From b3c2253a99ff9495a0132f466df825340ddf367c Mon Sep 17 00:00:00 2001
From: GN2
Date: Wed, 5 Sep 2018 03:38:46 -0500
Subject: Production updates

---
 .DS_Store                                          | Bin 6148 -> 0 bytes
 .gitignore                                         |  14 ---
 bin/genenetwork2                                   |   2 +-
 .../new/javascript/dataset_menu_structure.json     |  95 ++++++++++++++++++---
 4 files changed, 85 insertions(+), 26 deletions(-)
 delete mode 100644 .DS_Store

diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
index d992942f..00000000
Binary files a/.DS_Store and /dev/null differ
diff --git a/.gitignore b/.gitignore
index 0006d9a8..0d20b648 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,15 +1 @@
-# gitignore
 *.pyc
-*.orig
-*.bak
-*.cross
-*~
-genotype_files/genotype/HSNIH_copy.geno
-web/new_genotypes/HSNIH.json
-wqflask/secure_server.py
-build/
-dist/
-*.egg-info/
-EGG-INFO/
-wqflask/output/*
-wqflask/wqflask/static/output/*
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index b3a8d8c2..006e87ba 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -210,7 +210,7 @@ if [ "$1" = '-gunicorn-prod' ] ; then
     echo PYTHONPATH=$PYTHONPATH
     if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
     PID=$TMPDIR/gunicorn.$USER.pid
-    cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi"
+    cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 6000 --max-requests 1000 --timeout 1200 wsgi"
     echo RUNNING gunicorn $cmd
     gunicorn $cmd
     exit $?
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 81185136..d61168eb 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -2590,11 +2590,41 @@
                ]
             ],
             "Liver mRNA": [
+               [
+                  "852",
+                  "NIA-AgBXD-Liv_HFD-0818",
+                  "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **"
+               ],
+               [
+                  "857",
+                  "EPFLMouseLiverCDHFDRMA0818",
+                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+               ],
+               [
+                  "859",
+                  "EPFLMouseLiverCDRMA0818",
+                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+               ],
+               [
+                  "851",
+                  "NIA-AgBXD-Liv_CDHFD-0818",
+                  "NIA Aging BXD CD+HFD Liver Affy Clariom S Gene Level (Aug18) RMA **"
+               ],
+               [
+                  "853",
+                  "NIA-AgBXD-Liv_CD-0818",
+                  "NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA **"
+               ],
                [
                   "818",
                   "UCLA_BXD_Liv_Jan16",
                   "UCLA BXD Liver Affy M430 2.0 (Jan16) RMA"
                ],
+               [
+                  "858",
+                  "EPFLMouseLiverHFDRMA0818",
+                  "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+               ],
                [
                   "430",
                   "EPFLMouseLiverRMA0413",
@@ -2610,6 +2640,11 @@
                   "EPFLMouseLiverCDRMA0413",
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
                ],
+               [
+                  "848",
+                  "EPFLMouseLiverHFCEx0413",
+                  "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
                [
                   "433",
                   "EPFLMouseLiverBothExRMA0413",
@@ -2620,11 +2655,6 @@
                   "EPFLMouseLiverCDEx0413",
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
                ],
-               [
-                  "848",
-                  "EPFLMouseLiverHFCEx0413",
-                  "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
-               ],
                [
                   "700",
                   "UTHSC-VGX_MmBXDHepatocytesRMA1014",
@@ -3034,17 +3064,17 @@
                [
                   "843",
                   "UTHSC-BXD-Harv_Liv-0118",
-                  "UTHSC BXD Harvested Liver RNA-Seq (Jan18) Log2 **"
-               ],
-               [
-                  "842",
-                  "UTHSC-BXD-Liv-0917",
-                  "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **"
+                  "UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 **"
                ],
                [
                   "850",
                   "UTHSC-BXD-Liv-0818",
                   "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA **"
+               ],
+               [
+                  "842",
+                  "UTHSC-BXD-Liv-0917",
+                  "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **"
                ]
             ],
             "Phenotypes": [
@@ -3658,12 +3688,43 @@
       },
       "rat": {
          "HSNIH-Palmer": {
+            "Hippocampus mRNA": [
+               [
+                  "862",
+                  "HSNIH-Rat-LHB-RSeq-0818",
+                  "HSNIH-Palmer Lateral Habenula RNA-Seq (Aug18) rlog"
+               ]
+            ],
+            "Nucleus Accumbens mRNA": [
+               [
+                  "860",
+                  "HSNIH-Rat-Acbc-RSeq-0818",
+                  "HSNIH-Palmer Nucleus Accumbens Core RNA-Seq (Aug18) rlog"
+               ]
+            ],
             "Phenotypes": [
                [
                   "652",
                   "HSNIH-PalmerPublish",
                   "HSNIH-Palmer Published Phenotypes"
                ]
+            ],
+            "Prefrontal Cortex mRNA": [
+               [
+                  "864",
+                  "HSNIH-Rat-VoLo-RSeq-0818",
+                  "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog"
+               ],
+               [
+                  "863",
+                  "HSNIH-Rat-PL-RSeq-0818",
+                  "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) rlog"
+               ],
+               [
+                  "861",
+                  "HSNIH-Rat-IL-RSeq-0818",
+                  "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog"
+               ]
             ]
          },
          "HSNIH-RGSMC": {
@@ -5410,6 +5471,18 @@
             [
                "Phenotypes",
                "Phenotypes"
+            ],
+            [
+               "Hippocampus mRNA",
+               "Hippocampus mRNA"
+            ],
+            [
+               "Nucleus Accumbens mRNA",
+               "Nucleus Accumbens mRNA"
+            ],
+            [
+               "Prefrontal Cortex mRNA",
+               "Prefrontal Cortex mRNA"
             ]
          ],
          "HSNIH-RGSMC": [
-- 
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