Hi Luis, The latest (upon till r7467) files here <https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/> fixed the error. Thanks! Great software and great team.
Cheers, Roden On Monday, November 21, 2016 at 2:13:46 PM UTC-8, Luis wrote: > > Hello Roden, > Thank you for the detailed error report. We have identified and fixed the > issue, and will be included with the next release of TPP. > > Fortunately, and as you noted, it is not a fatal error (the models file > can be found in the directory and opened either directly or via the Petunia > interface). But, if you would like to have early access to this fix, just > update the code in your src/Visualization/PepXMLViewer/ directory with the > latest in our code repository, and re-make. > > Cheers, > --Luis > > > > On Wed, Nov 16, 2016 at 11:46 AM, Roden Luo <[email protected] > <javascript:>> wrote: > >> Hi, >> I followed this >> <https://groups.google.com/forum/#!topic/spctools-discuss/oKBB1lSk894> >> guide to install TPP5 on Ubuntu 16.04.01.All others I tested work well now. >> But when I view the pep.xml file by PepXML Viewer, I get the error msg >> (Shown below in ===Error Message IMG===). However, As you can see, I >> actually can view it and use all the display functions. The last two lines >> (shown below in ===Additional Debug Info===, these two lines added are in >> red) in error msg box shown up because I added two more lines in >> tpp/html/PepXMLViewer.html (shown). >> >> Versions: >> TPP 5.0.0 >> Ubuntu 16.04.01 >> Apache 2.4 >> Chrome Version 54.0.2840.98 (64-bit) >> >> Info I searched, one thread at here >> <https://groups.google.com/forum/#!topic/spctools-discuss/-oxQ9Ts1vJo>, >> seems not solved. Because of version difference, I start this new thread. >> One wiki >> <http://tools.proteomecenter.org/wiki/index.php?title=TPP:Installing_the_Trans-Proteomic_Pipeline_(TPP)_4.4.0_on_Mac_OS_X_10.6.4>, >> >> I do not get the solution there (Quoted below). If I understand it >> correctly, this triggers an error because of the missing "+", It masks the >> problem rather than solves the problem from the root. >> >> Look forward to seeing suggestions from you. Thanks very much! >> Best, >> Roden >> >> >> - ``` Quote from wiki >> >> <http://tools.proteomecenter.org/wiki/index.php?title=TPP:Installing_the_Trans-Proteomic_Pipeline_(TPP)_4.4.0_on_Mac_OS_X_10.6.4> >> - Error 1: *Unable to access xml file via webserver, so cannot check >> xml file for changes ()* >> >> Fixed by Ulrich: open /usr/local/tpp/html/PepXMLViewer.html and change >> line 115 from >> >> document.getElementById('msgs').innerHTML += " >> (URL: " + http_req.url + ")"; >> >> to >> >> document.getElementById('msgs').innerHTML += " >> (URL: " + http_req.url ")"; >> >> >> >> ``` >> >> ==========Error Message IMG========== >> >> >> <https://lh3.googleusercontent.com/-6xOpdQJNfOo/WCyyBpeeDBI/AAAAAAAAAcY/HvJ7WfJYo1kFrzkrJ-YPfTbJOVgd1myQACLcB/s1600/QQ20161116-0.png> >> >> ==========Error Message Ends========== >> >> >> ==========Additional Debug Info========== >> (dateorig: undefined) >> (lastupdate: undefined) >> >> ===File part for tpp/html/PepXMLViewer.html, Line 25-121, added two lines >> by me=== >> >> <!-- ajax starts here! --> >> >> <script language="JavaScript" type="text/javascript"> >> /* <![CDATA[ */ >> var http_req = false; >> var dateorig; >> var nretries = 0; >> >> >> // All-purpose wrapper for XMLHttpRequest call >> // if parameters=="GET" or "HEAD" request is GET/HEAD; otherwise >> POST >> function executeXHR(callback, url, parameters) { >> http_req = false; >> >> // branch for native XMLHttpRequest object >> if (window.XMLHttpRequest) { >> http_req = new XMLHttpRequest(); >> } // branch for IE/Windows ActiveX version >> else if (window.ActiveXObject) { >> try { >> http_req = new ActiveXObject("Msxml2.XMLHTTP"); >> } catch (e) { >> try { >> http_req = new ActiveXObject("Microsoft.XMLHTTP"); >> } catch (e) {} >> } >> } >> >> // warn if we cannot create this object >> if (!http_req) { >> document.getElementById('msgs').innerHTML = '-- Could not create >> XMLHttpRequest request object.<br/>'; >> return false; >> } >> >> http_req.onreadystatechange = callback; >> if (parameters=="GET" || parameters=="HEAD") { >> http_req.open(parameters, url, true); >> http_req.send(null); >> } >> else { >> http_req.open("POST", url, true); >> http_req.setRequestHeader("Content-type", >> "application/x-www-form-urlencoded"); >> http_req.setRequestHeader("Content-length", parameters.length); >> http_req.setRequestHeader("Connection", "close"); >> http_req.send(parameters); >> } >> } >> >> >> // Retrieve file info >> function getFileHeader() { >> var url = "__webserverAccessableFileName__"; >> var callback = processHeadRequest; >> executeXHR(callback, url, "HEAD"); >> } >> >> >> // response handler >> function processHeadRequest() { >> var t; >> // only if req shows "loaded" >> if (http_req.readyState == 4) { >> // only if "OK" >> if (http_req.status == 200) { >> >> var lastupdate = http_req.getResponseHeader("Last-Modified"); >> >> if (!lastupdate) { >> document.getElementById('messages').style.display = "block"; >> document.getElementById('msgs').innerHTML = "<b>Error requesting >> xml file information from webserver:</b><br/>"; >> document.getElementById('msgs').innerHTML += "<textarea rows='8' >> cols='90'>"+http_req.responseText +"</textarea>"; >> nretries++; >> } >> >> else if (!dateorig) { >> // first time >> dateorig = lastupdate; >> } >> >> else if (dateorig != lastupdate) { >> // warn user to refresh page >> document.getElementById('messages').style.display = "block"; >> document.getElementById('msgs').innerHTML = "<b>WARNING: This >> file has changed on disk!</b><br/>"; >> document.getElementById('msgs').innerHTML += "First update occurred >> at: "; >> document.getElementById('msgs').innerHTML += lastupdate; >> document.getElementById('msgs').innerHTML += "<br/>"; >> document.getElementById('msgs').innerHTML += "Please <b>Refresh</b> >> this page to ensure you are viewing current data<br/>"; >> nretries=5; // stop refreshing >> } >> >> } else { >> document.getElementById('messages').style.display = "block"; >> document.getElementById('msgs').innerHTML = "<b>Unable to access >> xml file via webserver, so cannot check xml file for changes (" + >> http_req.responseText + ")</b>"; >> document.getElementById('msgs').innerHTML += "<br/>Check webserver >> configuration if desired."; >> document.getElementById('msgs').innerHTML += "<br/>(URL: " + >> http_req.url + ")"; >> document.getElementById('msgs').innerHTML += "<br/>(dateorig: " + >> dateorig + ")"; >> document.getElementById('msgs').innerHTML += "<br/>(lastupdate: " + >> lastupdate + ")"; >> nretries++; >> } >> >> ==========Additional Debug Info Ends========== >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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