Help:WikiPathways Webservice

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== API Reference ==
== API Reference ==
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[[/API|API reference]]
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[[{{FULLPAGENAME}}/API|API reference]]
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=== Functions ===
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==== listOrganisms ====
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Get a list of all available organisms.
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{|class=wikitable
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|colspan=3 | '''returns'''
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|-
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|array of string
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|The names of the supported organisms
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|}
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==== listPathways ====
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Get a list of all available pathways.
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{|class=wikitable
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|colspan=3 | '''returns'''
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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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|}
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==== getPathway ====
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Download the pathway from WikiPathways.
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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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|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.
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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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|timestamp
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|Only get changes from after this time. Timestamp format: yyyymmddMMHHSS.
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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 changed pathways.
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|}
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==== login ====
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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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{|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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|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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Download a pathway in the specified file format.
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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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|fileType
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|The file format. This can be one of:
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* gpml
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* png
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* svg
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* pdf
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* txt
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* pwf
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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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|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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|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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==== 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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Find pathways using a textual search on the description and text labels of the pathway objects.
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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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|query
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|The search query (e.g. 'apoptosis' or 'p53').
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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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|-
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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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|}
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==== findPathwaysByXref ====
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Find pathways by searching on the external references of DataNodes (gene/protein/metabolite identifiers).
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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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|string
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|id
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|The DataNode identifier (e.g. 'P45985').
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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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|-
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|colspan=3 | ''Returns''
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|-
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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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|}
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=== Objects ===
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This section explains the different object classes defined in the WSDL.
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==== WSPathwayInfo ====
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Container for pathway metadata, such as name, organism and url.
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{|class=wikitable
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|colspan=3 | '''fields'''
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|-
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|name
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|string
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|The name of the pathway
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|-
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|species
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|string
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|The species (organism) of the pathway
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|-
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|url
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|string
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|The url to the pathway
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|-
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|revision
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|string
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|The revision number of the pathway ('0' can be used for the most recent revision)
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|}
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==== WSPathway ====
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'''Extends WSPathwayInfo'''.
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Container for pathway metadata and content. This object inherits all fields from WSPathwayInfo and
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has one additional field:
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{|class=wikitable
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|colspan=3 | '''fields'''
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|-
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|gpml
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|string
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|The content of the pathway (as [http://www.pathvisio.org/EverythingGPML GPML]).
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|}
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==== WSAuth ====
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Container for authentication data for a logged in WikiPathways session.
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{|class=wikitable
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|colspan=3 | '''fields'''
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|-
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|user
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|string
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|The username of a WikiPathways account
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|-
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|key
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|string
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|The authentication key of the session (can be obtained by calling the login function).
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|}
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==== WSSearchResult ====
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Container for a single search result.
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{|class=wikitable
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|colspan=3 | '''fields'''
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|-
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|score
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|double
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|The score of the search result
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|-
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|fields
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|array of object WSIndexField
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|An array of index fields that were returned with the search. The included fields may vary among different search functions.
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|}
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==== WSIndexField ====
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Container for a single index field.
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{|class=wikitable
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|colspan=3 | '''fields'''
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|-
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|name
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|string
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|The name of the index field.
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|-
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|fields
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|array of string
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|An array with the value(s) of the field.
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|}
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<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Frequently_Asked_Questions|Continue to FAQ]]</p>
<p>[[:Help:Frequently_Asked_Questions|Continue to FAQ]]</p>

Revision as of 13:36, 9 December 2008

Contents

Webservice documentation

WikiPathways can be accessed through a SOAP webservice. This page contains documentation for the webservice API.

WSDL

The WSDL file for the WikiPathways webservice can be downloaded from: http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl

Examples

Java

Check out the subversion repository for example code on how to call the webservice from Java with Apache Axis 2.

Taverna

You can use the WikiPathways webservice to integrate WikiPathways functions in your Taverna workflows. See myexperiment.org for a set of example workflows that show how to call WikiPathways from Taverna.

API Reference

API reference

Return to Help Contents

Continue to FAQ

Retrieved from "https://classic.wikipathways.org/index.php/Help:WikiPathways_Webservice"
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