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cytoscape / cyREST

Core App: REST API module for Cytoscape
https://github.com/cytoscape/cyREST/wiki
MIT License
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PDF Export Occasionally Crashes #37

Closed dotasek closed 6 years ago

dotasek commented 6 years ago 
import urllib, os
import requests

from IPython.display import display,Image
import numpy as np
from py2cytoscape.data.cyrest_client import CyRestClient

PORT_NUMBER = 1234
IP = 'localhost'
BASE = 'http://' + IP + ':' + str(PORT_NUMBER) + '/v1/'
HEADERS = {'Content-Type':'application/json'}

home_path = os.environ['HOME']
path = home_path + '/Desktop/

for x in range(1, 4):

    print x
    #if len(g.vs) > 1 and len(g.es) > 0:
    if 1 > 0:
        matrix1 = np.array([
            [0, 1, 1, 0],
            [0, 0, 1, 0],
            [0, 0, 0, 1],
            [0, 0, 0, 0]])
        name = 'binary sample ' + str(x)
        res1 = cy.network.create_from_ndarray(matrix1, name=name)

        suid = res1.get_id()
        network_id_map[name] = suid
        requests.get(BASE + 'apply/layouts/force-directed/' + str(suid))
        image_url = BASE + 'networks/' + str(suid) + '/views/first.pdf'
        outfile = path + name + '.network.pdf'
        res = urllib.urlretrieve(image_url,outfile)

If the chunk of code above is run, and then the for loop is executed more than once (in a Jupyter notebook for example), the following occurs intermittently, resulting in a broken script:

qtp931099874-80 - /v1/networks/180/views/first.pdf WARN [org.eclipse.jetty.servlet.ServletHandler] - 
javax.servlet.ServletException: javax.ws.rs.InternalServerErrorException: HTTP 500 Internal Server Error
    at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:489)
    at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
    at com.eclipsesource.jaxrs.publisher.internal.ServletContainerBridge.service(ServletContainerBridge.java:76)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
    at org.ops4j.pax.web.service.jetty.internal.HttpServiceServletHandler.doHandle(HttpServiceServletHandler.java:69)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
    at org.ops4j.pax.web.service.jetty.internal.HttpServiceContext.doHandle(HttpServiceContext.java:240)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
    at org.ops4j.pax.web.service.jetty.internal.JettyServerHandlerCollection.handle(JettyServerHandlerCollection.java:75)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
    at org.eclipse.jetty.server.Server.handle(Server.java:366)
    at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
    at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971)
    at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
    at java.lang.Thread.run(Thread.java:748)
Caused by: javax.ws.rs.InternalServerErrorException: HTTP 500 Internal Server Error
    at org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:90)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1130)
    at org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:711)
    at org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:444)
    at org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:490)
    at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:334)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
    at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
    at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
    at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
    ... 31 more
Caused by: org.glassfish.jersey.message.internal.MessageBodyProviderNotFoundException: MessageBodyWriter not found for media type=image/pdf, type=class org.cytoscape.ci.model.CIResponse, genericType=class org.cytoscape.ci.model.CIResponse.
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:247)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:106)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:86)
    ... 46 more
qtp931099874-80 - /v1/networks/180/views/first.pdf WARN [org.eclipse.jetty.servlet.ServletHandler] - /v1/networks/180/views/first.pdf
javax.ws.rs.InternalServerErrorException: HTTP 500 Internal Server Error
    at org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:90)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1130)
    at org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:711)
    at org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:444)
    at org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:490)
    at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:334)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
    at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
    at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
    at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
    at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
    at com.eclipsesource.jaxrs.publisher.internal.ServletContainerBridge.service(ServletContainerBridge.java:76)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
    at org.ops4j.pax.web.service.jetty.internal.HttpServiceServletHandler.doHandle(HttpServiceServletHandler.java:69)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
    at org.ops4j.pax.web.service.jetty.internal.HttpServiceContext.doHandle(HttpServiceContext.java:240)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
    at org.ops4j.pax.web.service.jetty.internal.JettyServerHandlerCollection.handle(JettyServerHandlerCollection.java:75)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
    at org.eclipse.jetty.server.Server.handle(Server.java:366)
    at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
    at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971)
    at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.glassfish.jersey.message.internal.MessageBodyProviderNotFoundException: MessageBodyWriter not found for media type=image/pdf, type=class org.cytoscape.ci.model.CIResponse, genericType=class org.cytoscape.ci.model.CIResponse.
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:247)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:106)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:86)
    ... 46 more
dotasek commented 6 years ago

Possibly related, from the framework-cytoscape.log:

java.lang.IllegalArgumentException: No rendering engine.
    at org.cytoscape.rest.internal.resource.NetworkViewResource.imageGenerator(NetworkViewResource.java:454)
    at org.cytoscape.rest.internal.resource.NetworkViewResource.getImage(NetworkViewResource.java:391)
    at org.cytoscape.rest.internal.resource.NetworkViewResource.getFirstImageAsPng(NetworkViewResource.java:349)
    at sun.reflect.GeneratedMethodAccessor63.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
    at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
    at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
    at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
    at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
    at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
    at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
    at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
    at com.eclipsesource.jaxrs.publisher.internal.ServletContainerBridge.service(ServletContainerBridge.java:76)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
    at org.ops4j.pax.web.service.jetty.internal.HttpServiceServletHandler.doHandle(HttpServiceServletHandler.java:69)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
    at org.ops4j.pax.web.service.jetty.internal.HttpServiceContext.doHandle(HttpServiceContext.java:240)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
    at org.ops4j.pax.web.service.jetty.internal.JettyServerHandlerCollection.handle(JettyServerHandlerCollection.java:75)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
    at org.eclipse.jetty.server.Server.handle(Server.java:366)
    at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
    at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971)
    at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
    at java.lang.Thread.run(Thread.java:748)
dotasek commented 6 years ago

Updated the python code that generates the error, and found that this will most likely happen when graphs are quickly generated.

import urllib, os
import requests
import time
from IPython.display import display,Image
import numpy as np
from py2cytoscape.data.cyrest_client import CyRestClient

PORT_NUMBER = 1234
IP = 'localhost'
BASE = 'http://' + IP + ':' + str(PORT_NUMBER) + '/v1/'
HEADERS = {'Content-Type':'application/json'}

home_path = os.environ['HOME']
path = home_path + '/Desktop/'
y = 0;
repeats = 20;

network_id_map = {}

cy = CyRestClient()

for x in range(y, y + repeats):

    print x
    if 1 > 0:
        matrix1 = np.array([
            [0, 1, 1, 0],
            [0, 0, 1, 0],
            [0, 0, 0, 1],
            [0, 0, 0, 0]])
        name = 'binary sample ' + str(x)
        res1 = cy.network.create_from_ndarray(matrix1, name=name)
        suid = res1.get_id()
        network_id_map[name] = suid
        #time.sleep(2)
        image_url = BASE + 'networks/' + str(suid) + '/views/first.pdf'
        outfile = path + name + '.network.pdf'
        res = urllib.urlretrieve(image_url,outfile)
y = y + repeats

Within this code is also a workaround: uncommenting the time.sleep(2) instruction causes Python to sleep, which appears to behave differently from putting a thread to sleep in Cytoscape, and allows the renderer time to initialise and be registered.

I suspect the source of this error is that adding a new network triggers an event and returns, and the event eventually registers the renderer, but not before other apps can ask for it.

dotasek commented 6 years ago

Solved in 7e7b8b4

Awaiting release

dotasek commented 6 years ago

Closed in 3.6.1 release