Re: Dockerization of Taverna Server - Vimig Socrates
Hi, Thank you all for your help. It turns out I just needed to increase the memory limit on the Docker container. I am not sure how that manifested itself in a 127.0.0.1 Connection Refused error. Thank you for your help however. -- Vimig Socrates Case Western Reserve University Class of 2018 On Fri, Apr 5, 2019 at 4:09 PM Vimig Socrates wrote: > I'm unsure which port those subprocesses are run on. I have tried curling > for port 80 and I receive a Connection Refused. I saw in the admin console > that the RMI server runs on port 1099, but that doesn't seem to work > either. Is that the correct approach? > > Thanks for the help! > > -- > Vimig Socrates > Case Western Reserve University Class of 2018 > > > On Fri, Apr 5, 2019 at 9:27 AM Stian Soiland-Reyes > wrote: > >> While running, the Taverna Server spawns up sub-processes that talk back >> to the Taverna Server to set the status of the workflow run etc. >> >> I think what we're facing here is that the server gets confused as to >> its apparance outside vs inside the docker container. Taverna Server >> will normally pick up its own hostname from the very first REST HTTP >> call from the outside. >> >> That said, 127.0.0.1 should still work inside the same container? >> >> Are you able to use "docker exec" to jump inside and try to test with >> curl? >> >> On Thu, 4 Apr 2019 19:58:19 -0400, Vimig Socrates >> wrote: >> > Hi, >> > >> > Yes, I gave that a shot too. I quickly realized that I can't run that on >> > Docker on Mac. I have to figure out if my program needs to be supported >> on >> > Mac and Windows as well. >> > >> > If that is the case, I have thought about communicating between >> containers >> > but I run into a usability issue for non-developers there. Thanks for >> the >> > help! >> > >> > >> > -- >> > Vimig Socrates >> > Case Western Reserve University Class of 2018 >> > >> > >> > On Thu, Apr 4, 2019 at 8:13 AM Ian Dunlop wrote: >> > >> > > Hello, >> > > >> > > >> > > >> > > I wonder if using --network="host" in your docker run command would >> help. >> > > That should make the docker container use the host network. Of course >> it >> > > might break other things in the TavServ container and it only works on >> > > linux. https://docs.docker.com/network/host/ >> > > >> > > >> > > >> > > Cheers, >> > > >> > > >> > > >> > > Ian >> > > >> > > >> > > >> > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for >> > > Windows 10 >> > > >> > > >> > > >> > > *From: *Vimig Socrates >> > > *Sent: *04 April 2019 00:42 >> > > *To: *users@taverna.incubator.apache.org >> > > *Subject: *Re: Dockerization of Taverna Server - Vimig Socrates >> > > >> > > >> > > >> > > Hi, >> > > >> > > >> > > >> > > Yes, I incorporated a portion of the Dockerfile from the released >> > > taverna-server Docker container. After some more digging, looks like >> it is >> > > an issue with my workflow file. >> > > >> > > >> > > >> > > I try to connect to the * >> http://localhost:8080/tavernaserver/rest/runs >> > > <http://localhost:8080/tavernaserver/rest/runs>* endpoint using a >> REST >> > > service in my workflow and since Docker sees localhost as the host >> machine, >> > > that doesn't work. Has anyone else run into this issue? >> > > >> > > >> > > >> > > If so, any help would be appreciated! Thank you! >> > > >> > > >> > > >> > > >> > > -- >> > > >> > > Vimig Socrates >> > > >> > > Case Western Reserve University Class of 2018 >> > > >> > > >> > > >> > > >> > > >> > > On Wed, Apr 3, 2019 at 5:52 AM Ian Dunlop >> wrote: >> > > >> > > Hello, >> > > >> > > >> > > >> > > Hi Vimig. Have you had a look at >> > > https://hub.docker.com/r/taverna/taverna-server/ which is a taverna >> > > server in Tomcat 8. I haven’t used
Re: Dockerization of Taverna Server - Vimig Socrates
I'm unsure which port those subprocesses are run on. I have tried curling for port 80 and I receive a Connection Refused. I saw in the admin console that the RMI server runs on port 1099, but that doesn't seem to work either. Is that the correct approach? Thanks for the help! -- Vimig Socrates Case Western Reserve University Class of 2018 On Fri, Apr 5, 2019 at 9:27 AM Stian Soiland-Reyes wrote: > While running, the Taverna Server spawns up sub-processes that talk back > to the Taverna Server to set the status of the workflow run etc. > > I think what we're facing here is that the server gets confused as to > its apparance outside vs inside the docker container. Taverna Server > will normally pick up its own hostname from the very first REST HTTP > call from the outside. > > That said, 127.0.0.1 should still work inside the same container? > > Are you able to use "docker exec" to jump inside and try to test with > curl? > > On Thu, 4 Apr 2019 19:58:19 -0400, Vimig Socrates > wrote: > > Hi, > > > > Yes, I gave that a shot too. I quickly realized that I can't run that on > > Docker on Mac. I have to figure out if my program needs to be supported > on > > Mac and Windows as well. > > > > If that is the case, I have thought about communicating between > containers > > but I run into a usability issue for non-developers there. Thanks for the > > help! > > > > > > -- > > Vimig Socrates > > Case Western Reserve University Class of 2018 > > > > > > On Thu, Apr 4, 2019 at 8:13 AM Ian Dunlop wrote: > > > > > Hello, > > > > > > > > > > > > I wonder if using --network="host" in your docker run command would > help. > > > That should make the docker container use the host network. Of course > it > > > might break other things in the TavServ container and it only works on > > > linux. https://docs.docker.com/network/host/ > > > > > > > > > > > > Cheers, > > > > > > > > > > > > Ian > > > > > > > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > > > Windows 10 > > > > > > > > > > > > *From: *Vimig Socrates > > > *Sent: *04 April 2019 00:42 > > > *To: *users@taverna.incubator.apache.org > > > *Subject: *Re: Dockerization of Taverna Server - Vimig Socrates > > > > > > > > > > > > Hi, > > > > > > > > > > > > Yes, I incorporated a portion of the Dockerfile from the released > > > taverna-server Docker container. After some more digging, looks like > it is > > > an issue with my workflow file. > > > > > > > > > > > > I try to connect to the *http://localhost:8080/tavernaserver/rest/runs > > > <http://localhost:8080/tavernaserver/rest/runs>* endpoint using a REST > > > service in my workflow and since Docker sees localhost as the host > machine, > > > that doesn't work. Has anyone else run into this issue? > > > > > > > > > > > > If so, any help would be appreciated! Thank you! > > > > > > > > > > > > > > > -- > > > > > > Vimig Socrates > > > > > > Case Western Reserve University Class of 2018 > > > > > > > > > > > > > > > > > > On Wed, Apr 3, 2019 at 5:52 AM Ian Dunlop > wrote: > > > > > > Hello, > > > > > > > > > > > > Hi Vimig. Have you had a look at > > > https://hub.docker.com/r/taverna/taverna-server/ which is a taverna > > > server in Tomcat 8. I haven’t used this recently but I think it used to > > > work. Are you required to use Tomcat 7? What workflow were you trying > to > > > run. It looks like the code that is causing the issue are: > > > > > > > > > > > > at > > > > org.taverna.server.master.worker.RemoteRunDelegate.getStatus(RemoteRunDelegate.java:214) > > > > > > at > > > > org.taverna.server.master.worker.RunDatabase.checkForFinishNow(RunDatabase.java:83) > > > > > > > > > > > > though I don’t know why they are trying to connect to 127.0.0.1. I’m > not > > > sure if its the workflow causing the problem or the TavServ itself. > > > > > > > > > > > > Cheers, > > > > > > > > > > > > Ian > > &g
Re: Dockerization of Taverna Server - Vimig Socrates
Hi, Yes, I gave that a shot too. I quickly realized that I can't run that on Docker on Mac. I have to figure out if my program needs to be supported on Mac and Windows as well. If that is the case, I have thought about communicating between containers but I run into a usability issue for non-developers there. Thanks for the help! -- Vimig Socrates Case Western Reserve University Class of 2018 On Thu, Apr 4, 2019 at 8:13 AM Ian Dunlop wrote: > Hello, > > > > I wonder if using --network="host" in your docker run command would help. > That should make the docker container use the host network. Of course it > might break other things in the TavServ container and it only works on > linux. https://docs.docker.com/network/host/ > > > > Cheers, > > > > Ian > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Vimig Socrates > *Sent: *04 April 2019 00:42 > *To: *users@taverna.incubator.apache.org > *Subject: *Re: Dockerization of Taverna Server - Vimig Socrates > > > > Hi, > > > > Yes, I incorporated a portion of the Dockerfile from the released > taverna-server Docker container. After some more digging, looks like it is > an issue with my workflow file. > > > > I try to connect to the *http://localhost:8080/tavernaserver/rest/runs > <http://localhost:8080/tavernaserver/rest/runs>* endpoint using a REST > service in my workflow and since Docker sees localhost as the host machine, > that doesn't work. Has anyone else run into this issue? > > > > If so, any help would be appreciated! Thank you! > > > > > -- > > Vimig Socrates > > Case Western Reserve University Class of 2018 > > > > > > On Wed, Apr 3, 2019 at 5:52 AM Ian Dunlop wrote: > > Hello, > > > > Hi Vimig. Have you had a look at > https://hub.docker.com/r/taverna/taverna-server/ which is a taverna > server in Tomcat 8. I haven’t used this recently but I think it used to > work. Are you required to use Tomcat 7? What workflow were you trying to > run. It looks like the code that is causing the issue are: > > > > at > org.taverna.server.master.worker.RemoteRunDelegate.getStatus(RemoteRunDelegate.java:214) > > at > org.taverna.server.master.worker.RunDatabase.checkForFinishNow(RunDatabase.java:83) > > > > though I don’t know why they are trying to connect to 127.0.0.1. I’m not > sure if its the workflow causing the problem or the TavServ itself. > > > > Cheers, > > > > Ian > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Vimig Socrates > *Sent: *03 April 2019 03:56 > *To: *users@taverna.incubator.apache.org > *Subject: *Dockerization of Taverna Server - Vimig Socrates > > > > Hello everyone! > > > > I am currently trying to Dockerize a Taverna Server v2.5.4 deployed on a > Tomcat 7 server. I am having some issues when I actually try to run a > workflow. I get a *Connection Refused *error as below: > > > java.rmi.ConnectException: Connection refused to host: 127.0.0.1; nested > exception is: > java.net.ConnectException: Connection refused (Connection refused) > at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:619) > at > sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:216) > ... > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) > Caused by: java.net.ConnectException: Connection refused (Connection > refused) > at java.net.PlainSocketImpl.socketConnect(Native Method) > > ... > at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:613) > ... 21 more > > > > > > I've attached the full *tavserv.out* file for reference. I believe the > reason is that 127.0.0.1 refers to the host computer through the Docker > bridge, but I am not sure how to fix that. Do I need to add something to > the tavernaserver.properties file? Thanks for the help! > > > > -- > > Vimig Socrates > > Case Western Reserve University Class of 2018 > > > > >
Re: Dockerization of Taverna Server - Vimig Socrates
Hi, Yes, I incorporated a portion of the Dockerfile from the released taverna-server Docker container. After some more digging, looks like it is an issue with my workflow file. I try to connect to the *http://localhost:8080/tavernaserver/rest/runs <http://localhost:8080/tavernaserver/rest/runs>* endpoint using a REST service in my workflow and since Docker sees localhost as the host machine, that doesn't work. Has anyone else run into this issue? If so, any help would be appreciated! Thank you! -- Vimig Socrates Case Western Reserve University Class of 2018 On Wed, Apr 3, 2019 at 5:52 AM Ian Dunlop wrote: > Hello, > > > > Hi Vimig. Have you had a look at > https://hub.docker.com/r/taverna/taverna-server/ which is a taverna > server in Tomcat 8. I haven’t used this recently but I think it used to > work. Are you required to use Tomcat 7? What workflow were you trying to > run. It looks like the code that is causing the issue are: > > > > at > org.taverna.server.master.worker.RemoteRunDelegate.getStatus(RemoteRunDelegate.java:214) > > at > org.taverna.server.master.worker.RunDatabase.checkForFinishNow(RunDatabase.java:83) > > > > though I don’t know why they are trying to connect to 127.0.0.1. I’m not > sure if its the workflow causing the problem or the TavServ itself. > > > > Cheers, > > > > Ian > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Vimig Socrates > *Sent: *03 April 2019 03:56 > *To: *users@taverna.incubator.apache.org > *Subject: *Dockerization of Taverna Server - Vimig Socrates > > > > Hello everyone! > > > > I am currently trying to Dockerize a Taverna Server v2.5.4 deployed on a > Tomcat 7 server. I am having some issues when I actually try to run a > workflow. I get a *Connection Refused *error as below: > > > java.rmi.ConnectException: Connection refused to host: 127.0.0.1; nested > exception is: > java.net.ConnectException: Connection refused (Connection refused) > at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:619) > at > sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:216) > ... > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) > Caused by: java.net.ConnectException: Connection refused (Connection > refused) > at java.net.PlainSocketImpl.socketConnect(Native Method) > > ... > at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:613) > ... 21 more > > > > > > I've attached the full *tavserv.out* file for reference. I believe the > reason is that 127.0.0.1 refers to the host computer through the Docker > bridge, but I am not sure how to fix that. Do I need to add something to > the tavernaserver.properties file? Thanks for the help! > > > > -- > > Vimig Socrates > > Case Western Reserve University Class of 2018 > > >
Dockerization of Taverna Server - Vimig Socrates
Hello everyone! I am currently trying to Dockerize a Taverna Server v2.5.4 deployed on a Tomcat 7 server. I am having some issues when I actually try to run a workflow. I get a *Connection Refused *error as below: java.rmi.ConnectException: Connection refused to host: 127.0.0.1; nested exception is: java.net.ConnectException: Connection refused (Connection refused) at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:619) at sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:216) ... at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.net.ConnectException: Connection refused (Connection refused) at java.net.PlainSocketImpl.socketConnect(Native Method) ... at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:613) ... 21 more I've attached the full *tavserv.out* file for reference. I believe the reason is that 127.0.0.1 refers to the host computer through the Docker bridge, but I am not sure how to fix that. Do I need to add something to the tavernaserver.properties file? Thanks for the help! -- Vimig Socrates Case Western Reserve University Class of 2018 tavserv.out Description: Binary data
Re: Taverna Server 2.5.4 Provenance File Location
Hi,
I thought that 2.5.5 was the most recent release of the Taverna
(pre-Apache). I don't see it on the Github repo either. Please let me know
where the war file is. Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2019
On Sun, Feb 24, 2019 at 4:11 PM Vimig Socrates wrote:
> Hi,
>
> I thought that 2.5.5 was the most recent release of the Taverna
> (pre-Apache). I don't see any on the Github repo either. Please let me know
> where the war file is. Thanks!
>
>
> --
> Vimig Socrates
> Case Western Reserve University Class of 2018
>
>
> On Fri, Feb 22, 2019 at 4:47 AM Ian Dunlop wrote:
>
>> Hi Vimig,
>>
>>
>>
>> I see you are using 2.5.4 . However, in the 2.5.5 server the provenance
>> is also contained in the run bundle for the workflow run via
>> /runs/{id}/run-bundle. It’s detailed in
>> http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/{id}/run-bundle
>> <http://dev.mygrid.org.uk/wiki/display/tav250/REST+API#RESTAPI-Resource:/runs/%7Bid%7D/run-bundle>.
>> Maybe it’s worth switching the 2.5.5 to give it a try. I’ve never tried
>> this provenance/run-bundle API call though so fingers crossed.
>>
>>
>>
>> Cheers,
>>
>>
>>
>> Ian
>>
>>
>>
>> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
>> Windows 10
>>
>>
>>
>> *From: *Vimig Socrates
>> *Sent: *19 February 2019 22:22
>> *To: *users@taverna.incubator.apache.org
>> *Subject: *Taverna Server 2.5.4 Provenance File Location
>>
>>
>>
>> Hi,
>>
>>
>>
>> I was wondering if there was a way to change the location that the files
>> are generated from calling with REST /generate-provenance from Taverna
>> Server 2.5.4. They seem to be currently placed in /tmp on Ubuntu16.04 and
>> those get deleted every day.
>>
>>
>>
>> I'd like access to the .wfbundle file so I can rerun the workflow easily.
>> Thanks!
>>
>>
>>
>>
>>
>> --
>>
>> Vimig Socrates
>>
>> Case Western Reserve University Class of 2018
>>
>>
>>
>
Taverna Server 2.5.4 Provenance File Location
Hi, I was wondering if there was a way to change the location that the files are generated from calling with REST /generate-provenance from Taverna Server 2.5.4. They seem to be currently placed in /tmp on Ubuntu16.04 and those get deleted every day. I'd like access to the .wfbundle file so I can rerun the workflow easily. Thanks! -- Vimig Socrates Case Western Reserve University Class of 2018
Taverna 3.1.0 vs Taverna 2.5.4
Hello, I am thinking about switching to Taverna 3.1.0. Are there other major changes, apart from those listed on this blog post? https://cwiki.apache.org/confluence/display/TAVERNADEV/2018/01/17/Apache+Taverna+Server+3.1.0-incubating+released If so, please point me in the right direction to the release notes. Thanks! -- Vimig Socrates Case Western Reserve University Class of 2018
Get UUID during Workflow Run
Hello, Is there a way to get the Taverna workflow UUID in Taverna 2.5 within the workflow? I want to create a file named with a unique identifier per run. Thank you! -- Vimig Socrates Case Western Reserve
Re: Resources to create UI using Workflow on Workbench
Hi, Just following up on this email. As a recap, I would like to embed the image of the workflow (that I see on the Workbench) from the Taverna Server 2.5 into my Django app. What is my best bet in doing this? Thanks! -- Vimig Socrates Case Western Reserve University Class of 2018 On Sat, Sep 22, 2018 at 2:28 AM Vimig Socrates wrote: > Thank you for your fast reply Donal. > > In a related note, what if I want just the workflow image but don't need > to update? I cannot use the Taverna Player plugin since the website I'm > developing is made with Django, not Rails. The Taverna Player REST API also > seems to not give an image of the workflow. > > Thank you all for your help so far! > > -- > Vimig Socrates > Case Western Reserve University Class of 2018 > > > On Thu, Sep 20, 2018 at 3:49 PM Donal K. Fellows < > donal.k.fell...@manchester.ac.uk> wrote: > >> On 20/09/2018 16:45, Ian Dunlop wrote: >> > I’m not sure how to get deep inside an actual workflow run. Donal >> > Fellows, the person who wrote most of the server code, might be able to >> > help (if he is still reading these emails!). I can’t think of any >> better >> > suggestions beyond loading the code into a debugger. Although I think >> > the actual workflow status, rather than workflow run status, is >> probably >> > handled by other code. >> > >> >> I *sometimes* read these things. :-) >> >> When I last worked with the Server (some time ago) there wasn't a >> mechanism for directly querying what the status of the parts of a >> workflow were when it was running (because the workflow execution engine >> process didn't publish that info; it only wrote things out at the end). >> I believe we worked around this by modifying the workflows to >> occasionally write something relating to their status to a “known >> location” (either files or services would work for this) that the >> exterior service could poll periodically. That's not a general solution, >> not without a mechanism for automatically creating the operations for >> recording the status (possible, but not something that existed the last >> time I looked), but it will work fine if one is only supporting a >> defined set of workflows. >> >> Or at least that's my first set of thoughts on how to do this. >> >> Donal. >> >
Re: Resources to create UI using Workflow on Workbench
Thank you for your fast reply Donal. In a related note, what if I want just the workflow image but don't need to update? I cannot use the Taverna Player plugin since the website I'm developing is made with Django, not Rails. The Taverna Player REST API also seems to not give an image of the workflow. Thank you all for your help so far! -- Vimig Socrates Case Western Reserve University Class of 2018 On Thu, Sep 20, 2018 at 3:49 PM Donal K. Fellows < donal.k.fell...@manchester.ac.uk> wrote: > On 20/09/2018 16:45, Ian Dunlop wrote: > > I’m not sure how to get deep inside an actual workflow run. Donal > > Fellows, the person who wrote most of the server code, might be able to > > help (if he is still reading these emails!). I can’t think of any better > > suggestions beyond loading the code into a debugger. Although I think > > the actual workflow status, rather than workflow run status, is probably > > handled by other code. > > > > I *sometimes* read these things. :-) > > When I last worked with the Server (some time ago) there wasn't a > mechanism for directly querying what the status of the parts of a > workflow were when it was running (because the workflow execution engine > process didn't publish that info; it only wrote things out at the end). > I believe we worked around this by modifying the workflows to > occasionally write something relating to their status to a “known > location” (either files or services would work for this) that the > exterior service could poll periodically. That's not a general solution, > not without a mechanism for automatically creating the operations for > recording the status (possible, but not something that existed the last > time I looked), but it will work fine if one is only supporting a > defined set of workflows. > > Or at least that's my first set of thoughts on how to do this. > > Donal. >
Re: Resources to create UI using Workflow on Workbench
Hi,
I did look at the Taverna 2.5 equivalent (
http://dev.mygrid.org.uk/wiki/display/tav250/REST+API). However, I didn't
see any calls there that would give me the statuses beyond what you
mentioned in your gitter message (Initial, initialized, operating,
finished, destroyed & stopped).
I believe this is functionality I will need and it seems feasible since the
workbench provides this capability. Could you point me in the right
direction, if I wanted to make changes to the server code to get finer
grain updates? Thank you!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Wed, Sep 19, 2018 at 9:11 AM Ian Dunlop wrote:
> Hello,
>
>
>
> If you have a look at
> https://taverna.incubator.apache.org/documentation/server/3.1/usage you
> can see all the REST calls detailed. I’m assuming its much the same for 2.5.
>
>
>
> Cheers,
>
>
>
> Ian
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Vimig Socrates
> *Sent: *17 September 2018 05:15
> *To: *users@taverna.incubator.apache.org
> *Subject: *Re: Resources to create UI using Workflow on Workbench
>
>
>
> Hi,
>
>
>
> Sorry for the late response. I tried running the player portal in docker
> and am having an issue. None of my workflows are running and whenever I
> try, the portal says "Server full - please wait; run will start soon".
>
>
>
> With some debugging I've found that it is the Taverna Server that won't
> allow me to run anything on it. Using a REST client, I get a "503 Service
> Unavailable" error with the body as "failed to build workflow run worker".
>
>
>
> As an *additional question*, I looked through the Rails code for the
> polling REST call, but don't see it. What REST endpoint should I hit to get
> an update of where along the workflow the system currently is?
>
>
>
> Please let me know. Thanks!
>
>
>
>
>
>
>
> --
>
> Vimig Socrates
>
> Case Western Reserve University Class of 2018
>
>
>
> On Tue, Sep 4, 2018 at 1:16 PM, Ian Dunlop wrote:
>
> Hello,
>
>
>
> Have a look at https://github.com/taverna-extras/taverna-player-portal.
> This is a UI that uses the taverna server to run workflows and update
> progress.
>
> I think there is some ruby code to get a png of the workflow diagram in
> it. There should also be some java code somewhere – anyone know where?
>
>
>
> Cheers,
>
>
>
> Ian
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Vimig Socrates
> *Sent: *04 September 2018 18:11
> *To: *users@taverna.incubator.apache.org
> *Subject: *Resources to create UI using Workflow on Workbench
>
>
>
> Hi everyone,
>
>
>
> I am looking to run Taverna Server *version 2.5* and create a user
> interface accessible from the internet that will update as the workflow
> progresses. To that end, I would need an API that I could access to get an
> update of a running workflow.
>
>
>
> Can I do that with /runs/{id}/listeners and only using the given
> */runs/{id}/listeners/io/properties/stdout
> *output? What if I want the entire workflow diagram to be shown in a web
> interface? Is there any support for that?
>
>
>
> Thanks!
>
>
>
>
> --
>
> Vimig Socrates
>
> Case Western Reserve University Class of 2018
>
>
>
>
>
>
>
Re: Resources to create UI using Workflow on Workbench
Hi,
Sorry for the late response. I tried running the player portal in docker
and am having an issue. None of my workflows are running and whenever I
try, the portal says "Server full - please wait; run will start soon".
With some debugging I've found that it is the Taverna Server that won't
allow me to run anything on it. Using a REST client, I get a "503 Service
Unavailable" error with the body as "failed to build workflow run worker".
As an *additional question*, I looked through the Rails code for the
polling REST call, but don't see it. What REST endpoint should I hit to get
an update of where along the workflow the system currently is?
Please let me know. Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
On Tue, Sep 4, 2018 at 1:16 PM, Ian Dunlop wrote:
> Hello,
>
>
>
> Have a look at https://github.com/taverna-extras/taverna-player-portal.
> This is a UI that uses the taverna server to run workflows and update
> progress.
>
> I think there is some ruby code to get a png of the workflow diagram in
> it. There should also be some java code somewhere – anyone know where?
>
>
>
> Cheers,
>
>
>
> Ian
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Vimig Socrates
> *Sent: *04 September 2018 18:11
> *To: *users@taverna.incubator.apache.org
> *Subject: *Resources to create UI using Workflow on Workbench
>
>
>
> Hi everyone,
>
>
>
> I am looking to run Taverna Server *version 2.5* and create a user
> interface accessible from the internet that will update as the workflow
> progresses. To that end, I would need an API that I could access to get an
> update of a running workflow.
>
>
>
> Can I do that with /runs/{id}/listeners and only using the given
> */runs/{id}/listeners/io/properties/stdout
> *output? What if I want the entire workflow diagram to be shown in a web
> interface? Is there any support for that?
>
>
>
> Thanks!
>
>
>
>
> --
>
> Vimig Socrates
>
> Case Western Reserve University Class of 2018
>
>
>
Resources to create UI using Workflow on Workbench
Hi everyone,
I am looking to run Taverna Server *version 2.5* and create a user
interface accessible from the internet that will update as the workflow
progresses. To that end, I would need an API that I could access to get an
update of a running workflow.
Can I do that with /runs/{id}/listeners and only using the given
*/runs/{id}/listeners/io/properties/stdout
*output? What if I want the entire workflow diagram to be shown in a web
interface? Is there any support for that?
Thanks!
--
Vimig Socrates
Case Western Reserve University Class of 2018
How to Use Beanshells and Lists
Hi, I've looked across the internet, but can't find a good example on this. I am trying to take json output from the body of a web service module (called *jsonedffiles*) here and then output a single element under the key "fileList" as a JsonArray and I am getting the following error. Processor 'Beanshell' - Port 'outputVal': Error accessing beanshell input/output data for net.sf.taverna.t2.activities. beanshell.BeanshellActivity$1@680a8ae1 I am unsure on why this is, and there is no stack trace for me to debug with. Any help would be much appreciated. Thank you. -- Vimig Socrates
Re: Taverna 2.54 Server POST Request HTTP Error 415
I think being able to post the objects as a t2flow object or JSON are more than enough. I don't see much benefit in making them form-data. -- Vimig Socrates Case Western Reserve University Class of 2018 On Tue, Apr 10, 2018 at 4:21 AM, Stian Soiland-Reyes <st...@apache.org> wrote: > Great! I checked > https://taverna.incubator.apache.org/documentation/server/3.1/usage > and none of the Server API calls currently support form-data, only > JSON or XML (as well as the t2flow upload). > > Do you think support for form-data would be beneficial for Taverna > Server or do the current options suffice? > > On 9 April 2018 at 18:26, Vimig Socrates <vsocra...@case.edu> wrote: > > Thank you. That basically worked. I had to post as a binary object as > > opposed to form-data. > > > > -- > > Vimig Socrates > > Case Western Reserve University Class of 2018 > > > > On Mon, Apr 9, 2018 at 10:33 AM, Stian Soiland-Reyes <st...@apache.org> > > wrote: > >> > >> Hi, > >> > >> POSTing with Content-Type application/vnd.taverna.t2flow+xml is indeed > >> the recommended way to upload the t2flow workflow. > >> > >> Could you try to remove the second Content-Type header of > >> multipart/form-data inserted by Postman? That is probably breaking it. > >> > >> > >> > >> > >> On 6 April 2018 at 00:11, Vimig Socrates <vsocra...@case.edu> wrote: > >> > Hi everyone! > >> > > >> > I just started using Taverna and have Taverna 2.54 Server setup on an > >> > Ubuntu > >> > 16.04 VM but I don't understand how to post a workflow to it. I am > using > >> > the > >> > old t2flow format, but I get a 415 Unsupported Media Type server error > >> > when > >> > I POST with the file attached using Postman HTTP Client. > >> > > >> > Am I missing a setting? > >> > > >> > Here is the cURL code snippet produced by Postman. > >> > > >> > curl -X POST \ > >> > http://pqhs-vimig.case.edu:8080/tavernaserver/rest/runs \ > >> > -H 'Authorization: Basic dGF2ZXJuYTp0YXZlcm5h' \ > >> > -H 'Cache-Control: no-cache' \ > >> > -H 'Content-Type: application/vnd.taverna.t2flow+xml' \ > >> > -H 'Postman-Token: 80a0ed49-e86e-5d2b-14cc-1530c5f9e5fd' \ > >> > -H 'content-type: multipart/form-data; > >> > boundary=WebKitFormBoundary7MA4YWxkTrZu0gW' \ > >> > -F =@/.../conversion_workflow.t2flow > >> > > >> > > >> > Please let me know! Thanks! > >> > > >> > -- > >> > Vimig Socrates > >> > >> > >> > >> -- > >> Stian Soiland-Reyes > >> http://orcid.org/-0001-9842-9718 > > > > > > > > -- > Stian Soiland-Reyes > http://orcid.org/-0001-9842-9718 >
Re: Taverna 2.54 Server POST Request HTTP Error 415
Thank you. That basically worked. I had to post as a binary object as opposed to form-data. -- Vimig Socrates Case Western Reserve University Class of 2018 On Mon, Apr 9, 2018 at 10:33 AM, Stian Soiland-Reyes <st...@apache.org> wrote: > Hi, > > POSTing with Content-Type application/vnd.taverna.t2flow+xml is indeed > the recommended way to upload the t2flow workflow. > > Could you try to remove the second Content-Type header of > multipart/form-data inserted by Postman? That is probably breaking it. > > > > > On 6 April 2018 at 00:11, Vimig Socrates <vsocra...@case.edu> wrote: > > Hi everyone! > > > > I just started using Taverna and have Taverna 2.54 Server setup on an > Ubuntu > > 16.04 VM but I don't understand how to post a workflow to it. I am using > the > > old t2flow format, but I get a 415 Unsupported Media Type server error > when > > I POST with the file attached using Postman HTTP Client. > > > > Am I missing a setting? > > > > Here is the cURL code snippet produced by Postman. > > > > curl -X POST \ > > http://pqhs-vimig.case.edu:8080/tavernaserver/rest/runs \ > > -H 'Authorization: Basic dGF2ZXJuYTp0YXZlcm5h' \ > > -H 'Cache-Control: no-cache' \ > > -H 'Content-Type: application/vnd.taverna.t2flow+xml' \ > > -H 'Postman-Token: 80a0ed49-e86e-5d2b-14cc-1530c5f9e5fd' \ > > -H 'content-type: multipart/form-data; > > boundary=WebKitFormBoundary7MA4YWxkTrZu0gW' \ > > -F =@/.../conversion_workflow.t2flow > > > > > > Please let me know! Thanks! > > > > -- > > Vimig Socrates > > > > -- > Stian Soiland-Reyes > http://orcid.org/-0001-9842-9718 >
Taverna 2.54 Server POST Request HTTP Error 415
Hi everyone! I just started using Taverna and have Taverna 2.54 Server setup on an Ubuntu 16.04 VM but I don't understand how to post a workflow to it. I am using the old t2flow format, but I get a 415 Unsupported Media Type server error when I POST with the file attached using Postman HTTP Client. Am I missing a setting? Here is the cURL code snippet produced by Postman. curl -X POST \ http://pqhs-vimig.case.edu:8080/tavernaserver/rest/runs \ -H 'Authorization: Basic dGF2ZXJuYTp0YXZlcm5h' \ -H 'Cache-Control: no-cache' \ -H 'Content-Type: application/vnd.taverna.t2flow+xml' \ -H 'Postman-Token: 80a0ed49-e86e-5d2b-14cc-1530c5f9e5fd' \ -H 'content-type: multipart/form-data; boundary=WebKitFormBoundary7MA4YWxkTrZu0gW' \ -F =@/.../conversion_workflow.t2flow Please let me know! Thanks! -- Vimig Socrates
