diff options
| -rw-r--r-- | issues/genenetwork1/gn1-network-graph.gmi | 58 | ||||
| -rw-r--r-- | issues/genenetwork1/gn1-pairscan.gmi | 1 | ||||
| -rw-r--r-- | issues/genenetwork1/gn1-production-system-issues.gmi | 20 |
3 files changed, 76 insertions, 3 deletions
diff --git a/issues/genenetwork1/gn1-network-graph.gmi b/issues/genenetwork1/gn1-network-graph.gmi new file mode 100644 index 0000000..4011ecc --- /dev/null +++ b/issues/genenetwork1/gn1-network-graph.gmi @@ -0,0 +1,58 @@ +# Fix GN1 Network Graph + +Status: the network graph works on production. PDF output is empty, however. + +## Tags + +* bug +* in progress +* assigned: pjotrp, zachs +* kanban: pjotrp + +## Tracking + +To reproduce this bug: select a 'shopping basket' and click on network graph. No image is shown. + +We needed to revert on + +=> https://github.com/genenetwork/genenetwork1/commit/88a6cb549cc318a961325666aed06f3196a5475d Commenting out functionality + +Reverting on that code still won't show the image contained in + +``` +<img border="0" alt="the graph" src="/image/tmpzmtq88.gif" usemap="#webqtlGraph" /> +``` + +The interesting thing is that files exist for tmpzmtq88, including PDF, but no GIF. + +ripgrep has a useful subsetting command: + +```rg --color always --type py image|less -R ``` + +this got me to web/webqtl/networkGraph/networkGraphPageBody.py with + +``` +web/webqtl/networkGraph/networkGraphPageBody.py: def __init__(self, fd, matrix, traits, imageHtmlName, imageName, pdfName, nodes, +web/webqtl/networkGraph/networkGraphPageBody.py: a <a href="%s" class="normalsize" target="_blank">PDF file</a>.</p> ''' % (imageName, pdfName) +``` + +The PDF link works but is an empty page! So something is going wrong with generating this image in an earlier step. The page says it is using GraphViz +which brings up + +``` +web/webqtl/networkGraph/networkGraphPageBody.py +128: #Adds the html generated by graphviz that displays the graph itself +652: body += ''' <p>This graph took %s seconds to generate with the <a href="http://www.research.att.com/sw/tools/graphviz/" class="normalsize" target="_blank"> 653: GraphViz</a> visualization toolkit from <a href="http://www.research.att.com" class="normalsize" target="_blank">AT&T Research</a>.</p>''' % (round(totalTime, 2)) +``` + +So it uses graphviz, but we are not using a python module. There is a tool graphml2gv, but not used. This is used ```import networkGraphUtils```. Ah, I may have found it: + +``` +neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename) +``` + +hard coded bin path is wrong! And of course there are no checks there is any output in the first place :/. There are more local paths - and the good news is that these tools are in the GUIX profile already. + +=> Commit aa4048af0f633101f2e723d86b5e99590885f2df fixes the network graph + +Still, the PDF is empty. ps2pdf is used - but I think the ps file is missing. diff --git a/issues/genenetwork1/gn1-pairscan.gmi b/issues/genenetwork1/gn1-pairscan.gmi new file mode 100644 index 0000000..b99b603 --- /dev/null +++ b/issues/genenetwork1/gn1-pairscan.gmi @@ -0,0 +1 @@ +# GN1 Pairscan diff --git a/issues/genenetwork1/gn1-production-system-issues.gmi b/issues/genenetwork1/gn1-production-system-issues.gmi index 1dc06c3..c519357 100644 --- a/issues/genenetwork1/gn1-production-system-issues.gmi +++ b/issues/genenetwork1/gn1-production-system-issues.gmi @@ -1,12 +1,26 @@ # GN1 Production -# Description +We are facing a number of issues with GN1 running on production (tux01). This is the meta-index to track resolving them. -We are facing a number of issues with GN1 running on production (tux01). Here we track resolving them. +This list does not include stuff that needs to be ported to GN2(!). See the GN2 tracker for that. -# Tags +## Tags * critical bug * in progress * assigned: pjotrp, zachs, robw * kanban: pjotrp + +## List of outstanding issues + +(see also E-mail Rob 14 Sep 2021) + +* [ ] Fix annotating metadata - until we have GN2 alternative +=> ./gn1-network-graph.gmi [ ] Fix network graph (it does not display image) +=> ./gn1-pairscan.gmi [ ] Pairscan not working +* [ ] Fix annotation link +* [ ] Enable time machines +* [ ] Disable galaxy URL +* [ ] Disable EC2 URL +* [ ] Disable GN mailing list URL +* [ ] Disable all defunct URLs |