Difference between revisions of "Pathway"

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Line 13: Line 13:
|/pathway
|/pathway
|
|
''optional parameter "delimiter" for<br />
text/csv only, default value: ","''
|''text/html''
|''text/html''


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''text/plain''
''text/plain''
''text/csv''
|List of all pathways of all packages that the user has permission to read.
|List of all pathways of all packages that the user has permission to read.
|200 - OK
|200 - OK
Line 24: Line 28:
|/package/<id>/pathway
|/package/<id>/pathway
|
|
''optional parameter "delimiter" for<br />
text/csv only, default value: ","''
|''text/html''
|''text/html''


Line 29: Line 35:


''text/plain''
''text/plain''
''text/csv''
|List of all pathways of all the package given by the URI.
|List of all pathways of all the package given by the URI.
|200 - OK
|200 - OK
Line 38: Line 46:
|/package/<id>/pathway/<id>
|/package/<id>/pathway/<id>
|
|
''optional parameter "delimiter" for<br />
text/csv only, default value: ","''
|''text/html''
|''text/html''


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''text/plain''
''text/plain''


''text/csv''
|The pathway identified by the URI.
|The pathway identified by the URI.
|200 - OK
|200 - OK
Line 65: Line 76:
500 - Internal Server Error
500 - Internal Server Error
|}
|}


== POST ==
== POST ==
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''name''
''name''
''description''
''rootOnly''


''selectedSetting''
''selectedSetting''
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''<settingParams>''
''<settingParams>''
|
|
|Creates a new predicted pathway in the default package. The redirect points to the URI of the new pathway.
|Creates a new predicted pathway in the default package. The redirect points to the URI of the new pathway. If rootOnly is set to true the generated pathway is empty(only contains the root).


There are 3 ways to select the [[Settings|setting]] for the pathway:
There are 3 ways to select the [[Settings|setting]] for the pathway:
Line 115: Line 129:
|/package/<id>/pathway/<id>
|/package/<id>/pathway/<id>
|''pathwayName''
|''pathwayName''
''setAsDefaultName''


''pathwayDescription''
''pathwayDescription''
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''scenario'' - URI of the scenario
''scenario'' - URI of the scenario
|
|
|Modify the compound identified by the URI.  
|Modify the pathway identified by the URI. Set setAsDefaultName to "setAsDefaultName" to use the new alias as default name.
| 200 - OK
| 200 - OK


Line 138: Line 154:
''nodeDepth''
''nodeDepth''
|
|
|Adds a new node to the pathway
|Adds a new node to the pathway.
| 200 - OK
| 200 - OK


Line 149: Line 165:
|/package/<id>/pathway/<id>/node/<id>
|/package/<id>/pathway/<id>/node/<id>
|''nodeName''
|''nodeName''
''setAsDefaultName''


''nodeDescription''
''nodeDescription''
|
|
|Modify the node identified by the URI.  
|Modify the node identified by the URI. Set setAsDefaultName to "setAsDefaultName" to use the new alias as default name.
| 200 - OK
| 200 - OK


Line 172: Line 190:
''multistep''
''multistep''
|
|
|Adds a new edge to the pathway
|Adds a new edge to the pathway.
| 200 - OK
| 200 - OK


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|/package/<id>/pathway/<id>/edge/<id>
|/package/<id>/pathway/<id>/edge/<id>
|''edgeName''
|''edgeName''
''setAsDefaultName''


''edgeDescription''
''edgeDescription''
|
|
|Modify the edge identified by the URI.  
|Modify the edge identified by the URI. Set setAsDefaultName to "setAsDefaultName" to use the new alias as default name.
| 200 - OK
| 200 - OK



Latest revision as of 14:59, 25 January 2016

REST Operations

GET

URI Parameter Accept Types Result Status Codes
/pathway

optional parameter "delimiter" for
text/csv only, default value: ","

text/html

application/json

text/plain

text/csv

List of all pathways of all packages that the user has permission to read. 200 - OK

500 - Internal Server Error

/package/<id>/pathway

optional parameter "delimiter" for
text/csv only, default value: ","

text/html

application/json

text/plain

text/csv

List of all pathways of all the package given by the URI. 200 - OK

401 - Unauthorized

500 - Internal Server Error

/package/<id>/pathway/<id>

optional parameter "delimiter" for
text/csv only, default value: ","

text/html

application/json

text/plain

text/csv

The pathway identified by the URI. 200 - OK

401 - Unauthorized

404 - Not Found

500 - Internal Server Error

/package/<id>/pathway/<id>?status application/json The status of the pathway identified by the URI. 200 - OK

401 - Unauthorized

404 - Not Found

500 - Internal Server Error

POST

URI Parameter Accept Types Result Status Codes
/pathway smilesinput

reverse

name

description

rootOnly

selectedSetting

<settingParams>

Creates a new predicted pathway in the default package. The redirect points to the URI of the new pathway. If rootOnly is set to true the generated pathway is empty(only contains the root).

There are 3 ways to select the setting for the pathway:

* Do not specify any setting options (uses default setting)
* Provide a setting URI with selectedSetting
* Provide further setting parameters to create a new setting as defined in the Setting REST API.
303 - See Other

500 - Internal Server Error

/package/<id>/pathway smilesinput

reverse

name

selectedSetting

<settingParams>

Creates a new predicted pathway in the package given by the URI. The redirect points to the URI of the new pathway. 303 - See Other

401 - Unauthorized

500 - Internal Server Error

/package/<id>/pathway/<id> pathwayName

setAsDefaultName

pathwayDescription

scenario - URI of the scenario

Modify the pathway identified by the URI. Set setAsDefaultName to "setAsDefaultName" to use the new alias as default name. 200 - OK

401 - Unauthorized

404 - Not Found

500 - Internal Server Error

/package/<id>/pathway/<id>/node nodeAsSmiles

nodeReason

nodeName

nodeDepth

Adds a new node to the pathway. 200 - OK

401 - Unauthorized

404 - Not Found

500 - Internal Server Error

/package/<id>/pathway/<id>/node/<id> nodeName

setAsDefaultName

nodeDescription

Modify the node identified by the URI. Set setAsDefaultName to "setAsDefaultName" to use the new alias as default name. 200 - OK

401 - Unauthorized

404 - Not Found

500 - Internal Server Error

/package/<id>/pathway/<id>/edge edgeAsSmirks

edgeReason

products

educts

multistep

Adds a new edge to the pathway. 200 - OK

401 - Unauthorized

404 - Not Found

500 - Internal Server Error

/package/<id>/pathway/<id>/edge/<id> edgeName

setAsDefaultName

edgeDescription

Modify the edge identified by the URI. Set setAsDefaultName to "setAsDefaultName" to use the new alias as default name. 200 - OK

401 - Unauthorized

404 - Not Found

500 - Internal Server Error

DELETE

URI Parameter Accept Types Result Status Codes
/pathway Delete all pathways the user has write access on (does not delete created compounds or reactions). 303 - See Other

500 - Internal Server Error

/package/<id>/pathway Delete all pathways in the package given by the URI. 303 - See Other

401 - Unauthorized

500 - Internal Server Error

/package/<id>/pathway/<id> Delete the pathway identified by the URI. 303 - See Other
401 - Unauthorized
404 - Not Found
500 - Internal Server Error
/package/<id>/pathway/<id>/node/<id> Remove node from pathway. 303 - See Other

401 - Unauthorized

500 - Internal Server Error

/package/<id>/pathway/<id>/edge/<id> Remove edge from pathway. 303 - See Other

401 - Unauthorized

500 - Internal Server Error

PUT

Not Implemented.