they are the same parameters as are
|
||||
used in the web form, like 'link_data_only' and etc.
|
||||
|
||||
The request and response format should be considered alpha and are subject to change.
|
||||
|
||||
|
||||
@@ -0,0 +1,185 @@
|
||||
Quickstart
|
||||
==========
|
||||
|
||||
Log in as your user, navigate to the API Keys page in the User menu, and
|
||||
generate a new API key. Make a note of the API key, and then pull up a
|
||||
terminal. Now we'll use the display.py script in your galaxy/scripts/api
|
||||
directory for a short example::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories
|
||||
Collection Members
|
||||
------------------
|
||||
#1: /api/histories/8c49be448cfe29bc
|
||||
name: Unnamed history
|
||||
id: 8c49be448cfe29bc
|
||||
#2: /api/histories/33b43b4e7093c91f
|
||||
name: output test
|
||||
id: 33b43b4e7093c91f
|
||||
|
||||
The result is a Collection of the histories of the user specified by the API
|
||||
key (you). To look at the details of a particular history, say #1 above, do
|
||||
the following::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc
|
||||
Member Information
|
||||
------------------
|
||||
state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
|
||||
state: ok
|
||||
contents_url: /api/histories/8c49be448cfe29bc/contents
|
||||
id: 8c49be448cfe29bc
|
||||
name: Unnamed history
|
||||
|
||||
This gives detailed information about the specific member in question, in this
|
||||
case the History. To view history contents, do the following::
|
||||
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents
|
||||
Collection Members
|
||||
------------------
|
||||
#1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
|
||||
name: Pasted Entry
|
||||
type: file
|
||||
id: 6f91353f3eb0fa4a
|
||||
|
||||
What we have here is another Collection of items containing all of the datasets
|
||||
in this particular history. Finally, to view details of a particular dataset
|
||||
in this collection, execute the following::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
|
||||
Member Information
|
||||
------------------
|
||||
misc_blurb: 1 line
|
||||
name: Pasted Entry
|
||||
data_type: txt
|
||||
deleted: False
|
||||
file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
|
||||
state: ok
|
||||
download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
|
||||
visible: True
|
||||
genome_build: ?
|
||||
model_class: HistoryDatasetAssociation
|
||||
file_size: 17
|
||||
metadata_data_lines: 1
|
||||
id: 6f91353f3eb0fa4a
|
||||
misc_info: uploaded txt file
|
||||
metadata_dbkey: ?
|
||||
|
||||
And now you've successfully used the API to request and select a history,
|
||||
browse the contents of that history, and then look at detailed information
|
||||
about a particular dataset.
|
||||
|
||||
For a more comprehensive Data Library example, set the following option in your
|
||||
galaxy.ini as well, and restart galaxy again::
|
||||
|
||||
admin_users = you@example.org
|
||||
library_import_dir = /path/to/some/directory
|
||||
|
||||
In the directory you specified for 'library_import_dir', create some
|
||||
subdirectories, and put (or symlink) files to import into Galaxy into those
|
||||
subdirectories.
|
||||
|
||||
In Galaxy, create an account that matches the address you put in 'admin_users',
|
||||
then browse to that user's preferences and generate a new API Key. Copy the
|
||||
key to your clipboard and then use these scripts::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries
|
||||
Collection Members
|
||||
------------------
|
||||
|
||||
0 elements in collection
|
||||
|
||||
% ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006
|
||||
name: api_test
|
||||
id: f3f73e481f432006
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006
|
||||
name: api_test
|
||||
id: f3f73e481f432006
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
|
||||
Member Information
|
||||
------------------
|
||||
synopsis: None
|
||||
contents_url: /api/libraries/f3f73e481f432006/contents
|
||||
description: API Test Library
|
||||
name: api_test
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
|
||||
name: /
|
||||
type: folder
|
||||
id: 28202595c0d2591f61ddda595d2c3670
|
||||
|
||||
% ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
|
||||
name: api_test_folder1
|
||||
id: 28202595c0d2591fa4f9089d2303fd89
|
||||
|
||||
% ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
name: 2.bed
|
||||
id: e9ef7fdb2db87d7b
|
||||
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
|
||||
name: 3.bed
|
||||
id: 3b7f6a31f80a5018
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
|
||||
name: /
|
||||
type: folder
|
||||
id: 28202595c0d2591f61ddda595d2c3670
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
|
||||
name: /api_test_folder1
|
||||
type: folder
|
||||
id: 28202595c0d2591fa4f9089d2303fd89
|
||||
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
name: /api_test_folder1/2.bed
|
||||
type: file
|
||||
id: e9ef7fdb2db87d7b
|
||||
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
|
||||
name: /api_test_folder1/3.bed
|
||||
type: file
|
||||
id: 3b7f6a31f80a5018
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
Member Information
|
||||
------------------
|
||||
misc_blurb: 68 regions
|
||||
metadata_endCol: 3
|
||||
data_type: bed
|
||||
metadata_columns: 6
|
||||
metadata_nameCol: 4
|
||||
uploaded_by: nate@...
|
||||
metadata_strandCol: 6
|
||||
name: 2.bed
|
||||
genome_build: hg19
|
||||
metadata_comment_lines: None
|
||||
metadata_startCol: 2
|
||||
metadata_chromCol: 1
|
||||
file_size: 4272
|
||||
metadata_data_lines: 68
|
||||
message:
|
||||
metadata_dbkey: hg19
|
||||
misc_info: uploaded bed file
|
||||
date_uploaded: 2010-06-22T17:01:51.266119
|
||||
metadata_column_types: str, int, int, str, int, str
|
||||
|
||||
Other parameters are valid when uploading, they are the same parameters as are
|
||||
used in the web form, like 'link_data_only' and etc.
|
||||
|
||||
The request and response format should be considered alpha and are subject to change.
|
||||
|
||||
+6
-187
@@ -1,8 +1,6 @@
|
||||
Galaxy API Documentation
|
||||
************************
|
||||
========================
|
||||
|
||||
Background
|
||||
==========
|
||||
In addition to being accessible through a web interface, Galaxy can also be
|
||||
accessed programmatically, through shell scripts and other programs. The web
|
||||
interface is appropriate for things like exploratory analysis, visualization,
|
||||
@@ -20,191 +18,12 @@ The Galaxy API addresses these and other situations by exposing Galaxy
|
||||
internals through an additional interface, known as an Application Programming
|
||||
Interface, or API.
|
||||
|
||||
Quickstart
|
||||
==========
|
||||
|
||||
Log in as your user, navigate to the API Keys page in the User menu, and
|
||||
generate a new API key. Make a note of the API key, and then pull up a
|
||||
terminal. Now we'll use the display.py script in your galaxy/scripts/api
|
||||
directory for a short example::
|
||||
.. toctree::
|
||||
:maxdepth: 3
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories
|
||||
Collection Members
|
||||
------------------
|
||||
#1: /api/histories/8c49be448cfe29bc
|
||||
name: Unnamed history
|
||||
id: 8c49be448cfe29bc
|
||||
#2: /api/histories/33b43b4e7093c91f
|
||||
name: output test
|
||||
id: 33b43b4e7093c91f
|
||||
Galaxy API Quickstart <api/quickstart>
|
||||
|
||||
The result is a Collection of the histories of the user specified by the API
|
||||
key (you). To look at the details of a particular history, say #1 above, do
|
||||
the following::
|
||||
Galaxy API Guidelines <api/guidelines>
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc
|
||||
Member Information
|
||||
------------------
|
||||
state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
|
||||
state: ok
|
||||
contents_url: /api/histories/8c49be448cfe29bc/contents
|
||||
id: 8c49be448cfe29bc
|
||||
name: Unnamed history
|
||||
|
||||
This gives detailed information about the specific member in question, in this
|
||||
case the History. To view history contents, do the following::
|
||||
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents
|
||||
Collection Members
|
||||
------------------
|
||||
#1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
|
||||
name: Pasted Entry
|
||||
type: file
|
||||
id: 6f91353f3eb0fa4a
|
||||
|
||||
What we have here is another Collection of items containing all of the datasets
|
||||
in this particular history. Finally, to view details of a particular dataset
|
||||
in this collection, execute the following::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
|
||||
Member Information
|
||||
------------------
|
||||
misc_blurb: 1 line
|
||||
name: Pasted Entry
|
||||
data_type: txt
|
||||
deleted: False
|
||||
file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
|
||||
state: ok
|
||||
download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
|
||||
visible: True
|
||||
genome_build: ?
|
||||
model_class: HistoryDatasetAssociation
|
||||
file_size: 17
|
||||
metadata_data_lines: 1
|
||||
id: 6f91353f3eb0fa4a
|
||||
misc_info: uploaded txt file
|
||||
metadata_dbkey: ?
|
||||
|
||||
And now you've successfully used the API to request and select a history,
|
||||
browse the contents of that history, and then look at detailed information
|
||||
about a particular dataset.
|
||||
|
||||
For a more comprehensive Data Library example, set the following option in your
|
||||
galaxy.ini as well, and restart galaxy again::
|
||||
|
||||
admin_users = you@example.org
|
||||
library_import_dir = /path/to/some/directory
|
||||
|
||||
In the directory you specified for 'library_import_dir', create some
|
||||
subdirectories, and put (or symlink) files to import into Galaxy into those
|
||||
subdirectories.
|
||||
|
||||
In Galaxy, create an account that matches the address you put in 'admin_users',
|
||||
then browse to that user's preferences and generate a new API Key. Copy the
|
||||
key to your clipboard and then use these scripts::
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries
|
||||
Collection Members
|
||||
------------------
|
||||
|
||||
0 elements in collection
|
||||
|
||||
% ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006
|
||||
name: api_test
|
||||
id: f3f73e481f432006
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006
|
||||
name: api_test
|
||||
id: f3f73e481f432006
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
|
||||
Member Information
|
||||
------------------
|
||||
synopsis: None
|
||||
contents_url: /api/libraries/f3f73e481f432006/contents
|
||||
description: API Test Library
|
||||
name: api_test
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
|
||||
name: /
|
||||
type: folder
|
||||
id: 28202595c0d2591f61ddda595d2c3670
|
||||
|
||||
% ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
|
||||
name: api_test_folder1
|
||||
id: 28202595c0d2591fa4f9089d2303fd89
|
||||
|
||||
% ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
|
||||
Response
|
||||
--------
|
||||
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
name: 2.bed
|
||||
id: e9ef7fdb2db87d7b
|
||||
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
|
||||
name: 3.bed
|
||||
id: 3b7f6a31f80a5018
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
|
||||
Collection Members
|
||||
------------------
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
|
||||
name: /
|
||||
type: folder
|
||||
id: 28202595c0d2591f61ddda595d2c3670
|
||||
/api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
|
||||
name: /api_test_folder1
|
||||
type: folder
|
||||
id: 28202595c0d2591fa4f9089d2303fd89
|
||||
/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
name: /api_test_folder1/2.bed
|
||||
type: file
|
||||
id: e9ef7fdb2db87d7b
|
||||
/api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
|
||||
name: /api_test_folder1/3.bed
|
||||
type: file
|
||||
id: 3b7f6a31f80a5018
|
||||
|
||||
% ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
|
||||
Member Information
|
||||
------------------
|
||||
misc_blurb: 68 regions
|
||||
metadata_endCol: 3
|
||||
data_type: bed
|
||||
metadata_columns: 6
|
||||
metadata_nameCol: 4
|
||||
uploaded_by: nate@...
|
||||
metadata_strandCol: 6
|
||||
name: 2.bed
|
||||
genome_build: hg19
|
||||
metadata_comment_lines: None
|
||||
metadata_startCol: 2
|
||||
metadata_chromCol: 1
|
||||
file_size: 4272
|
||||
metadata_data_lines: 68
|
||||
message:
|
||||
metadata_dbkey: hg19
|
||||
misc_info: uploaded bed file
|
||||
date_uploaded: 2010-06-22T17:01:51.266119
|
||||
metadata_column_types: str, int, int, str, int, str
|
||||
|
||||
Other parameters are valid when uploading, they are the same parameters as are
|
||||
used in the web form, like 'link_data_only' and etc.
|
||||
|
||||
The request and response format should be considered alpha and are subject to change.
|
||||
|
||||
.. include:: api/guidelines.rst
|
||||
|
||||
.. include:: lib/galaxy.webapps.galaxy.api.rst
|
||||
Galaxy API Documentation <lib/galaxy.webapps.galaxy.api>
|
||||
|
||||
@@ -1,8 +1,6 @@
|
||||
Tool Shed API Documentation
|
||||
***************************
|
||||
===========================
|
||||
|
||||
Introduction
|
||||
============
|
||||
The Galaxy Tool Shed can be accessed programmatically using API described
|
||||
here via shell scripts and other programs.
|
||||
To interact with the API you first need to log in as your user, navigate
|
||||
@@ -13,7 +11,7 @@ key you have to attach to every request as a parameter. Example:
|
||||
|
||||
GET https://toolshed.g2.bx.psu.edu/api/repositories?q=fastq?key=SOME_KEY_HERE
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 3
|
||||
|
||||
.. include:: api/guidelines.rst
|
||||
|
||||
.. include:: lib/galaxy.webapps.tool_shed.api.rst
|
||||
Toolshed API Documentation <lib/galaxy.webapps.tool_shed.api>
|
||||
|
||||
Reference in New Issue
Block a user