Help:WikiPathways Webservice
From WikiPathways
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[http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl] | [http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl] | ||
| - | == Objects == | + | == Examples == |
| + | === Java === | ||
| + | Check out [http://svn.bigcat.unimaas.nl/pathvisio/trunk/tools/soap-axis2/ the subversion repository] for example code on how to call the webservice from Java with [http://ws.apache.org/axis2/ Apache Axis 2]. | ||
| + | === Taverna === | ||
| + | You can use the WikiPathways webservice to integrate WikiPathways functions in your Taverna workflows. See [http://www.myexperiment.org/packs/30 myexperiment.org] for a set of example workflows that show how to call WikiPathways from Taverna. | ||
| + | |||
| + | == API Reference == | ||
| + | === Objects === | ||
This section explains the different object classes defined in the WSDL. | This section explains the different object classes defined in the WSDL. | ||
| - | === WSPathwayInfo === | + | ==== WSPathwayInfo ==== |
Container for pathway metadata, such as name, organism and url. | Container for pathway metadata, such as name, organism and url. | ||
{|class=wikitable | {|class=wikitable | ||
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|} | |} | ||
| - | === WSPathway === | + | ==== WSPathway ==== |
'''Extends WSPathwayInfo'''. | '''Extends WSPathwayInfo'''. | ||
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|} | |} | ||
| - | === WSAuth === | + | ==== WSAuth ==== |
Container for authentication data for a logged in WikiPathways session. | Container for authentication data for a logged in WikiPathways session. | ||
{|class=wikitable | {|class=wikitable | ||
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|} | |} | ||
| - | === WSSearchResult === | + | ==== WSSearchResult ==== |
Container for a single search result. | Container for a single search result. | ||
{|class=wikitable | {|class=wikitable | ||
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|} | |} | ||
| - | === WSIndexField === | + | ==== WSIndexField ==== |
Container for a single index field. | Container for a single index field. | ||
{|class=wikitable | {|class=wikitable | ||
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|} | |} | ||
| - | == Functions == | + | === Functions === |
| - | === listOrganisms === | + | ==== listOrganisms ==== |
Get a list of all available organisms. | Get a list of all available organisms. | ||
{|class=wikitable | {|class=wikitable | ||
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|The names of the supported organisms | |The names of the supported organisms | ||
|} | |} | ||
| - | === listPathways === | + | ==== listPathways ==== |
Get a list of all available pathways. | Get a list of all available pathways. | ||
{|class=wikitable | {|class=wikitable | ||
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|The available pathways. | |The available pathways. | ||
|} | |} | ||
| - | === getPathway === | + | ==== getPathway ==== |
Download the pathway from WikiPathways. | Download the pathway from WikiPathways. | ||
{|class=wikitable | {|class=wikitable | ||
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|| The available pathways. | || The available pathways. | ||
|} | |} | ||
| - | === getRecentChanges === | + | ==== 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. | 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. | ||
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|| The changed pathways. | || The changed pathways. | ||
|} | |} | ||
| - | === login === | + | ==== 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). | 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). | ||
{|class=wikitable | {|class=wikitable | ||
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|} | |} | ||
| - | === getPathwayAs === | + | === getPathwayAs ==== |
| - | === updatePathway = | + | ==== updatePathway ==== |
| - | + | ==== findPathwaysByText ==== | |
| - | === | + | ==== findPathwaysByXref ==== |
| - | + | ||
| - | + | ||
| - | === | + | |
| - | + | ||
| - | == | + | |
| - | + | ||
Revision as of 11:53, 16 September 2008
This page is under construction
WikiPathways can be accessed through a SOAP webservice. This page contains documentation for the webservice API.
Contents |
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
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. |
Functions
listOrganisms
Get a list of all available organisms.
| returns | ||
| array of string | The names of the supported organisms | |
listPathways
Get a list of all available pathways.
| returns | ||
| array of object WSPathwayInfo | The available pathways. | |
getPathway
Download the pathway from WikiPathways.
| Arguments | ||
| Type | Name | Description |
| string | pwName | The pathway name |
| string | pwSpecies | The pathway species |
| integer | revision | The revision number of the pathway (use '0' for most recent version) |
| Returns | ||
| array of object WSPathwayInfo | The available pathways. | |
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 | ||
| Type | Name | Description |
| string | timestamp | Only get changes from after this time. Timestamp format: yyyymmddMMHHSS. |
| Returns | ||
| array of object WSPathwayInfo | The changed pathways. | |
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 | ||
| Type | Name | Description |
| string | name | The username of the WikiPathways account |
| string | pass | The password of the WikiPathways account |
| Returns | ||
| string | The authentication code for this session | |
