<html><head><base href="x-msg://1210/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Gavin</div><div><br></div><div>Please be patient when using the dev list and always keep the conversation on the list, un-invited off list contact is unacceptable (see posting guidelines attached).</div><div><br></div><div>wrt the error you have found, it seems that this fix has been hanging around in my local repository for a while and missed check in for some reason. I have now checked in the updated methods on the head. You can try checking out the head code and simply copying the Helper.pm to your v67 checkout. </div><div><br></div><div>Thanks</div><div><br></div><div><div style="font-size: 12px; ">Nathan Johnson</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Senior Scientific Programmer</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Ensembl Regulation</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">European Bioinformatics Institute</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Wellcome Trust Genome Campus</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Hinxton</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; ">Cambridge CB10 1SD</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><a href="http://www.ensembl.info/">http://www.ensembl.info/</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><a href="http://twitter.com/#!/ensembl">http://twitter.com/#!/ensembl</a></div></div><div><br></div><div><br>Ensembl dev posting guidelines<br><br>The Ensembl dev mailing list (<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>) is a forum for users of the <br>Ensembl API, website and data including users maintaining Ensembl mirrors<br>or developing applications based on the Ensembl code. 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All Ensembl team members will reply with the dev list in copy and<br>dev messages should not be sent directly to members of the<br>Ensembl team.<br><br>- Normal standards of professional behaviour are expected in all messages. <br>Comments that are deemed rude or insulting are not acceptable.<br><br>- Uninvited off-list contact for commercial or other purposes is not acceptable.<br><br>- Messages sent to <a href="mailto:dev@ensembl.org">dev@ensembl.org</a> will be archived. These are indexed and<br>searchable via sources such as google.<br><br>- Job postings for Ensembl project positions at the EBI and Sanger may be<br>occasionally be sent to the list. Other jobs postings are not appropriate for the list.</div><div><br></div><div><br></div><div><br></div><div><br></div><br><div><div>On 11 Jul 2012, at 10:53, Oliver, Gavin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Hi Nathan,<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><br>Sorry to contact you directly but I am not having much luck on the mailing list.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I am leaving Almac in a couple of weeks (off to the Mayo Clinic) and have been asked to update our array annotations before I go. I have not updated the annotations/APIs etc since v60 and am now trying to update to v67.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I have got as far as the RunTranscriptXrefs stage but then it is failing when the Helper.pm module looks for the transcript_stable_id table which appears to have been removed from the core schema after v64.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 22px; "><span lang="EN-US" style="font-size: 10pt; line-height: 19px; font-family: Arial, sans-serif; ">Are there any known issues with the current API version?<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 22px; "><span lang="EN-US" style="font-size: 10pt; line-height: 19px; font-family: Arial, sans-serif; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 22px; "><span lang="EN-US" style="font-size: 10pt; line-height: 19px; font-family: Arial, sans-serif; ">Best,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 22px; "><span lang="EN-US" style="font-size: 10pt; line-height: 19px; font-family: Arial, sans-serif; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 22px; "><span lang="EN-US" style="font-size: 10pt; line-height: 19px; font-family: Arial, sans-serif; ">Gavin<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; text-align: center; "><span lang="EN-US" style="font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div><font face="Tahoma" size="2"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><strong><b><span style="color: blue; font-size: 12pt; "><font face="Times New Roman"> </font></span></b></strong></div><strong><b><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><font color="#000000"><span lang="EN-GB" style="font-family: 'Times New Roman'; ">The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><font color="#0000ff"><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Group (UK) Limited, registered no. NI061368.<span> <span class="Apple-converted-space"> </span></span>Almac Sciences Limited, registered no. NI041550.<span> <span class="Apple-converted-space"> </span></span>Almac Discovery Limited, registered no. NI046249.<span class="Apple-converted-space"> </span><span> </span>Almac Pharma Services Limited, registered no. NI045055.<span> <span class="Apple-converted-space"> </span></span>Almac Clinical Services Limited, registered no. NI041905.<span> <span class="Apple-converted-space"> </span></span>Almac Clinical Technologies Limited, registered no. NI061202.<span class="Apple-converted-space"> </span><span> </span>Almac Diagnostics Limited, registered no. NI043067.<span> </span>All preceding companies are registered in<span class="Apple-converted-space"> </span><st1:country-region w:st="on">Northern Ireland</st1:country-region><span class="Apple-converted-space"> </span>with a registered office address of Almac House, 20 Seagoe Industrial Estate,<span class="Apple-converted-space"> </span><st1:place w:st="on"><st1:city w:st="on">Craigavon</st1:city>,<span class="Apple-converted-space"> </span><st1:postalcode w:st="on">BT63 5QD</st1:postalcode>,<span class="Apple-converted-space"> </span><st1:country-region w:st="on">UK</st1:country-region></st1:place>.<span class="Apple-converted-space"> </span><span> </span><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in<span class="Apple-converted-space"> </span><st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region><span class="Apple-converted-space"> </span>no. SC154034.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac Diagnostics LLC are<st1:state w:st="on"><st1:place w:st="on">Delaware</st1:place></st1:state><span class="Apple-converted-space"> </span>limited liability companies and Almac Group Incorporated is a Delaware Corporation.<span> <span class="Apple-converted-space"> </span></span>More information on the Almac Group can be found on the Almac website:<span class="Apple-converted-space"> </span><a href="http://www.almacgroup.com" style="color: blue; text-decoration: underline; ">www.almacgroup.com</a><o:p></o:p></span></div></b></strong></font></div></span></blockquote></div><br><div>
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