From 1a3a456eb7635337a966913f2e2e75c8a89bb92e Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Wed, 17 Jul 2013 23:06:32 +0000
Subject: Fixed gen_select_dataset.py Appended redis installation info to notes
---
misc/gn_installation_notes.txt | 40 +++++
wqflask/base/webqtlConfigLocal.py | 4 +-
wqflask/maintenance/gen_select_dataset.py | 2 +-
.../new/javascript/dataset_menu_structure.json | 176 ++++++++++-----------
4 files changed, 131 insertions(+), 91 deletions(-)
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
index 7545a5b8..913021db 100644
--- a/misc/gn_installation_notes.txt
+++ b/misc/gn_installation_notes.txt
@@ -181,6 +181,46 @@ ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key
============================================
+Installing redis server
+
+In the dls directory:
+$ wget http://redis.googlecode.com/files/redis-2.6.14.tar.gz
+$ tar xzf redis-2.6.14.tar.gz
+$ cd redis-2.6.14
+$ make
+
+Run redis (from inside redis-2.6.14 directory):
+src/redis-server
+
+For the rest of the installation instructions, refer to:
+http://redis.io/topics/quickstart
+
+To continue installation (from the README):
+
+In order to install Redis binaries into /usr/local/bin just use:
+
+ % make install
+
+Make install will just install binaries in your system, but will not configure
+init scripts and configuration files in the appropriate place. This is not
+needed if you want just to play a bit with Redis, but if you are installing
+it the proper way for a production system, we have a script doing this
+for Ubuntu and Debian systems:
+
+ % cd utils
+ % ./install_server
+
+The script will ask you a few questions and will setup everything you need
+to run Redis properly as a background daemon that will start again on
+system reboots.
+
+In the redis config file (/etc/redis/6379.conf) uncomment the following line:
+bind 127.0.0.1
+
+This is so only the local computer has access
+
+============================================
+
Using Yolk
Install Yolk:
diff --git a/wqflask/base/webqtlConfigLocal.py b/wqflask/base/webqtlConfigLocal.py
index abaeff93..cc53866b 100755
--- a/wqflask/base/webqtlConfigLocal.py
+++ b/wqflask/base/webqtlConfigLocal.py
@@ -5,12 +5,12 @@
MYSQL_SERVER = 'gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com'
DB_NAME = 'db_webqtl'
DB_USER = 'webqtl'
-DB_PASSWD = 'f2ZypIflRM'
+DB_PASSWD = 'zK150dVzyvclGY5aCzavcK'
MYSQL_UPDSERVER = 'gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com'
DB_UPDNAME = 'db_webqtl'
DB_UPDUSER = 'webqtl'
-DB_UPDPASSWD = 'f2ZypIflRM'
+DB_UPDPASSWD = 'zK150dVzyvclGY5aCzavcK'
GNROOT = '/home/zas1024/gene/'
ROOT_URL = 'http://50.16.251.170'
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 4c544192..b6bf5bfd 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -41,7 +41,6 @@ from pprint import pformat as pf
from base import webqtlConfig
-
# build MySql database connection
Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,
host=webqtlConfig.MYSQL_SERVER,
@@ -148,6 +147,7 @@ def build_datasets(species, group, type_name):
def main():
"""Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
+
species = get_species()
groups = get_groups(species)
types = get_types(groups)
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 88bdcb11..a4d88ab2 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -63,14 +63,14 @@
]
],
"Leaf": [
- [
- "B1LI0809M5",
- "Barley1 Leaf INOC TTKS (Aug09) MAS5"
- ],
[
"B1LI0809R",
"Barley1 Leaf INOC TTKS (Aug09) RMA"
],
+ [
+ "B1LI0809M5",
+ "Barley1 Leaf INOC TTKS (Aug09) MAS5"
+ ],
[
"B1MI0809M5",
"Barley1 Leaf MOCK TTKS (Aug09) MAS5"
@@ -113,13 +113,13 @@
"B30_K_1206_M",
"Barley1 Leaf MAS 5.0 SCRI (Dec06)"
],
- [
- "B30_K_1206_R",
- "Barley1 Leaf gcRMA SCRI (Dec06)"
- ],
[
"B30_K_1206_Rn",
"Barley1 Leaf gcRMAn SCRI (Dec06)"
+ ],
+ [
+ "B30_K_1206_R",
+ "Barley1 Leaf gcRMA SCRI (Dec06)"
]
],
"Phenotypes": [
@@ -211,14 +211,14 @@
},
"AD-cases-controls-Myers": {
"Brain": [
- [
- "GSE15222_F_N_RI_0409",
- "GSE15222 Human Brain Normal Myers (Apr09) RankInv"
- ],
[
"GSE15222_F_A_RI_0409",
"GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv"
],
+ [
+ "GSE15222_F_N_RI_0409",
+ "GSE15222 Human Brain Normal Myers (Apr09) RankInv"
+ ],
[
"GSE15222_F_RI_0409",
"GSE15222 Human Brain Myers (Apr09) RankInv"
@@ -547,13 +547,13 @@
"NCI_Agil_Mam_Tum_RMA_0409",
"NCI Mammary LMT miRNA v2 (Apr09) RMA"
],
- [
- "MA_M_0704_M",
- "NCI Mammary mRNA M430 (July04) MAS5"
- ],
[
"MA_M_0704_R",
"NCI Mammary mRNA M430 (July04) RMA"
+ ],
+ [
+ "MA_M_0704_M",
+ "NCI Mammary mRNA M430 (July04) MAS5"
]
],
"Phenotypes": [
@@ -597,13 +597,13 @@
]
],
"Liver": [
- [
- "LVF2_M_0704_M",
- "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
- ],
[
"LVF2_M_0704_R",
"(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
+ ],
+ [
+ "LVF2_M_0704_M",
+ "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
]
],
"Phenotypes": [
@@ -631,13 +631,13 @@
"BRF2_M_0304_P",
"OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
],
- [
- "BRF2_M_0304_M",
- "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
- ],
[
"BRF2_M_0304_R",
"OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
+ ],
+ [
+ "BRF2_M_0304_M",
+ "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
]
],
"Genotypes": [
@@ -727,6 +727,10 @@
]
],
"Striatum": [
+ [
+ "SA_M2_0905_R",
+ "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
+ ],
[
"SA_M2_0905_M",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
@@ -734,37 +738,33 @@
[
"SA_M2_0905_P",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
- ],
- [
- "SA_M2_0905_R",
- "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
]
]
},
"BHF2": {
"Adipose": [
- [
- "UCLA_BHF2_ADIPOSE_FEMALE",
- "UCLA BHF2 Adipose Female mlratio"
- ],
[
"UCLA_BHF2_ADIPOSE_MALE",
"UCLA BHF2 Adipose Male mlratio"
],
+ [
+ "UCLA_BHF2_ADIPOSE_FEMALE",
+ "UCLA BHF2 Adipose Female mlratio"
+ ],
[
"UCLA_BHF2_ADIPOSE_0605",
"UCLA BHF2 Adipose (June05) mlratio"
]
],
"Brain": [
- [
- "UCLA_BHF2_BRAIN_FEMALE",
- "UCLA BHF2 Brain Female mlratio"
- ],
[
"UCLA_BHF2_BRAIN_MALE",
"UCLA BHF2 Brain Male mlratio"
],
+ [
+ "UCLA_BHF2_BRAIN_FEMALE",
+ "UCLA BHF2 Brain Female mlratio"
+ ],
[
"UCLA_BHF2_BRAIN_0605",
"UCLA BHF2 Brain (June05) mlratio"
@@ -777,28 +777,28 @@
]
],
"Liver": [
- [
- "UCLA_BHF2_LIVER_FEMALE",
- "UCLA BHF2 Liver Female mlratio"
- ],
[
"UCLA_BHF2_LIVER_MALE",
"UCLA BHF2 Liver Male mlratio"
],
+ [
+ "UCLA_BHF2_LIVER_FEMALE",
+ "UCLA BHF2 Liver Female mlratio"
+ ],
[
"UCLA_BHF2_LIVER_0605",
"UCLA BHF2 Liver (June05) mlratio"
]
],
"Muscle": [
- [
- "UCLA_BHF2_MUSCLE_FEMALE",
- "UCLA BHF2 Muscle Female mlratio **"
- ],
[
"UCLA_BHF2_MUSCLE_MALE",
"UCLA BHF2 Muscle Male mlratio **"
],
+ [
+ "UCLA_BHF2_MUSCLE_FEMALE",
+ "UCLA BHF2 Muscle Female mlratio **"
+ ],
[
"UCLA_BHF2_MUSCLE_0605",
"UCLA BHF2 Muscle (June05) mlratio **"
@@ -923,6 +923,10 @@
"BR_U_1105_P",
"UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
],
+ [
+ "BR_U_0805_M",
+ "UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
+ ],
[
"BR_U_0805_R",
"UTHSC Brain mRNA U74Av2 (Aug05) RMA"
@@ -931,10 +935,6 @@
"BR_U_0805_P",
"UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
],
- [
- "BR_U_0805_M",
- "UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
- ],
[
"CB_M_0204_P",
"INIA Brain mRNA M430 (Feb04) PDNN"
@@ -955,6 +955,10 @@
]
],
"Cerebellum": [
+ [
+ "CB_M_1004_M",
+ "SJUT Cerebellum mRNA M430 (Oct04) MAS5"
+ ],
[
"CB_M_1004_R",
"SJUT Cerebellum mRNA M430 (Oct04) RMA"
@@ -963,10 +967,6 @@
"CB_M_1004_P",
"SJUT Cerebellum mRNA M430 (Oct04) PDNN"
],
- [
- "CB_M_1004_M",
- "SJUT Cerebellum mRNA M430 (Oct04) MAS5"
- ],
[
"CB_M_1003_M",
"SJUT Cerebellum mRNA M430 (Oct03) MAS5"
@@ -1131,13 +1131,13 @@
"MA_M2_0806_P",
"Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN"
],
- [
- "MA_M2_0706_R",
- "Mouse Kidney M430v2 (Jul06) RMA"
- ],
[
"MA_M2_0706_P",
"Mouse Kidney M430v2 (Jul06) PDNN"
+ ],
+ [
+ "MA_M2_0706_R",
+ "Mouse Kidney M430v2 (Jul06) RMA"
]
],
"Leucocytes": [
@@ -1155,6 +1155,10 @@
"GenEx_BXD_liverEt_M5_0912",
"GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes **"
],
+ [
+ "GenEx_BXD_liverSal_RMA_F_0211",
+ "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **"
+ ],
[
"GenEx_BXD_liverEt_M5F_0912",
"GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females **"
@@ -1163,10 +1167,6 @@
"GenEx_BXD_liverEt_M5M_0912",
"GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Males **"
],
- [
- "GenEx_BXD_liverSal_RMA_F_0211",
- "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **"
- ],
[
"GenEx_BXD_liverSal_RMA_M_0211",
"GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **"
@@ -1227,14 +1227,14 @@
]
],
"Neocortex": [
- [
- "DevNeocortex_ILM6.2P3RInv_1111",
- "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
- ],
[
"DevNeocortex_ILM6.2P14RInv_1111",
"BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
],
+ [
+ "DevNeocortex_ILM6.2P3RInv_1111",
+ "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
+ ],
[
"HQFNeoc_1210v2_RankInv",
"HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
@@ -1247,13 +1247,13 @@
"HQFNeoc_0208_RankInv",
"HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv"
],
- [
- "DevNeocortex_ILM6.2P14RInv_1110",
- "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
- ],
[
"DevNeocortex_ILM6.2P3RInv_1110",
"BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
+ ],
+ [
+ "DevNeocortex_ILM6.2P14RInv_1110",
+ "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
]
],
"Nucleus Accumbens": [
@@ -1293,6 +1293,10 @@
]
],
"Prefrontal Cortex": [
+ [
+ "VCUEtOH_1206_R",
+ "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA"
+ ],
[
"VCUSal_1206_R",
"VCU BXD PFC Sal M430 2.0 (Dec06) RMA"
@@ -1301,10 +1305,6 @@
"VCUSal_1006_R",
"VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore"
],
- [
- "VCUEtOH_1206_R",
- "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA"
- ],
[
"VCU_PF_Air_0111_R",
"VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **"
@@ -1447,6 +1447,10 @@
]
],
"Ventral Tegmental Area": [
+ [
+ "VCUEtOH_0609_R",
+ "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **"
+ ],
[
"VCUSal_0609_R",
"VCU BXD VTA Sal M430 2.0 (Jun09) RMA **"
@@ -1454,10 +1458,6 @@
[
"VCUEtvsSal_0609_R",
"VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **"
- ],
- [
- "VCUEtOH_0609_R",
- "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **"
]
]
},
@@ -1573,13 +1573,13 @@
]
],
"Hippocampus": [
- [
- "HC_M2CB_1205_P",
- "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
- ],
[
"HC_M2CB_1205_R",
"Hippocampus Consortium M430v2 CXB (Dec05) RMA"
+ ],
+ [
+ "HC_M2CB_1205_P",
+ "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
]
],
"Phenotypes": [
@@ -1711,6 +1711,10 @@
]
],
"Prefrontal Cortex": [
+ [
+ "VCUEtOH_0806_R",
+ "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **"
+ ],
[
"VCUSal_0806_R",
"VCU LXS PFC Sal M430A 2.0 (Aug06) RMA"
@@ -1718,10 +1722,6 @@
[
"VCUEt_vs_Sal_0806_R",
"VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **"
- ],
- [
- "VCUEtOH_0806_R",
- "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **"
]
]
},
@@ -1733,13 +1733,13 @@
]
],
"Hippocampus": [
- [
- "HC_M2_0606_MDP",
- "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
- ],
[
"UMUTAffyExon_0209_RMA_MDP",
"UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
+ ],
+ [
+ "HC_M2_0606_MDP",
+ "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
]
],
"Liver": [
--
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