Help:WikiPathways Webservice/API

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(New page: === Functions === ==== listOrganisms ==== Get a list of all available organisms. {|class=wikitable |colspan=3 | '''returns''' |- |array of string |The names of the supported organisms ...)
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=== Functions ===
=== Functions ===
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==== listOrganisms ====
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{{WSFunction
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Get a list of all available organisms.
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|name=listOrganisms
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{|class=wikitable
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|descr=Get a list of all available organisms.
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|colspan=3 | '''returns'''
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|returns=
-
|-
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{{WSFunction/Return|type=array of string|descr=The names of the supported organisms.}}
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|array of string
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}}
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|The names of the supported organisms
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-
|}
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{{WSFunction
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==== listPathways ====
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|name=listPathways
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Get a list of all available pathways.
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|descr=Get a list of all available pathways.
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{|class=wikitable
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|returns=
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|colspan=3 | '''returns'''
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{{WSFunction/Return|type=array of [[Help:WikiPathways_Webservice#WSPathwayInfo|WSPathwayInfo]]|descr=The available pathways.}}
-
|-
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}}
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|array of object [[Help:WikiPathways_Webservice#WSPathwayInfo|WSPathwayInfo]]
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|The available pathways.
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{{WSFunction
-
|}
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|name=getPathway
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==== getPathway ====
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|descr=Download the pathway from WikiPathways.
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Download the pathway from WikiPathways.
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|args=
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{|class=wikitable
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{{WSFunction/Argument|name=pwId|type=string|descr=The pathway identifier.}}
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|colspan=3 | ''Arguments''
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{{WSFunction/Argument|name=revision|type=integer|descr=The revision number of the pathway (use '0' for most recent version).}}
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|-
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|returns=
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|'''Type'''
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{{WSFunction/Return|type=[[Help:WikiPathways_Webservice#WSPathway|WSPathway]]|descr=The pathway.}}
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|'''Name'''
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}}
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|'''Description'''
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|-
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{{WSFunction
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|string
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|name=getRecentChanges
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|pwName
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|descr=Get the recently changed pathways.
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|The pathway name
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|-
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|string
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|pwSpecies
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|The pathway species
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-
|-
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|integer
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|revision
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|The revision number of the pathway (use '0' for most recent version)
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-
|-
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|colspan=3 | ''Returns''
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-
|-
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|colspan=2 | array of object [[Help:WikiPathways_Webservice#WSPathwayInfo|WSPathwayInfo]]
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|| The available pathways.
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-
|}
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==== getRecentChanges ====
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-
Get the recently changed pathways.  
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'''Note:''' the recent changes table only retains items for a limited time (2 months), so there is no guarantee that you will get all changes when the timestamp points to a date that is more than 2 months in the past.
'''Note:''' the recent changes table only retains items for a limited time (2 months), so there is no guarantee that you will get all changes when the timestamp points to a date that is more than 2 months in the past.
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{|class=wikitable
 
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|colspan=3 | ''Arguments''
 
-
|-
 
-
|'''Type'''
 
-
|'''Name'''
 
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|'''Description'''
 
-
|-
 
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|string
 
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|timestamp
 
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|Only get changes from after this time. Timestamp format: yyyymmddMMHHSS.
 
-
|-
 
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|colspan=3 | ''Returns''
 
-
|-
 
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|colspan=2 | array of object [[Help:WikiPathways_Webservice#WSPathwayInfo|WSPathwayInfo]]
 
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|| The changed pathways.
 
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|}
 
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==== login ====
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|args=
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Start a logged in session, using an existing WikiPathways account. This function will return an authentication code that can be used to excecute methods that need authentication (e.g. updatePathway).
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{{WSFunction/Argument|name=timestamp|type=string|descr=Only get changes from after this time. Timestamp format: yyyymmddMMHHSS.}}
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{|class=wikitable
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|returns=
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|colspan=3 | ''Arguments''
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{{WSFunction/Return|type=array of [[Help:WikiPathways_Webservice#WSPathwayInfo|WSPathwayInfo]]|descr=The changed pathways.}}
-
|-
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}}
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|'''Type'''
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|'''Name'''
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|'''Description'''
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|-
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|string
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|name
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|The username of the WikiPathways account
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-
|-
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|string
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|pass
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|The password of the WikiPathways account
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-
|-
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|colspan=3 | ''Returns''
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-
|-
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|colspan=2 | string
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| The authentication code for this session
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-
|}
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==== getPathwayAs ====
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{{WSFunction
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Download a pathway in the specified file format.
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|name=login
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{|class=wikitable
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|descr=Start a logged in session, using an existing WikiPathways account. This function will return an authentication code that can be used to excecute methods that need authentication (e.g. updatePathway).
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|colspan=3 | ''Arguments''
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|args=
-
|-
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{{WSFunction/Argument|name=name|type=string|descr=The username of the WikiPathways account.}}
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|'''Type'''
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{{WSFunction/Argument|name=pass|type=string|descr=The password of the WikiPathways account.}}
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|'''Name'''
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|returns=
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|'''Description'''
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{{WSFunction/Return|type=string|descr=The authentication code for this session.}}
-
|-
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}}
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|string
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|fileType
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{{WSFunction
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|The file format. This can be one of:
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|name=getPathwayAs
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|descr=Download a pathway in the specified file format.
 +
|args=
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{{WSFunction/Argument|name=fileType|type=string|descr=Download a pathway in the specified file format.
* gpml
* gpml
* png
* png
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* txt
* txt
* pwf
* pwf
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See [[Download_Pathways | the download page]] for an explanation of these file formats.
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See [[Download_Pathways | the download page]] for an explanation of these file formats.}}
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|-
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{{WSFunction/Argument|name=pwId|type=string|descr=The pathway identifier.}}
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|string
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|returns=
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|pwName
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{{WSFunction/Return|type=base64Binary|descr=The file contents (base64 encoded).}}
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|The pathway name
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}}
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|-
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|string
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|pwSpecies
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|The pathway species
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-
|-
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|integer
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|revision
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|The revision number of the pathway (use '0' for most recent version)
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-
|-
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|colspan=3 | ''Returns''
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-
|-
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|colspan=2 | base64Binary  
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|The file contents (base64 encoded)
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-
|}
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-
 
+
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==== updatePathway ====
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Update a pathway on the wiki with the given GPML code.
+
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{|class=wikitable
+
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|colspan=3 | ''Arguments''
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-
|-
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|'''Type'''
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-
|'''Name'''
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|'''Description'''
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-
|-
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|string
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|pwName
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|The pathway name
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-
|-
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|string
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|pwSpecies
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|The pathway species
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|-
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|string
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|description
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|A description of the modifications
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|-
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|string
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|gpml
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|The updated GPML code
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|-
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|integer
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|revision
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|The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it.
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|-
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|object [[Help:WikiPathways_Webservice#WSAuth|WSAuth]]
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|auth
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|The authentication info.
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|-
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|colspan=3 | ''Returns''
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|-
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|colspan=2 | boolean
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|True if the pathway was updated sucessfully.
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-
|}
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==== findPathwaysByText ====
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{{WSFunction
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Find pathways using a textual search on the description and text labels of the pathway objects.
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|name=updatePathway
 +
|descr=Update a pathway on the wiki with the given GPML code.
 +
|args=
 +
{{WSFunction/Argument|name=pwId|type=string|descr=The pathway identifier.}}
 +
{{WSFunction/Argument|name=description|type=string|descr=A description of the modifications.}}
 +
{{WSFunction/Argument|name=pass|type=string|descr=The updated GPML code.}}
 +
{{WSFunction/Argument|name=revision|type=integer|descr=The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it.}}
 +
{{WSFunction/Argument|name=auth|type=string|descr=The authentication info.}}
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|returns=
 +
{{WSFunction/Return|type=boolean|descr=True if the pathway was updated successfully.}}
 +
}}
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{|class=wikitable
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{{WSFunction
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|colspan=3 | ''Arguments''
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|name=findPathwaysByText
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|-
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|descr=Find pathways using a textual search on the description and text labels of the pathway objects.
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|'''Type'''
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|args=
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|'''Name'''
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{{WSFunction/Argument|name=query|type=string|descr=The search query (e.g. 'apoptosis' or 'p53').}}
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|'''Description'''
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{{WSFunction/Argument|name=species|type=string|descr=The species to limit the search to (leave blank to search on all species).}}
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|-
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{{WSFunction/Argument|name=pass|type=string|descr=The updated GPML code.}}
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|string
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{{WSFunction/Argument|name=revision|type=integer|descr=The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it.}}
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|query
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|returns=
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|The search query (e.g. 'apoptosis' or 'p53').
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{{WSFunction/Return|type=array of [[Help:WikiPathways_Webservice#WSSearchResult|WSSearchResult]]|descr=An array of search results.}}
-
|-
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}}
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|string
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|species
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|The species to limit the search to (leave blank to search on all species).
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-
|-
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|colspan=3 | ''Returns''
+
-
|-
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|colspan=2 | array of object [[Help:WikiPathways_Webservice#WSSearchResult|WSSearchResult]]  
+
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|An array of search results.
+
-
|}
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==== findPathwaysByXref ====
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-
Find pathways by searching on the external references of DataNodes (gene/protein/metabolite identifiers).
+
-
{|class=wikitable
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{{WSFunction
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|colspan=3 | ''Arguments''
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|name=findPathwaysByXref
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|-
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|descr=Find pathways by searching on the external references of DataNodes (gene/protein/metabolite identifiers).
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|'''Type'''
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|args=
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|'''Name'''
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{{WSFunction/Argument|name=id|type=string|descr=The DataNode identifier (e.g. 'P45985').}}
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|'''Description'''
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{{WSFunction/Argument|name=code|type=string|descr=The code of the database system to limit the search to. Leave blank to search on all database systems. See [http://www.pathvisio.org/Help_1.1#Supported_database_systems this page] for an overview of available system codes.}}
-
|-
+
{{WSFunction/Argument|name=pass|type=string|descr=The updated GPML code.}}
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|string
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{{WSFunction/Argument|name=revision|type=integer|descr=The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it.}}
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|id
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|returns=
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|The DataNode identifier (e.g. 'P45985').
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{{WSFunction/Return|type=array of [[Help:WikiPathways_Webservice#WSSearchResult|WSSearchResult]]|descr=An array of search results.}}
-
|-
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}}
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|string
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|code
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|The code of the database system to limit the search to. Leave blank to search on all database systems. See [http://www.pathvisio.org/Help_1.1#Supported_database_systems this page] for an overview of available system codes.
+
-
|-
+
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|colspan=3 | ''Returns''
+
-
|-
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|colspan=2 | array of object [[Help:WikiPathways_Webservice#WSSearchResult|WSSearchResult]]  
+
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|An array of search results.
+
-
|}
+
=== Objects ===
=== Objects ===

Revision as of 12:05, 17 December 2008

Contents

Functions

listOrganisms

Get a list of all available organisms.



listPathways

Get a list of all available pathways.



getPathway

Download the pathway from WikiPathways.


Arguments:

  • string pwId
    • The pathway identifier.
  • integer revision
    • The revision number of the pathway (use '0' for most recent version).


getRecentChanges

Get the recently changed pathways.

Note: the recent changes table only retains items for a limited time (2 months), so there is no guarantee that you will get all changes when the timestamp points to a date that is more than 2 months in the past.


Arguments:

  • string timestamp
    • Only get changes from after this time. Timestamp format: yyyymmddMMHHSS.


login

Start a logged in session, using an existing WikiPathways account. This function will return an authentication code that can be used to excecute methods that need authentication (e.g. updatePathway).


Arguments:

  • string name
    • The username of the WikiPathways account.
  • string pass
    • The password of the WikiPathways account.


getPathwayAs

Download a pathway in the specified file format.


Arguments:

  • string fileType
    • Download a pathway in the specified file format.
  • gpml
  • png
  • svg
  • pdf
  • txt
  • pwf

See the download page for an explanation of these file formats.

  • string pwId
    • The pathway identifier.


updatePathway

Update a pathway on the wiki with the given GPML code.


Arguments:

  • string pwId
    • The pathway identifier.
  • string description
    • A description of the modifications.
  • string pass
    • The updated GPML code.
  • integer revision
    • The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it.
  • string auth
    • The authentication info.


findPathwaysByText

Find pathways using a textual search on the description and text labels of the pathway objects.


Arguments:

  • string query
    • The search query (e.g. 'apoptosis' or 'p53').
  • string species
    • The species to limit the search to (leave blank to search on all species).
  • string pass
    • The updated GPML code.
  • integer revision
    • The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it.


findPathwaysByXref

Find pathways by searching on the external references of DataNodes (gene/protein/metabolite identifiers).


Arguments:

  • string id
    • The DataNode identifier (e.g. 'P45985').
  • string code
    • The code of the database system to limit the search to. Leave blank to search on all database systems. See this page for an overview of available system codes.
  • string pass
    • The updated GPML code.
  • integer revision
    • The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it.


Objects

This section explains the different object classes defined in the WSDL.

WSPathwayInfo

Container for pathway metadata, such as name, organism and url.

fields
name string The name of the pathway
species string The species (organism) of the pathway
url string The url to the pathway
revision string The revision number of the pathway ('0' can be used for the most recent revision)

WSPathway

Extends WSPathwayInfo.

Container for pathway metadata and content. This object inherits all fields from WSPathwayInfo and has one additional field:

fields
gpml string The content of the pathway (as GPML).

WSAuth

Container for authentication data for a logged in WikiPathways session.

fields
user string The username of a WikiPathways account
key string The authentication key of the session (can be obtained by calling the login function).

WSSearchResult

Container for a single search result.

fields
score double The score of the search result
fields array of object WSIndexField An array of index fields that were returned with the search. The included fields may vary among different search functions.

WSIndexField

Container for a single index field.

fields
name string The name of the index field.
fields array of string An array with the value(s) of the field.
Retrieved from "https://classic.wikipathways.org/index.php/Help:WikiPathways_Webservice/API"
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