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]> 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]. > To post to this group, send email to [email protected]. > 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. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
