<div dir="ltr">Both ran fine. -angel</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Aug 8, 2013 at 4:09 PM, Tolmie, David A <span dir="ltr"><<a href="mailto:dtolmie@fhcrc.org" target="_blank">dtolmie@fhcrc.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
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<div>Angel,</div>
<div><br>
</div>
<div>Was it the update script or the data management script that had been failing for you? The update is running just fine for me, it's the data migration script that's complaining.</div>
<div><br>
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<div>Thanks,</div>
<div><br>
</div>
<div>-Dave</div>
<div>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><u></u> <u></u></p>
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<span style="font-weight:bold">From: </span>Angel Pizarro <<a href="mailto:angel@itmat.upenn.edu" target="_blank">angel@itmat.upenn.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:angel@upenn.edu" target="_blank">angel@upenn.edu</a>" <<a href="mailto:angel@upenn.edu" target="_blank">angel@upenn.edu</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, August 8, 2013 12:52 PM<br>
<span style="font-weight:bold">To: </span>"Cheng, Sophia" <<a href="mailto:Sophia_Cheng@hms.harvard.edu" target="_blank">Sophia_Cheng@hms.harvard.edu</a>><br>
<span style="font-weight:bold">Cc: </span>Faith Coldren <<a href="mailto:fcoldren@mail.med.upenn.edu" target="_blank">fcoldren@mail.med.upenn.edu</a>>, David Tolmie <<a href="mailto:dtolmie@fhcrc.org" target="_blank">dtolmie@fhcrc.org</a>>, "<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>"
<<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>>, "<a href="mailto:ross.davis@Vanderbilt.Edu" target="_blank">ross.davis@Vanderbilt.Edu</a>" <<a href="mailto:ross.davis@vanderbilt.edu" target="_blank">ross.davis@vanderbilt.edu</a>>, "<a href="mailto:sukie@dartmouth.edu" target="_blank">sukie@dartmouth.edu</a>"
<<a href="mailto:sukie@dartmouth.edu" target="_blank">sukie@dartmouth.edu</a>>, "Neiman, David" <<a href="mailto:David_Neiman@hms.harvard.edu" target="_blank">David_Neiman@hms.harvard.edu</a>>, "Cole, Julian C" <<a href="mailto:Julian_Cole@hms.harvard.edu" target="_blank">Julian_Cole@hms.harvard.edu</a>>,
"Ciriello, Marc" <<a href="mailto:Marc_Ciriello@hms.harvard.edu" target="_blank">Marc_Ciriello@hms.harvard.edu</a>><div><div class="h5"><br>
<span style="font-weight:bold">Subject: </span>Re: [Eagle-i-admins] New process and data migration issues & clarification of properties [2.0-MS2.14]<br>
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<div dir="ltr">The update ran fine for us once we took care of the changed values in the respective properties files. -angel</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Thu, Aug 8, 2013 at 3:45 PM, Cheng, Sophia <span dir="ltr">
<<a href="mailto:Sophia_Cheng@hms.harvard.edu" target="_blank">Sophia_Cheng@hms.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Faith,</div>
<div><br>
</div>
<div>Have you had trouble using the data migration script with the latest (2.0-MS2.14) version?</div>
<div><br>
</div>
<div>-Sophia</div>
<div><br>
</div>
<span>
<div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>Faith Coldren <<a href="mailto:fcoldren@mail.med.upenn.edu" target="_blank">fcoldren@mail.med.upenn.edu</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, August 8, 2013 3:43 PM<br>
<span style="font-weight:bold">To: </span>Sophia <<a href="mailto:sophia_cheng@hms.harvard.edu" target="_blank">sophia_cheng@hms.harvard.edu</a>><br>
<span style="font-weight:bold">Cc: </span>"Tolmie, David A" <<a href="mailto:dtolmie@fhcrc.org" target="_blank">dtolmie@fhcrc.org</a>>, "<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>" <<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>>,
"<a href="mailto:ross.davis@Vanderbilt.Edu" target="_blank">ross.davis@Vanderbilt.Edu</a>" <<a href="mailto:ross.davis@vanderbilt.edu" target="_blank">ross.davis@vanderbilt.edu</a>>, "<a href="mailto:angel@itmat.upenn.edu" target="_blank">angel@itmat.upenn.edu</a>"
<<a href="mailto:angel@itmat.upenn.edu" target="_blank">angel@itmat.upenn.edu</a>>, "<a href="mailto:fcoldren@mail.med.upenn.edu" target="_blank">fcoldren@mail.med.upenn.edu</a>" <<a href="mailto:fcoldren@mail.med.upenn.edu" target="_blank">fcoldren@mail.med.upenn.edu</a>>,
"<a href="mailto:sukie@dartmouth.edu" target="_blank">sukie@dartmouth.edu</a>" <<a href="mailto:sukie@dartmouth.edu" target="_blank">sukie@dartmouth.edu</a>>, "Neiman, David" <<a href="mailto:David_Neiman@hms.harvard.edu" target="_blank">David_Neiman@hms.harvard.edu</a>>,
"Cole, Julian C" <<a href="mailto:Julian_Cole@hms.harvard.edu" target="_blank">Julian_Cole@hms.harvard.edu</a>>, "Ciriello, Marc" <<a href="mailto:Marc_Ciriello@hms.harvard.edu" target="_blank">Marc_Ciriello@hms.harvard.edu</a>>
<div>
<div><br>
<span style="font-weight:bold">Subject: </span>Re: [Eagle-i-admins] New process and data migration issues & clarification of properties [2.0-MS2.14]<br>
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<div><br>
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<div dir="ltr">
<div>We aren't running java 1.6. We have the following configuration:</div>
<div><br>
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<div>java version "1.7.0_05-icedtea"</div>
<div>OpenJDK Runtime Environment (rhel-2.2.1.el6_3.3-x86_64)</div>
<div>OpenJDK 64-Bit Server VM (build 23.0-b21, mixed mode)</div>
<div class="gmail_extra">
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<div dir="ltr"></div>
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<div class="gmail_quote">On Thu, Aug 8, 2013 at 3:07 PM, Cheng, Sophia <span dir="ltr">
<<a href="mailto:Sophia_Cheng@hms.harvard.edu" target="_blank">Sophia_Cheng@hms.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Hello everyone,</div>
<div><br>
</div>
<div>This is a bit of a shot in the dark, but has anyone else running java 1.6 with OpenJDK as the Java? If so, have you been able to run the migration scripts?</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Sophia</div>
<div><br>
</div>
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<div style="border-width:1pt medium medium;border-style:solid none none;padding:3pt 0in 0in;text-align:left;font-size:11pt;font-family:Calibri;border-top-color:rgb(181,196,223)">
<span style="font-weight:bold">From: </span><Tolmie>, David A <<a href="mailto:dtolmie@fhcrc.org" target="_blank">dtolmie@fhcrc.org</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, August 8, 2013 1:21 PM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>" <<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>>,
"<a href="mailto:ross.davis@Vanderbilt.Edu" target="_blank">ross.davis@Vanderbilt.Edu</a>" <<a href="mailto:ross.davis@Vanderbilt.Edu" target="_blank">ross.davis@Vanderbilt.Edu</a>>, "<a href="mailto:angel@itmat.upenn.edu" target="_blank">angel@itmat.upenn.edu</a>"
<<a href="mailto:angel@itmat.upenn.edu" target="_blank">angel@itmat.upenn.edu</a>>, "<a href="mailto:fcoldren@mail.med.upenn.edu" target="_blank">fcoldren@mail.med.upenn.edu</a>" <<a href="mailto:fcoldren@mail.med.upenn.edu" target="_blank">fcoldren@mail.med.upenn.edu</a>>,
"<a href="mailto:sukie@dartmouth.edu" target="_blank">sukie@dartmouth.edu</a>" <<a href="mailto:sukie@dartmouth.edu" target="_blank">sukie@dartmouth.edu</a>><br>
<span style="font-weight:bold">Cc: </span>"Neiman, David" <<a href="mailto:David_Neiman@hms.harvard.edu" target="_blank">David_Neiman@hms.harvard.edu</a>>, "Cole, Julian C" <<a href="mailto:Julian_Cole@hms.harvard.edu" target="_blank">Julian_Cole@hms.harvard.edu</a>>,
"Ciriello, Marc" <<a href="mailto:Marc_Ciriello@hms.harvard.edu" target="_blank">Marc_Ciriello@hms.harvard.edu</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [Eagle-i-admins] New process and data migration issues & clarification of properties [2.0-MS2.14]<br>
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<div>Hi folks,</div>
<div><br>
</div>
<div>I'm back to trying to upgrade eagle-I, and I'm receiving the same kind of output as before when running the data migration script. See attached. The script claims to have run successfully, but shows command usage info as if underlying commands were not
called correctly. Nothing was written to any of the logs.</div>
<div><br>
</div>
<div>I'm doing this with the repository and data migrations tools from 2.0-MS2.16 this time. I made certain there were no old instances of the eagle-i-datatools-datamanagement.jar before downloading the jar for the newest release.</div>
<div><br>
</div>
<div>Any thoughts or suggestions?</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>-Dave</div>
<div><br>
</div>
<div>
<div style="font-family:Calibri;font-size:medium">
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<p style="margin:0in 0in 0.0001pt;font-size:11pt"><span style="font-size:18pt;color:rgb(31,35,62)">David Tolmie</span><span style="font-size:18pt;color:rgb(31,35,62)"><u></u><u></u></span></p>
<p style="margin:0in 0in 0.0001pt;font-size:11pt"><b><span style="font-size:14pt;color:rgb(198,159,48)">Systems Librarian</span></b><b><span style="color:rgb(198,159,48)"> </span></b><b><span style="font-size:14pt;color:rgb(198,159,48)"><u></u><u></u></span></b></p>
<p style="margin:0in 0in 0.0001pt;font-size:11pt"><b><span style="font-size:10pt;color:rgb(106,145,144)">Arnold Library | Fred Hutchinson Cancer Research Center | Seattle, WA<u></u><u></u></span></b></p>
<p style="margin:0in 0in 0.0001pt;font-size:11pt"><b><span style="font-size:10pt;color:rgb(106,145,144)"><a href="mailto:dtolmie@fhcrc.org" style="color:purple" target="_blank"><span style="color:rgb(106,145,144)">dtolmie@fhcrc.org</span></a> | tel
<a href="tel:206.667.6852" value="+12066676852" target="_blank">206.667.6852</a> | fax
<a href="tel:206.667.4737" value="+12066674737" target="_blank">206.667.4737</a></span></b><b><span style="color:rgb(138,169,169)"><u></u><u></u></span></b></p>
<p style="margin:0in 0in 0.0001pt;font-size:11pt"><a href="http://library.fhcrc.org/" style="color:purple" target="_blank"><span style="color:blue;text-decoration:none"><img border="0" width="234" height="51" alt="Description: Description: Description: Description: AL-Logo-color" type="image/png"></span></a><u></u><u></u></p>
<p style="margin:0in 0in 0.0001pt;font-size:11pt"><u></u> <u></u></p>
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<span style="font-weight:bold">From: </span><Cheng>, "Cheng, Sophia" <<a href="mailto:Sophia_Cheng@hms.harvard.edu" target="_blank">Sophia_Cheng@hms.harvard.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>"<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>" <<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, July 23, 2013 4:51 PM<br>
<span style="font-weight:bold">To: </span>David Tolmie <<a href="mailto:dtolmie@fhcrc.org" target="_blank">dtolmie@fhcrc.org</a>>, "<a href="mailto:ross.davis@Vanderbilt.Edu" target="_blank">ross.davis@Vanderbilt.Edu</a>" <<a href="mailto:ross.davis@Vanderbilt.Edu" target="_blank">ross.davis@Vanderbilt.Edu</a>>,
"<a href="mailto:angel@itmat.upenn.edu" target="_blank">angel@itmat.upenn.edu</a>" <<a href="mailto:angel@itmat.upenn.edu" target="_blank">angel@itmat.upenn.edu</a>>, "<a href="mailto:fcoldren@mail.med.upenn.edu" target="_blank">fcoldren@mail.med.upenn.edu</a>"
<<a href="mailto:fcoldren@mail.med.upenn.edu" target="_blank">fcoldren@mail.med.upenn.edu</a>>, "<a href="mailto:sukie@dartmouth.edu" target="_blank">sukie@dartmouth.edu</a>" <<a href="mailto:sukie@dartmouth.edu" target="_blank">sukie@dartmouth.edu</a>><br>
<span style="font-weight:bold">Cc: </span>"Ciriello, Marc" <<a href="mailto:Marc_Ciriello@hms.harvard.edu" target="_blank">Marc_Ciriello@hms.harvard.edu</a>>, "Bourges, Daniela" <<a href="mailto:Daniela_Bourges@hms.harvard.edu" target="_blank">Daniela_Bourges@hms.harvard.edu</a>>,
"Cole, Julian C" <<a href="mailto:Julian_Cole@hms.harvard.edu" target="_blank">Julian_Cole@hms.harvard.edu</a>>, "Neiman, David" <<a href="mailto:David_Neiman@hms.harvard.edu" target="_blank">David_Neiman@hms.harvard.edu</a>>, "<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>"
<<a href="mailto:eagle-i-admins@open.med.harvard.edu" target="_blank">eagle-i-admins@open.med.harvard.edu</a>><br>
<span style="font-weight:bold">Subject: </span>New process and data migration issues & clarification of properties [2.0-MS2.14]<br>
</div>
<div><br>
</div>
<div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:12px;white-space:normal;font-family:Consolas,monospace;word-spacing:0px">
Now, regarding some of the issues that have been encountered:</div>
<div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:12px;white-space:normal;font-family:Consolas,monospace;word-spacing:0px">
(1) Some of you have reported having issues running the data-migration.sh for the latest release, 2.0-MS2.14. This issue manifests with notification of incorrect/missing parameters during the execution of the script, but the script does not fail. The output
looks similar to the attached file. I have been unable to reproduce the error using the files that were mentioned in the initial email:</div>
<div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:12px;white-space:normal;font-family:Consolas,monospace;word-spacing:0px">
<div>Datamangement Toolkit - <a href="http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-datatools-datamanagement/" target="_blank">http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-datatools-datamanagement/</a> </div>
<div>Repository - <a href="http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-repository-dist/" target="_blank">http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-repository-dist/</a> </div>
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<div style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;text-transform:none;font-size:12px;white-space:normal;font-family:Consolas,monospace;word-spacing:0px">
Not everyone has run into this problem, so I'm wondering if I could ask those of you who have had problems to remove your existing eagle-i-datatools-datamanagement.jar, re-download the jar and try the script again.</div>
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