From users-return-245-archive-asf-public=cust-asf.ponee.io@taverna.incubator.apache.org Thu Apr 4 23:58:53 2019 Return-Path: X-Original-To: archive-asf-public@cust-asf.ponee.io Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by mx-eu-01.ponee.io (Postfix) with SMTP id 5D94018065B for ; Fri, 5 Apr 2019 01:58:52 +0200 (CEST) Received: (qmail 27065 invoked by uid 500); 4 Apr 2019 23:58:51 -0000 Mailing-List: contact users-help@taverna.incubator.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: users@taverna.incubator.apache.org Delivered-To: mailing list users@taverna.incubator.apache.org Received: (qmail 27055 invoked by uid 99); 4 Apr 2019 23:58:51 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd1-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Thu, 04 Apr 2019 23:58:51 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd1-us-west.apache.org (ASF Mail Server at spamd1-us-west.apache.org) with ESMTP id 18CC9C5EA0 for ; Thu, 4 Apr 2019 23:58:51 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd1-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: 2 X-Spam-Level: ** X-Spam-Status: No, score=2 tagged_above=-999 required=6.31 tests=[HTML_MESSAGE=2, RCVD_IN_DNSWL_NONE=-0.0001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001] autolearn=disabled Received: from mx1-lw-us.apache.org ([10.40.0.8]) by localhost (spamd1-us-west.apache.org [10.40.0.7]) (amavisd-new, port 10024) with ESMTP id uS8fxEz5an2D for ; Thu, 4 Apr 2019 23:58:49 +0000 (UTC) Received: from mpv3-2015.case.edu (mpv3-2015.CWRU.Edu [129.22.103.194]) by mx1-lw-us.apache.org (ASF Mail Server at mx1-lw-us.apache.org) with ESMTPS id 1B01B5F1A0 for ; Thu, 4 Apr 2019 23:58:48 +0000 (UTC) Received: from mpv6-2015.CWRU.Edu (EHLO mpv6-2015.case.edu) ([129.22.103.202]) by mpv3-2015.case.edu (MOS 4.4.8-GA FastPath queued) with ESMTP id AWZ10452; Thu, 04 Apr 2019 19:58:47 -0400 (EDT) Received: from mail-io1-f43.google.com (EHLO mail-io1-f43.google.com) ([209.85.166.43]) by mpv6-2015.case.edu (MOS 4.4.8-GA FastPath queued) with ESMTP id CQA77530 (AUTH vsocrates); Thu, 04 Apr 2019 19:58:47 -0400 (EDT) Received: by mail-io1-f43.google.com with SMTP id p23so2940606iol.13 for ; Thu, 04 Apr 2019 16:58:47 -0700 (PDT) X-Gm-Message-State: APjAAAVhLuqOeLIso0o1OPgnR5QT9eSRZYg/aimTyrsWlIpG4kHSaWFW 9jA+AoYvLekMKFGcBz0+uyifuQQsAXleDqLXz6c= X-Google-Smtp-Source: APXvYqyVYYBUmDzFtSYyJy87mUk0TChCv0ehnmAZabzQJ1TUE0Bj2ZOKZrDo5pnITdWlDbg79cdRH+i0eplKsIhISeI= X-Received: by 2002:a5d:9291:: with SMTP id s17mr5953729iom.209.1554422327320; Thu, 04 Apr 2019 16:58:47 -0700 (PDT) MIME-Version: 1.0 References: <5ca4825b.1c69fb81.78e38.f4b5@mx.google.com> <5ca5f4e6.1c69fb81.6dc21.2354@mx.google.com> In-Reply-To: <5ca5f4e6.1c69fb81.6dc21.2354@mx.google.com> From: Vimig Socrates Date: Thu, 4 Apr 2019 19:58:19 -0400 X-Gmail-Original-Message-ID: Message-ID: Subject: Re: Dockerization of Taverna Server - Vimig Socrates To: users@taverna.incubator.apache.org Content-Type: multipart/alternative; boundary="000000000000a6a7a70585bd26cb" X-Junkmail-Status: score=7/90, host=mpv3-2015.case.edu X-Junkmail-PrAS-Raw: score=7/90, refid=2.7.2:2019.4.4.223916:17:7.944, ip=, rules=__YOUTUBE_RCVD, __MIME_VERSION, __REFERENCES, __IN_REP_TO, __HAS_FROM, FROM_EDU_TLD, DATE_TZ_NA, __HAS_MSGID, __SANE_MSGID, __SUBJ_REPLY, __BOUNCE_CHALLENGE_SUBJ, __BOUNCE_NDR_SUBJ_EXEMPT, __SUBJ_ALPHA_END, __TO_MALFORMED_2, __TO_NO_NAME, __CT, __CTYPE_MULTIPART_ALT, __HEX28_LC_BOUNDARY, __CTYPE_HAS_BOUNDARY, __CTYPE_MULTIPART, __MIME_TEXT_P2, __MIME_TEXT_H2, __ANY_URI, __HTTPS_URI, __URI_WITH_PATH, __FRAUD_BODY_WEBMAIL, __URI_NO_WWW, __HIGHBITS, __CP_URI_IN_BODY, __FRAUD_MONEY_CURRENCY_DOLLAR, __SUBJ_ALPHA_NEGATE, __MULTIPLE_URI_TEXT, __URI_IN_BODY, __URI_NOT_IMG, __MULTIPLE_URI_HTML, __HTML_AHREF_TAG, __FORWARDED_MSG, __HAS_HTML, __HTML_TAG_DIV, BODY_SIZE_10000_PLUS, BODYTEXTH_SIZE_3000_MORE, BODYTEXTH_SIZE_10000_LESS, __MIME_TEXT_H1, __MIME_TEXT_P1, __MIME_HTML, __URI_NS, HTML_50_70, HEX28_LC_NOT_GOOGLE, __FRAUD_MONEY_CURRENCY, __FRAUD_WEBMAIL, [TRUNCATED], so=2010-03-03 19:42:08, dmn=2016-08-03-0138 --000000000000a6a7a70585bd26cb Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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=3D"host" in your docker run command would hel= p. > 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 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 i= s > an issue with my workflow file. > > > > I try to connect to the *http://localhost:8080/tavernaserver/rest/runs > * endpoint using a REST > service in my workflow and since Docker sees localhost as the host machin= e, > 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=E2=80=99t used this recently but I think it u= sed 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(RemoteRunDel= egate.java:214) > > at > org.taverna.server.master.worker.RunDatabase.checkForFinishNow(RunDatabas= e.java:83) > > > > though I don=E2=80=99t know why they are trying to connect to 127.0.0.1. = I=E2=80=99m not > sure if its the workflow causing the problem or the TavServ itself. > > > > Cheers, > > > > Ian > > > > Sent from Mail 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.jav= a: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 > > > > > --000000000000a6a7a70585bd26cb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
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= =20 if my program needs to be supported on Mac and Windows as well.
<= br>
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=20 the help!


--
= Vimig Socrates
Case Western Reserv= e University Class of 2018


On Thu, Apr 4, 2019 = at 8:13 AM Ian Dunlop <ianwdunlo= p@gmail.com> wrote:

Hello,

= =C2=A0

I wonder if using --network=3D"= ;host" in your docker run command would help. That should make the doc= ker container use the host network. Of course it might break other things i= n the TavServ container and it only works on linux. https://docs.docker.com/networ= k/host/

=C2=A0

Cheers,

=C2=A0

Ian

=C2=A0

Sent from Mail for Windows 10

=C2=A0

From: Vimig Socrates
Sent: 04 April 2019 00:42
To: users@taverna.incubator.apache.org
Subject: Re: Dockeri= zation of Taverna Server - Vimig Socrates

<= u>=C2=A0

Hi,

<= p class=3D"MsoNormal">=C2=A0

Yes, I incorporated a portion of the Dockerfile from the released tave= rna-server Docker container. After some more digging, looks like it is an i= ssue with my workflow file.

= =C2=A0

I try to connect to the = http://localhost:8080/tavernaserver/rest/runs endpoint using a = REST service in my workflow and since Docker sees localhost as the host mac= hine, that doesn't work. Has anyone else run into this=C2=A0issue?

=

=C2=A0

If so, any help would be appreciated! Thank you!

=C2=A0


--

Vimig Socrates=

Case Western Reserve University Class of 2018

=C2=A0

<= p class=3D"MsoNormal">=C2=A0

On Wed, Apr 3, 2019 at 5:52 AM Ian Dunlop <ianwdunlop@gmail.com> wrote:

=

Hello,

=C2=A0

Hi Vimig. Have you had a look at https://hub.do= cker.com/r/taverna/taverna-server/ which is a taverna server in Tomcat = 8. I haven=E2=80=99t used this recently but I think it used to work. Are yo= u required to use Tomcat 7? What workflow were you trying to run. It looks = like the code that is causing the issue are:

=C2= =A0

at org.taverna.server.master.worker.RemoteRun= Delegate.getStatus(RemoteRunDelegate.java:214)

= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 at org.taverna.server.master.worker.RunDatabase.checkForFin= ishNow(RunDatabase.java:83)

=C2=A0

though I don=E2=80=99t know why they are trying to connect to 1= 27.0.0.1. I=E2=80=99m not sure if its the workflow causing the problem or t= he TavServ itself.

=C2=A0

Cheers,

=C2=A0

Ian

=C2=A0

Sent from Mai= l for Windows 10

=C2=A0

From: Vimig Socrates
Sent:= 03 April 2019 03:56
To: users@taverna.incubator.apache.org<= br>Subject: Dockerization of Taverna Server - Vimig Socrates

=C2=A0

He= llo everyone!

=C2=A0

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: <= /p>


java.rm= i.ConnectException: Connection refused to host: 127.0.0.1; nested exception= is:
=C2=A0=C2=A0=C2=A0 java.net.ConnectException: Connection refused (= Connection refused)
=C2=A0=C2=A0=C2=A0 at sun.rmi.transport.tcp.TCPEndpo= int.newSocket(TCPEndpoint.java:619)
=C2=A0=C2=A0=C2=A0 at sun.rmi.transp= ort.tcp.TCPChannel.createConnection(TCPChannel.java:216)
...
=C2=A0= =C2=A0=C2=A0 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPo= olExecutor.java:624)
=C2=A0=C2=A0=C2=A0 at java.lang.Thread.run(Thread.j= ava:748)
Caused by: java.net.ConnectException: Connection refused (Conne= ction refused)
=C2=A0=C2=A0=C2=A0 at java.net.PlainSocketImpl.socketConn= ect(Native Method)

...
=C2=A0=C2=A0=C2=A0 at sun.rmi.transport.tcp.TCPEndpoi= nt.newSocket(TCPEndpoint.java:613)
=C2=A0=C2=A0=C2=A0 ... 21 more

=C2=A0

=C2= =A0

I've attached the full tavs= erv.out file for reference. I believe the reason is that 127.0.0.1 refe= rs 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!

=C2=A0

--

Vimig Socrates

Case Western Reserve Univers= ity Class of 2018

=C2=A0

= =C2=A0

--000000000000a6a7a70585bd26cb--