[InterMine Dev] Reg:Array Atlas Datasource

Alex Kalderimis alex at intermine.org
Tue Feb 21 14:12:32 GMT 2012


Thanks for sending the stack trace Lenin,

looking at the json you link to, not all the objects have a arrayDesign 
property. Our converter currently makes the (perhaps unfounded) 
assumption that there will always be this property. Which fields out of 
the returned objects are you interested in?

Alex


On Tue 21 Feb 2012 13:31:54 GMT, it at reverseinformatics.com wrote:
> Hi,
>      We used the Array Express Atlas source in intermine to load
> Array express Atlas
> data from http://www.ebi.ac.uk/gxa/api/v1?experiment=%22E-GEOD-33091%22&format=json
> <http://www.ebi.ac.uk/gxa/api/v1?experiment=%22E-GEOD-33091%22&format=json> but
> when we integrate the source it replies the following stack trace:
>
> BUILD FAILED
> /home/administrator/Documents/intermine/branches/intermine_0_98/imbuild/integrate.xml:54:
> The following error occurred while executing this line:
> /home/administrator/Documents/intermine/branches/intermine_0_98/imbuild/source.xml:162:
> org.json.JSONException: JSONObject["arrayDesign"] not found.
> at
> org.apache.tools.ant.ProjectHelper.addLocationToBuildException(ProjectHelper.java:508)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:418)
> at org.intermine.task.Integrate.performAction(Integrate.java:223)
> at org.intermine.task.Integrate.performAction(Integrate.java:135)
> at org.intermine.task.Integrate.execute(Integrate.java:127)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:357)
> at org.apache.tools.ant.Target.performTasks(Target.java:385)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
> at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
> at org.apache.tools.ant.Main.runBuild(Main.java:758)
> at org.apache.tools.ant.Main.startAnt(Main.java:217)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
> Caused by:
> /home/administrator/Documents/intermine/branches/intermine_0_98/imbuild/source.xml:162:
> org.json.JSONException: JSONObject["arrayDesign"] not found.
> at
> org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:112)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:357)
> at org.apache.tools.ant.Target.performTasks(Target.java:385)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
> at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
> ... 19 more
> Caused by: org.json.JSONException: JSONObject["arrayDesign"] not found.
> at org.json.JSONObject.get(JSONObject.java:405)
> at org.json.JSONObject.getString(JSONObject.java:586)
> at
> org.intermine.bio.dataconversion.ArrayexpressAtlasConverter.process(ArrayexpressAtlasConverter.java:104)
> at
> org.intermine.bio.dataconversion.ArrayexpressAtlasConverter.process(ArrayexpressAtlasConverter.java:72)
> at
> org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
> ... 31 more
> --- Nested Exception ---
> /home/administrator/Documents/intermine/branches/intermine_0_98/imbuild/source.xml:162:
> org.json.JSONException: JSONObject["arrayDesign"] not found.
> at
> org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:112)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:357)
> at org.apache.tools.ant.Target.performTasks(Target.java:385)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
> at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
> at org.intermine.task.Integrate.performAction(Integrate.java:223)
> at org.intermine.task.Integrate.performAction(Integrate.java:135)
> at org.intermine.task.Integrate.execute(Integrate.java:127)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:357)
> at org.apache.tools.ant.Target.performTasks(Target.java:385)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
> at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
> at org.apache.tools.ant.Main.runBuild(Main.java:758)
> at org.apache.tools.ant.Main.startAnt(Main.java:217)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
> Caused by: org.json.JSONException: JSONObject["arrayDesign"] not found.
> at org.json.JSONObject.get(JSONObject.java:405)
> at org.json.JSONObject.getString(JSONObject.java:586)
> at
> org.intermine.bio.dataconversion.ArrayexpressAtlasConverter.process(ArrayexpressAtlasConverter.java:104)
> at
> org.intermine.bio.dataconversion.ArrayexpressAtlasConverter.process(ArrayexpressAtlasConverter.java:72)
> at
> org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
> ... 31 more
> --- Nested Exception ---
> org.json.JSONException: JSONObject["arrayDesign"] not found.
> at org.json.JSONObject.get(JSONObject.java:405)
> at org.json.JSONObject.getString(JSONObject.java:586)
> at
> org.intermine.bio.dataconversion.ArrayexpressAtlasConverter.process(ArrayexpressAtlasConverter.java:104)
> at
> org.intermine.bio.dataconversion.ArrayexpressAtlasConverter.process(ArrayexpressAtlasConverter.java:72)
> at
> org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:357)
> at org.apache.tools.ant.Target.performTasks(Target.java:385)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
> at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
> at org.intermine.task.Integrate.performAction(Integrate.java:223)
> at org.intermine.task.Integrate.performAction(Integrate.java:135)
> at org.intermine.task.Integrate.execute(Integrate.java:127)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:357)
> at org.apache.tools.ant.Target.performTasks(Target.java:385)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
> at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
> at org.apache.tools.ant.Main.runBuild(Main.java:758)
> at org.apache.tools.ant.Main.startAnt(Main.java:217)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
>
> Total time: 13 seconds
>
> Any thoughts?
>
> Thanks and Regards,
> Lenin
>
>
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