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-rw-r--r--wqflask/base/webqtlConfig.py2
-rw-r--r--wqflask/maintenance/gen_select_dataset.py2
-rw-r--r--wqflask/utility/tools.py40
-rw-r--r--wqflask/wqflask/database.py2
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py2
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py15
-rw-r--r--wqflask/wqflask/static/new/css/corr_scatter_plot2.css39
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json284
-rw-r--r--wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js122
-rw-r--r--wqflask/wqflask/templates/base.html2
-rw-r--r--wqflask/wqflask/templates/corr_scatterplot.html26
-rw-r--r--wqflask/wqflask/templates/error.html4
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html2
-rw-r--r--wqflask/wqflask/templates/show_trait.html1
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics.html5
-rw-r--r--wqflask/wqflask/user_manager.py26
-rw-r--r--wqflask/wqflask/views.py7
17 files changed, 399 insertions, 182 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 1e47e183..e5f10edf 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -65,7 +65,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp
# want to reach this base dir
assert_writable_dir(TEMPDIR)
-TMPDIR = mk_dir(TEMPDIR+'gn2')
+TMPDIR = mk_dir(TEMPDIR+'/gn2/')
assert_writable_dir(TMPDIR)
CACHEDIR = mk_dir(TMPDIR+'/cache/')
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index e5726656..a5fd86e2 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -57,7 +57,7 @@ import urlparse
from pprint import pformat as pf
-#Engine = sa.create_engine(zach_settings.SQLALCHEMY_DATABASE_URI)
+#Engine = sa.create_engine(zach_settings.SQL_URI)
# build MySql database connection
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index c28c617a..393ff2df 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -13,6 +13,11 @@ logger = logging.getLogger(__name__ )
OVERRIDES = {}
+def app_set(command_id, value):
+ """Set application wide value"""
+ app.config.setdefault(command_id,value)
+ value
+
def get_setting(command_id,guess=None):
"""Resolve a setting from the environment or the global settings in
app.config, with valid_path is a function checking whether the
@@ -40,6 +45,7 @@ def get_setting(command_id,guess=None):
def value(command):
if command:
# sys.stderr.write("Found "+command+"\n")
+ app_set(command_id,command)
return command
else:
return None
@@ -89,6 +95,18 @@ def valid_path(dir):
return dir
return None
+def js_path(module=None):
+ """
+ Find the JS module in the two paths
+ """
+ try_gn = get_setting("JS_GN_PATH")+"/"+module
+ if valid_path(try_gn):
+ return try_gn
+ try_guix = get_setting("JS_GUIX_PATH")+"/"+module
+ if valid_path(try_guix):
+ return try_guix
+ raise "No JS path found for "+module+" (check JS_GN_PATH)"
+
def pylmm_command(guess=None):
return valid_bin(get_setting("PYLMM_COMMAND",guess))
@@ -205,21 +223,27 @@ SQL_URI = get_setting('SQL_URI')
LOG_LEVEL = get_setting('LOG_LEVEL')
LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG')
LOG_SQL = get_setting_bool('LOG_SQL')
-LOG_SQLALCHEMY = get_setting_bool('LOG_SQLALCHEMY')
+LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY')
LOG_BENCH = get_setting_bool('LOG_BENCH')
LOG_FORMAT = "%(message)s" # not yet in use
USE_REDIS = get_setting_bool('USE_REDIS')
USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
-TEMP_TRAITS = get_setting('TEMP_TRAITS')
-
-PYLMM_COMMAND = pylmm_command()
-GEMMA_COMMAND = gemma_command()
-GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH')
-PLINK_COMMAND = plink_command()
+JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
+# assert_dir(JS_GUIX_PATH) - don't enforce right now
+JS_GN_PATH = get_setting('JS_GN_PATH')
+# assert_dir(JS_GN_PATH)
+
+PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command())
+GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
+PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
TEMPDIR = tempdir() # defaults to UNIX TMPDIR
+# ---- Handle specific JS modules
+JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))
+assert_dir(JS_TWITTER_POST_FETCHER_PATH)
+
from six import string_types
if os.environ.get('WQFLASK_OVERRIDES'):
@@ -234,5 +258,3 @@ if os.environ.get('WQFLASK_OVERRIDES'):
else:
OVERRIDES[k] = cmd
logger.debug(OVERRIDES)
-
-assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH"))
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index 4df872ad..96c2c301 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -22,8 +22,8 @@ def init_db():
# they will be registered properly on the metadata. Otherwise
# you will have to import them first before calling init_db()
#import yourapplication.models
+ logger.info("Initializing database connection")
import wqflask.model
- logger.debug("Creating all model metadata")
Base.metadata.create_all(bind=engine)
logger.info("Done creating all model metadata")
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 87532445..8882c515 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -37,7 +37,7 @@ from utility import temp_data
from utility.benchmark import Bench
from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
-from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, GEMMA_RESULTS_PATH, PLINK_COMMAND, TEMPDIR
+from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
from utility.external import shell
from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 49959a74..82a44796 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1018,7 +1018,7 @@ class MarkerRegression(object):
else:
if self.selectedChr > -1:
for i, qtlresult in enumerate(self.qtlresults):
- if qtlresult['Chr'] != self.selectedChr:
+ if qtlresult['chr'] != self.selectedChr:
continue
if i==0 and qtlresult['Mb'] >= Mb:
@@ -1027,7 +1027,7 @@ class MarkerRegression(object):
#the trait's position is between two traits
if i > 0 and self.qtlresults[i-1]['Mb'] < Mb and qtlresult['Mb'] >= Mb:
- locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['cM']+(qtlresult['cM']-self.qtlresults[i-1]['cM'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
+ locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['Mb']+(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
break
#the trait's position is on the right of the last genotype
@@ -1036,11 +1036,12 @@ class MarkerRegression(object):
else:
locPixel = xLeftOffset
for i, _chr in enumerate(self.ChrList):
- if _chr != Chr:
- locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
- else:
- locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
- break
+ if i < (len(self.ChrList)-1):
+ if _chr != Chr:
+ locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+ else:
+ locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
+ break
if locPixel >= 0 and self.plotScale == 'physic':
traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12))
canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
diff --git a/wqflask/wqflask/static/new/css/corr_scatter_plot2.css b/wqflask/wqflask/static/new/css/corr_scatter_plot2.css
index 92e777c2..5aa9b9bf 100644
--- a/wqflask/wqflask/static/new/css/corr_scatter_plot2.css
+++ b/wqflask/wqflask/static/new/css/corr_scatter_plot2.css
@@ -1,19 +1,40 @@
.nvd3 .nv-axis.nv-x text {
- font-size: 16px;
- font-weight: normal;
- fill: black;
+ font-size: 16px;
+ font-weight: normal;
+ fill: black;
}
.nvd3 .nv-axis.nv-y text {
- font-size: 16px;
- font-weight: normal;
- fill: black;
+ font-size: 16px;
+ font-weight: normal;
+ fill:black;
}
-.nv-y .tick.zero line {
- stroke: black;
+.nv-x .nv-axis g path.domain {
+ stroke: black;
+ stroke-width: 2;
}
.nv-y .nv-axis g path.domain {
- stroke: black;
+ stroke: black;
+ stroke-width: 2;
+}
+
+.nvd3 .nv-axis.nv-x path.domain {
+ stroke-opacity: 1;
+}
+
+.nvd3 .nv-axis.nv-y path.domain {
+ stroke-opacity: 1;
+}
+
+line.nv-regLine {
+ stroke: red !important;
+}
+
+.nv-axisMin-x,
+.nv-axisMax-x,
+.nv-axisMin-y,
+.nv-axisMax-y {
+ display: none;
}
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 861af3d6..f3712b5d 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1340,14 +1340,14 @@
"GSE9588 Human Liver Normal (Mar11) Both Sexes"
],
[
- "384",
- "HLCF_0311",
- "GSE9588 Human Liver Normal (Mar11) Females"
- ],
- [
"383",
"HLCM_0311",
"GSE9588 Human Liver Normal (Mar11) Males"
+ ],
+ [
+ "384",
+ "HLCF_0311",
+ "GSE9588 Human Liver Normal (Mar11) Females"
]
],
"Phenotypes": [
@@ -1493,6 +1493,15 @@
]
]
},
+ "Islets-Gerling": {
+ "Phenotypes": [
+ [
+ "None",
+ "Islets-GerlingPublish",
+ "Islets-Gerling Published Phenotypes"
+ ]
+ ]
+ },
"TIGEM-Retina-RNA-Seq": {
"Phenotypes": [
[
@@ -1561,6 +1570,11 @@
],
"Heart mRNA": [
[
+ "820",
+ "UCLA_AXB_BXA_Aor_Jan16",
+ "UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) RMA"
+ ],
+ [
"421",
"IRCM_AXBXA_HRI0213",
"IRCM AXB/BXA Mouse Heart ILM MouseRef-8 v2.0 (Feb13) RankInv"
@@ -1568,6 +1582,11 @@
],
"Liver mRNA": [
[
+ "822",
+ "UCLA_AXB_BXA_Liv_Jan16",
+ "UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA"
+ ],
+ [
"352",
"GSE16780AB_UCLA_ML0911",
"GSE16780 UCLA Mouse AXB/BXA Liver Affy HT M430A (Sep11) RMA"
@@ -1727,11 +1746,6 @@
],
"Striatum mRNA": [
[
- "85",
- "SA_M2_0905_P",
- "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
- ],
- [
"84",
"SA_M2_0905_R",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
@@ -1740,22 +1754,27 @@
"83",
"SA_M2_0905_M",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
+ ],
+ [
+ "85",
+ "SA_M2_0905_P",
+ "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
]
]
},
"BHF2": {
"Adipose mRNA": [
[
- "197",
- "UCLA_BHF2_ADIPOSE_FEMALE",
- "UCLA BHF2 Adipose Female mlratio"
- ],
- [
"196",
"UCLA_BHF2_ADIPOSE_MALE",
"UCLA BHF2 Adipose Male mlratio"
],
[
+ "197",
+ "UCLA_BHF2_ADIPOSE_FEMALE",
+ "UCLA BHF2 Adipose Female mlratio"
+ ],
+ [
"165",
"UCLA_BHF2_ADIPOSE_0605",
"UCLA BHF2 Adipose (June05) mlratio"
@@ -1763,16 +1782,16 @@
],
"Brain mRNA": [
[
- "199",
- "UCLA_BHF2_BRAIN_FEMALE",
- "UCLA BHF2 Brain Female mlratio"
- ],
- [
"198",
"UCLA_BHF2_BRAIN_MALE",
"UCLA BHF2 Brain Male mlratio"
],
[
+ "199",
+ "UCLA_BHF2_BRAIN_FEMALE",
+ "UCLA BHF2 Brain Female mlratio"
+ ],
+ [
"166",
"UCLA_BHF2_BRAIN_0605",
"UCLA BHF2 Brain (June05) mlratio"
@@ -1787,16 +1806,16 @@
],
"Liver mRNA": [
[
- "201",
- "UCLA_BHF2_LIVER_FEMALE",
- "UCLA BHF2 Liver Female mlratio"
- ],
- [
"200",
"UCLA_BHF2_LIVER_MALE",
"UCLA BHF2 Liver Male mlratio"
],
[
+ "201",
+ "UCLA_BHF2_LIVER_FEMALE",
+ "UCLA BHF2 Liver Female mlratio"
+ ],
+ [
"167",
"UCLA_BHF2_LIVER_0605",
"UCLA BHF2 Liver (June05) mlratio"
@@ -2000,11 +2019,6 @@
"UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
],
[
- "81",
- "BR_U_0805_P",
- "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
- ],
- [
"80",
"BR_U_0805_M",
"UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
@@ -2015,6 +2029,11 @@
"UTHSC Brain mRNA U74Av2 (Aug05) RMA"
],
[
+ "81",
+ "BR_U_0805_P",
+ "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
+ ],
+ [
"42",
"CB_M_0204_P",
"INIA Brain mRNA M430 (Feb04) PDNN"
@@ -2142,6 +2161,13 @@
"BXD Genotypes"
]
],
+ "Heart mRNA": [
+ [
+ "819",
+ "UCLA_BXD_Aor_Jan16",
+ "UCLA BXD Aorta Affy M430 2.0 (Jan16) RMA"
+ ]
+ ],
"Hematopoietic Cells mRNA": [
[
"149",
@@ -2218,6 +2244,26 @@
"UMUTAffy Hippocampus Exon (Feb09) RMA"
],
[
+ "814",
+ "UTHSC_ILM_BXD_hipp_NOSb_0217",
+ "UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) RankInv"
+ ],
+ [
+ "815",
+ "UTHSC_ILM_BXD_hipp_NOEb_0217",
+ "UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) RankInv"
+ ],
+ [
+ "816",
+ "UTHSC_ILM_BXD_hipp_RSSb_0217",
+ "UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) RankInv"
+ ],
+ [
+ "817",
+ "UTHSC_ILM_BXD_hipp_RSEb_0217",
+ "UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) RankInv"
+ ],
+ [
"780",
"UTHSC_ILM_BXD_hipp_NOEb_0216",
"UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb16) RankInv"
@@ -2391,14 +2437,24 @@
],
"Liver Proteome": [
[
+ "540",
+ "EPFLETHZBXDprotCD0514",
+ "EPFL/ETHZ BXD Liver, Chow Diet (Jun16) Top100 SWATH"
+ ],
+ [
+ "541",
+ "EPFLETHZBXDprotHFD0514",
+ "EPFL/ETHZ BXD Liver, High Fat Diet (Jun16) Top100 SWATH"
+ ],
+ [
"704",
"EPFLETHZBXDprotCD_LS1114",
- "EPFL/ETHZ BXD Liver, Chow Diet (Oct14) Light SWATH"
+ "EPFL/ETHZ BXD Liver, Chow Diet (Oct14) Top10 SWATH"
],
[
"705",
"EPFLETHZBXDprotHF_LS1114",
- "EPFL/ETHZ BXD Liver, High Fat Diet (Oct14) Light SWATH"
+ "EPFL/ETHZ BXD Liver, High Fat Diet Diet (Oct14) Top10 SWATH"
],
[
"703",
@@ -2414,20 +2470,15 @@
"489",
"EPFLBXDprotHFDRPN0214",
"EPFL/LISP BXD Liver, Soluble Proteins HFD (Feb14) SRM"
- ],
- [
- "540",
- "EPFLETHZBXDprotCD0514",
- "EPFL/ETHZ BXD Liver, Soluble Proteins CD (Jun14) SWATH"
- ],
- [
- "541",
- "EPFLETHZBXDprotHFD0514",
- "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (Jun14) SWATH"
]
],
"Liver mRNA": [
[
+ "818",
+ "UCLA_BXD_Liv_Jan16",
+ "UCLA BXD Liver Affy M430 2.0 (Jan16) RMA"
+ ],
+ [
"430",
"EPFLMouseLiverRMA0413",
"EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
@@ -2443,6 +2494,11 @@
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
],
[
+ "433",
+ "EPFLMouseLiverBothExRMA0413",
+ "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+ ],
+ [
"700",
"UTHSC-VGX_MmBXDHepatocytesRMA1014",
"UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA"
@@ -2466,6 +2522,51 @@
"702",
"SUH_Liv_RMAEx_0611",
"SUH BXD Liver CCl4-treated Affy Mouse Gene 1.0 ST Exon Level (Jun11) RMA"
+ ],
+ [
+ "256",
+ "GenEx_BXD_liverEt_M5_0912",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes"
+ ],
+ [
+ "257",
+ "GenEx_BXD_liverEt_M5M_0912",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Males"
+ ],
+ [
+ "258",
+ "GenEx_BXD_liverEt_M5F_0912",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females"
+ ],
+ [
+ "307",
+ "GenEx_BXD_liverEt_RMA_0211",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes"
+ ],
+ [
+ "308",
+ "GenEx_BXD_liverEt_RMA_M_0211",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males"
+ ],
+ [
+ "309",
+ "GenEx_BXD_liverEt_RMA_F_0211",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females"
+ ],
+ [
+ "310",
+ "GenEx_BXD_liverSal_RMA_0211",
+ "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes"
+ ],
+ [
+ "311",
+ "GenEx_BXD_liverSal_RMA_M_0211",
+ "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males"
+ ],
+ [
+ "312",
+ "GenEx_BXD_liverSal_RMA_F_0211",
+ "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females"
]
],
"Lung mRNA": [
@@ -2546,14 +2647,14 @@
"HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv"
],
[
- "275",
- "DevNeocortex_ILM6.2P14RInv_1110",
- "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
- ],
- [
"274",
"DevNeocortex_ILM6.2P3RInv_1110",
"BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
+ ],
+ [
+ "275",
+ "DevNeocortex_ILM6.2P14RInv_1110",
+ "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
]
],
"Nucleus Accumbens mRNA": [
@@ -2761,11 +2862,6 @@
],
"Ventral Tegmental Area mRNA": [
[
- "230",
- "VCUEtvsSal_0609_R",
- "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
- ],
- [
"229",
"VCUEtOH_0609_R",
"VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
@@ -2774,6 +2870,11 @@
"228",
"VCUSal_0609_R",
"VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
+ ],
+ [
+ "230",
+ "VCUEtvsSal_0609_R",
+ "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
]
]
},
@@ -2920,6 +3021,27 @@
]
]
},
+ "CIE-RMA": {
+ "Midbrain mRNA": [
+ [
+ "830",
+ "INIA_UTHSC_Mid_AffyMTA1_Apr17",
+ "INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) RMA"
+ ],
+ [
+ "834",
+ "INIA_UTHSC_Mid_AffyMTA1_Ex_May17",
+ "INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) RMA"
+ ]
+ ],
+ "Phenotypes": [
+ [
+ "None",
+ "CIE-RMAPublish",
+ "CIE-RMA Published Phenotypes"
+ ]
+ ]
+ },
"CMS": {
"Phenotypes": [
[
@@ -3021,6 +3143,13 @@
"CXB Genotypes"
]
],
+ "Heart mRNA": [
+ [
+ "821",
+ "UCLA_CXB_Aor_Jan16",
+ "UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA"
+ ]
+ ],
"Hippocampus mRNA": [
[
"100",
@@ -3033,6 +3162,13 @@
"Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
]
],
+ "Liver mRNA": [
+ [
+ "823",
+ "UCLA_CXB_Liv_Jan16",
+ "UCLA CXB Liver Affy M430 2.0 (Jan16) RMA"
+ ]
+ ],
"Phenotypes": [
[
"628",
@@ -3048,6 +3184,7 @@
]
]
},
+ "EMSR": {},
"HS": {
"Hippocampus mRNA": [
[
@@ -3545,6 +3682,10 @@
"Brain, Development: Normal Gene Expression (Yale/Sestan)"
],
[
+ "Islets-Gerling",
+ "Pancreatic: Islets (UTHSC/Gerling)"
+ ],
+ [
"TIGEM-Retina-RNA-Seq",
"Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)"
]
@@ -3616,7 +3757,11 @@
],
[
"CIE-INIA",
- "Chronic Intermittent Ethanol"
+ "Chronic Intermittent Ethanol Phase 1"
+ ],
+ [
+ "CIE-RMA",
+ "Chronic Intermittent Ethanol Phase 2"
],
[
"CMS",
@@ -3631,6 +3776,10 @@
"CXB"
],
[
+ "EMSR",
+ "Ethanol-Medicated Stress Reduction"
+ ],
+ [
"HS",
"Heterogeneous Stock"
],
@@ -4414,6 +4563,12 @@
"Ventrolateral Prefrontal Cortex mRNA"
]
],
+ "Islets-Gerling": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ]
+ ],
"TIGEM-Retina-RNA-Seq": [
[
"Phenotypes",
@@ -4630,6 +4785,10 @@
"Gastrointestinal mRNA"
],
[
+ "Heart mRNA",
+ "Heart mRNA"
+ ],
+ [
"Hematopoietic Cells mRNA",
"Hematopoietic Cells mRNA"
],
@@ -4780,6 +4939,16 @@
"LCM Brain Regions mRNA"
]
],
+ "CIE-RMA": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ],
+ [
+ "Midbrain mRNA",
+ "Midbrain mRNA"
+ ]
+ ],
"CMS": [
[
"Phenotypes",
@@ -4822,14 +4991,23 @@
"Genotypes"
],
[
+ "Heart mRNA",
+ "Heart mRNA"
+ ],
+ [
"Hippocampus mRNA",
"Hippocampus mRNA"
],
[
+ "Liver mRNA",
+ "Liver mRNA"
+ ],
+ [
"Spleen mRNA",
"Spleen mRNA"
]
],
+ "EMSR": [],
"HS": [
[
"Phenotypes",
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
index 7a5a86bd..96763aca 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
@@ -1,74 +1,64 @@
var chart;
nv.addGraph(function() {
- //
- chart = nv.models.scatterChart();
- //
- chart.showLegend(false);
- chart.duration(300);
- chart.color(d3.scale.category10().range());
- chart.pointRange([200,0]);
- //
- // chart.showDistX(true);
- // chart.showDistY(true);
- chart.xAxis.tickFormat(d3.format('.02f'));
- chart.yAxis.tickFormat(d3.format('.02f'));
- // chart.showXAxis(false);
- // chart.showYAxis(false);
- chart.xAxis.axisLabel(js_data.trait_1);
- chart.yAxis.axisLabel(js_data.trait_2);
- //
- xmin = d3.min(js_data.data[0]);
- xmax = d3.max(js_data.data[0]);
- xrange = xmax - xmin;
- ymin = d3.min(js_data.data[1]);
- ymax = d3.max(js_data.data[1]);
- yrange = ymax - ymin;
- chart.xDomain([xmin - xrange/10, xmax + xrange/10]);
- chart.yDomain([ymin - yrange/10, ymax + yrange/10]);
- //
- d3.select('#scatterplot2 svg').datum(nv.log(getdata())).call(chart);
- nv.utils.windowResize(chart.update);
- return chart;
+ //
+ chart = nv.models.scatterChart();
+ //
+ chart.showLegend(false);
+ chart.duration(300);
+ chart.color(d3.scale.category10().range());
+ chart.pointRange([200,0]);
+ //
+ chart.xAxis.axisLabel(js_data.trait_1);
+ chart.xAxis.axisLabelDistance(11);
+ chart.yAxis.axisLabel(js_data.trait_2);
+ chart.yAxis.axisLabelDistance(11);
+ //
+ xmin = d3.min(js_data.data[0]);
+ xmax = d3.max(js_data.data[0]);
+ xrange = xmax - xmin;
+ ymin = d3.min(js_data.data[1]);
+ ymax = d3.max(js_data.data[1]);
+ yrange = ymax - ymin;
+ chart.xDomain([xmin - xrange/10, xmax + xrange/10]);
+ chart.yDomain([ymin - yrange/10, ymax + yrange/10]);
+ chart.xAxis.tickFormat(d3.format(checkformat(xrange)));
+ chart.yAxis.tickFormat(d3.format(checkformat(yrange)));
+ //
+ chart.tooltip.contentGenerator(function (obj) {
+ return '<b style="font-size: 18px">(' + obj.point.x + ', ' + obj.point.y + ')</b>';
+ });
+ //
+ d3.select('#scatterplot2 svg').datum(nv.log(getdata())).call(chart);
+ nv.utils.windowResize(chart.update);
+ return chart;
});
function getdata () {
- var data = [];
- data.push({
- values: [],
- slope: js_data.slope,
- intercept: js_data.intercept
- });
- for (j = 0; j < js_data.data[0].length; j++) {
- data[0].values.push({
- x: js_data.data[0][j],
- y: js_data.data[1][j],
- size: 10,
- shape: 'circle'
- });
- }
- return data;
+ var data = [];
+ data.push({
+ values: [],
+ slope: js_data.slope,
+ intercept: js_data.intercept
+ });
+ for (j = 0; j < js_data.data[0].length; j++) {
+ data[0].values.push({
+ x: js_data.data[0][j],
+ y: js_data.data[1][j],
+ size: 10,
+ shape: 'circle'
+ });
+ }
+ return data;
}
-
-function randomData(groups, points) {
- var data = [],
- shapes = ['circle'],
- random = d3.random.normal();
- for (i = 0; i < groups; i++) {
- data.push({
- key: 'Group ' + i,
- values: [],
- slope: Math.random() - .01,
- intercept: Math.random() - .5
- });
- for (j = 0; j < points; j++) {
- data[i].values.push({
- x: random(),
- y: random(),
- size: Math.random(),
- shape: shapes[j % shapes.length]
- });
- }
- }
- return data;
+
+function checkformat (range) {
+ cell = range / 10.0;
+ if (cell >= 1) {
+ return ",r";
+ } else {
+ cell = -Math.log(cell);
+ n = cell.toString().split(".")[0].length;
+ return ",.0" + n + "f";
+ }
}
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ec55ebeb..9ca3d63a 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -144,7 +144,7 @@
<p>
Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <a href="https://webchat.freenode.net/">IRC</a> (#genenetwork channel).
{% if version: %}
- <p><small>GeneNetwork v{{ version }}</small></p>
+ <p><small>GeneNetwork {{ version }}</small></p>
{% endif %}
</div>
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 4464025e..05891c95 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -53,16 +53,6 @@
<h2>Correlation Scatterplot</h2>
-<table class="table">
- <tbody>
- <tr><th class="text-right">num overlap</th> <td>{{jsdata.num_overlap}}</td></tr>
- <tr><th class="text-right">slope</th> <td>{{jsdata.slope}}</td></tr>
- <tr><th class="text-right">intercept</th> <td>{{jsdata.intercept}}</td></tr>
- <tr><th class="text-right">r value</th> <td>{{jsdata.r_value}}</td></tr>
- <tr><th class="text-right">p value</th> <td>{{jsdata.p_value}}</td></tr>
- </tbody>
-</table>
-
<!--
<table class="table">
<tr>
@@ -85,12 +75,12 @@
-->
<div id="scatterplot2">
- <svg style="width: 1000px; height: 800px;"></svg>
+ <svg style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
</div>
<br>
-<div style="margin-left: 75px;">
+<div style="margin-left: 80px;">
{% if trait_1.dataset.type == "ProbeSet" %}
<div>
@@ -144,6 +134,18 @@
</div>
+<br>
+
+<table class="table table-hover table-striped table-bordered" style="width: 250px; margin-left: 80px;">
+ <tbody>
+ <tr><th>Number</th> <td>{{jsdata.num_overlap}}</td></tr>
+ <tr><th>Slope</th> <td>{{'%0.3f' % jsdata.slope}}</td></tr>
+ <tr><th>Intercept</th> <td>{{'%0.3f' % jsdata.intercept}}</td></tr>
+ <tr><th>R value</th> <td>{{'%0.3f' % jsdata.r_value}}</td></tr>
+ <tr><th>P value</th> <td>{{'%0.3e' % jsdata.p_value}}</td></tr>
+ </tbody>
+</table>
+
{% endblock %}
{% block js %}
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
index c707a4fc..2f1e06fa 100644
--- a/wqflask/wqflask/templates/error.html
+++ b/wqflask/wqflask/templates/error.html
@@ -35,7 +35,7 @@
</p>
<pre>
- GeneNetwork v{{ version }} {{ stack[0] }}
+ GeneNetwork {{ version }} {{ stack[0] }}
{{ message }} (error)
{{ stack[-3] }}
{{ stack[-2] }}
@@ -50,7 +50,7 @@
<a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a>
<div id="Stack" class="collapse">
<pre>
- GeneNetwork v{{ version }} {% for line in stack %} {{ line }}
+ GeneNetwork {{ version }} {% for line in stack %} {{ line }}
{% endfor %}
</pre>
</div>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 4cea51b2..65debd10 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -14,7 +14,7 @@
<input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
<input type="hidden" name="trait_id" value="{{ this_trait.name }}">
<input type="hidden" name="dataset" value="{{ dataset.name }}">
- {% if mapping_method == "reaper" %}
+ {% if mapping_method == "reaper" or mapping_method == "rqtl_geno" %}
<input type="hidden" name="genofile" value="{{ dataset.group.genofile }}">
{% endif %}
<input type="hidden" name="method" value="{{ mapping_method }}">
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 56b6cc62..5a880647 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -129,6 +129,7 @@
<script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
+ <script type="text/javascript" src="/static/new/js_external/saveSvgAsPng.js"></script>
<script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 0a0e9990..ac44b656 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -94,12 +94,15 @@
<div class="tab-pane" id="probability_plot">
<div style="padding: 20px" class="form-horizontal">
{% if sample_groups|length != 1 %}
+ Select Group:
<select class="prob_plot_samples_group">
{% for group, pretty_group in sample_group_types.items() %}
<option value="{{ group }}">{{ pretty_group }}</option>
{% endfor %}
</select>
- <br><br>
+ <button type="button" class="btn btn-default" id="down_prob_plot">Export as PNG</button>
+ <br>
+ <br>
{% endif %}
<div id="prob_plot_container">
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 1e831896..f7fcd2d0 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -46,7 +46,7 @@ from wqflask.database import db_session
from wqflask import model
from utility import Bunch, Struct, after
-from utility.tools import LOG_SQL, LOG_SQLALCHEMY
+from utility.tools import LOG_SQL, LOG_SQL_ALCHEMY
import logging
from utility.logger import getLogger
@@ -69,7 +69,7 @@ class AnonUser(object):
if self.cookie:
logger.debug("already is cookie")
self.anon_id = verify_cookie(self.cookie)
-
+
else:
logger.debug("creating new cookie")
self.anon_id, self.cookie = create_signed_cookie()
@@ -78,17 +78,17 @@ class AnonUser(object):
@after.after_this_request
def set_cookie(response):
response.set_cookie(self.cookie_name, self.cookie)
-
+
def add_collection(self, new_collection):
collection_dict = dict(name = new_collection.name,
created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
num_members = new_collection.num_members,
members = new_collection.get_members())
-
+
Redis.set(self.key, json.dumps(collection_dict))
Redis.expire(self.key, 60 * 60 * 24 * 5)
-
+
def delete_collection(self, collection_name):
existing_collections = self.get_collections()
updated_collections = []
@@ -106,7 +106,7 @@ class AnonUser(object):
updated_collections.append(this_collection)
Redis.set(self.key, json.dumps(updated_collections))
-
+
def get_collections(self):
json_collections = Redis.get(self.key)
if json_collections == None or json_collections == "None":
@@ -117,7 +117,7 @@ class AnonUser(object):
collection['created_timestamp'] = datetime.datetime.strptime(collection['created_timestamp'], '%b %d %Y %I:%M%p')
collection['changed_timestamp'] = datetime.datetime.strptime(collection['changed_timestamp'], '%b %d %Y %I:%M%p')
return collections
-
+
def import_traits_to_user(self):
collections_list = json.loads(Redis.get(self.key))
for collection in collections_list:
@@ -131,7 +131,7 @@ class AnonUser(object):
uc.members = json.dumps(collection['members'])
db_session.add(uc)
db_session.commit()
-
+
def display_num_collections(self):
"""
Returns the number of collections or a blank string if there are zero.
@@ -217,7 +217,7 @@ class UserSession(object):
"""Actual sqlalchemy record"""
# Only look it up once if needed, then store it
try:
- if LOG_SQLALCHEMY:
+ if LOG_SQL_ALCHEMY:
logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
# Already did this before
@@ -237,7 +237,7 @@ class UserSession(object):
def before_request():
g.user_session = UserSession()
g.cookie_session = AnonUser()
-
+
class UsersManager(object):
def __init__(self):
self.users = model.User.query.all()
@@ -541,9 +541,9 @@ class LoginUser(object):
import_col = "true"
else:
import_col = "false"
-
- #g.cookie_session.import_traits_to_user()
-
+
+ #g.cookie_session.import_traits_to_user()
+
return self.actual_login(user, import_collections=import_col)
else:
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 39f4a686..07151425 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -53,7 +53,7 @@ from wqflask.ctl import ctl_analysis
#from wqflask.trait_submission import submit_trait
from utility import temp_data
-from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION
+from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH
from utility.helper_functions import get_species_groups
from base import webqtlFormData
@@ -147,9 +147,8 @@ def tmp_page(img_path):
img_base64 = bytesarray )
@app.route("/twitter/<path:filename>")
-def bd_files(filename):
- bd_path = app.config['TWITTER_POST_FETCHER_JS_PATH']
- return send_from_directory(bd_path, filename)
+def twitter(filename):
+ return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename)
#@app.route("/data_sharing")
#def data_sharing_page():
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 19:34:27 +0000