From 360b4a832bbadb84b698e48e9d16884e809ed0a4 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 15 Sep 2021 04:21:24 -0500
Subject: GN1 network graph issue

---
 issues/genenetwork1/gn1-network-graph.gmi          | 58 ++++++++++++++++++++++
 issues/genenetwork1/gn1-pairscan.gmi               |  1 +
 .../genenetwork1/gn1-production-system-issues.gmi  | 20 ++++++--
 3 files changed, 76 insertions(+), 3 deletions(-)
 create mode 100644 issues/genenetwork1/gn1-network-graph.gmi
 create mode 100644 issues/genenetwork1/gn1-pairscan.gmi

(limited to 'issues')

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&amp;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
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