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-rwxr-xr-xbin/test-website7
-rw-r--r--test/lib/NavigationTest.rb46
-rw-r--r--wqflask/base/trait.py2
-rwxr-xr-xwqflask/wqflask/static/new/javascript/dataset_menu_structure.json187
4 files changed, 196 insertions, 46 deletions
diff --git a/bin/test-website b/bin/test-website
index 24274713..aeab459b 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -25,6 +25,10 @@ opts = OptionParser.new do |o|
o.on('-l','--link-checker', 'Check for dead links') do
options[:link_checker] = true
end
+
+ o.on('-n','--navigation-test', 'Check for navigation test results') do
+ options[:navigation_test] = true
+ end
o.separator ""
o.on_tail('-h', '--help', 'display this help and exit') do
@@ -63,4 +67,7 @@ else
require 'main_web_functionality'
end
+if options[:navigation_test]
+ require 'NavigationTest'
+end
diff --git a/test/lib/NavigationTest.rb b/test/lib/NavigationTest.rb
new file mode 100644
index 00000000..26080d28
--- /dev/null
+++ b/test/lib/NavigationTest.rb
@@ -0,0 +1,46 @@
+# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions).
+
+class NavigationTest
+end
+
+describe NavigationTest do
+ before do
+ @agent = Mechanize.new
+ @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt'
+ end
+
+ describe NavigationTest do
+ it "pyLMM mapping tool selection" do
+ page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P')
+#Navigates to http://localhost:5003/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P and clicks respective buttons.
+ link = page.link_with(text: 'pyLMM')
+ page = link.click
+ puts page.uri
+ link = page.link_with(text: 'Compute')
+ page = link.click
+ puts page.uri
+ probe_link.uri.to_s.must_equal "/marker_regression"
+
+
+ end
+ end
+
+end
+
+describe NavigationTest do
+ it "R/qtl mapping tool selection" do
+ page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P')
+ link = page.link_with(text: 'R/qtl')
+ page = link.click
+ puts page.uri
+ form.field_with(:name => 'Methods').options[2].select
+ link = page.link_with(text: 'Compute')
+ page = link.click
+ puts page.uri
+ probe_link.uri.to_s.must_equal "/marker_regression"
+
+
+ end
+ end
+
+
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 6c5ca8b2..6b4fff20 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -329,7 +329,7 @@ class GeneralTrait(object):
#
# description = self.pre_publication_description
- if len(description) > 0:
+ if description:
self.description_display = description.strip()
else:
self.description_display = ""
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 2b16383f..12a30e84 100755
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1596,6 +1596,11 @@
"B6D2F2": {
"Brain mRNA": [
[
+ "76",
+ "BRF2_M_0805_M",
+ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
+ ],
+ [
"78",
"BRF2_M_0805_P",
"OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
@@ -1606,11 +1611,6 @@
"OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA"
],
[
- "76",
- "BRF2_M_0805_M",
- "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
- ],
- [
"33",
"BRF2_M_0304_P",
"OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
@@ -1846,6 +1846,18 @@
]
},
"BXD": {
+ "Adipose Proteome": [
+ [
+ "797",
+ "EPFL_AdiPro0416",
+ "EPFL/ETHZ BXD Brown Adipose, Total Tissue Proteome, Chow Diet (Apr16) Light SWATH **"
+ ],
+ [
+ "798",
+ "EPFL_AdiMitPro0416",
+ "EPFL/ETHZ BXD Brown Adipose, Isolated Mitochondria Proteome, Chow Diet (Apr16) Light SWATH **"
+ ]
+ ],
"Adipose mRNA": [
[
"469",
@@ -1916,21 +1928,21 @@
[
"414",
"UCLA_BXD-on_Femur_0113_RSN",
- "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v2.0 (Jan13) RSN"
+ "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v1.1 (Jan13) RSN"
]
],
"Brain mRNA": [
[
- "164",
- "UTHSC_BXD_WB_RNASeq1112",
- "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed"
- ],
- [
"590",
"UTHSC_BXD_WB_RNASeqtrim1_1112",
"UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed 1.0"
],
[
+ "164",
+ "UTHSC_BXD_WB_RNASeq1112",
+ "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed"
+ ],
+ [
"394",
"UTHSC_BXD_WB_RNASeqEx1112",
"UTHSC Mouse BXD Whole Brain RNA Sequence Exon Level (Nov12) RPKM"
@@ -1946,6 +1958,11 @@
"UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
],
[
+ "82",
+ "BR_U_0805_R",
+ "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
+ ],
+ [
"81",
"BR_U_0805_P",
"UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
@@ -1956,11 +1973,6 @@
"UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
],
[
- "82",
- "BR_U_0805_R",
- "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
- ],
- [
"42",
"CB_M_0204_P",
"INIA Brain mRNA M430 (Feb04) PDNN"
@@ -2027,6 +2039,11 @@
"Eye M430v2 WT Gpnmb (Sep08) RMA"
],
[
+ "278",
+ "Eye_M2_0908_R_MT",
+ "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
+ ],
+ [
"382",
"Eye_M2_0908_WTWT",
"Eye M430v2 WT WT (Sep08) RMA"
@@ -2037,11 +2054,6 @@
"Eye M430v2 WT Tyrp1 (Sep08) RMA"
],
[
- "278",
- "Eye_M2_0908_R_MT",
- "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
- ],
- [
"400",
"DBA2J-ONH-1212",
"Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA"
@@ -2557,29 +2569,29 @@
],
"Retina mRNA": [
[
+ "267",
+ "Illum_Retina_BXD_RankInv0410",
+ "Full HEI Retina Illumina V6.2 (Apr10) RankInv"
+ ],
+ [
+ "302",
+ "G2NEI_ILM_Retina_BXD_RI0410",
+ "HEI Retina Normal Illumina V6.2 (Apr10) RankInv"
+ ],
+ [
"709",
"DoDCMMRPRetMoGene2_0515",
- "DoD CDMRP Retina Affy MoGene 2.0 ST (May15) RMA Gene Level"
+ "DoD Retina Normal Affy MoGene 2.0 ST (May15) RMA Gene Level"
],
[
"710",
"DoDCMMRPRetMoGene2Ex_0515",
- "DoD CDMRP Retina Affy MoGene 2.0 ST (May15) RMA Exon Level"
+ "DoD Retina Normal Affy MoGene 2.0 ST (May15) RMA Exon Level"
],
[
"385",
"ONCRetILM6_0412",
"ONC HEI Retina (April 2012) RankInv"
- ],
- [
- "302",
- "G2NEI_ILM_Retina_BXD_RI0410",
- "Normal HEI Retina (April 2010) RankInv"
- ],
- [
- "267",
- "Illum_Retina_BXD_RankInv0410",
- "Full HEI Retina (April 2010) RankInv"
]
],
"Spleen mRNA": [
@@ -2704,6 +2716,23 @@
"RTC_1106_R",
"HZI Treg M430v2 (Feb11) RMA"
]
+ ],
+ "Ventral Tegmental Area mRNA": [
+ [
+ "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"
+ ],
+ [
+ "229",
+ "VCUEtOH_0609_R",
+ "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
+ ]
]
},
"BXH": {
@@ -2810,6 +2839,16 @@
"170",
"UCLA_CTB6B6CTF2_ADIPOSE_2005",
"UCLA CTB6/B6CTF2 Adipose (2005) mlratio"
+ ],
+ [
+ "189",
+ "UCLA_CTB6B6CTF2_ADIPOSE_FEMALE",
+ "UCLA CTB6B6CTF2 Adipose Female mlratio"
+ ],
+ [
+ "188",
+ "UCLA_CTB6B6CTF2_ADIPOSE_MALE",
+ "UCLA CTB6B6CTF2 Adipose Male mlratio"
]
],
"Brain mRNA": [
@@ -2841,6 +2880,16 @@
"172",
"UCLA_CTB6B6CTF2_LIVER_2005",
"UCLA CTB6/B6CTF2 Liver (2005) mlratio"
+ ],
+ [
+ "193",
+ "UCLA_CTB6B6CTF2_LIVER_FEMALE",
+ "UCLA CTB6B6CTF2 Liver Female mlratio"
+ ],
+ [
+ "192",
+ "UCLA_CTB6B6CTF2_LIVER_MALE",
+ "UCLA CTB6B6CTF2 Liver Male mlratio"
]
],
"Muscle mRNA": [
@@ -2848,6 +2897,16 @@
"173",
"UCLA_CTB6B6CTF2_MUSCLE_2005",
"UCLA CTB6/B6CTF2 Muscle (2005) mlratio"
+ ],
+ [
+ "195",
+ "UCLA_CTB6B6CTF2_MUSCLE_FEMALE",
+ "UCLA CTB6B6CTF2 Muscle Female mlratio"
+ ],
+ [
+ "194",
+ "UCLA_CTB6B6CTF2_MUSCLE_MALE",
+ "UCLA CTB6B6CTF2 Muscle Male mlratio"
]
],
"Phenotypes": [
@@ -2942,6 +3001,11 @@
],
"Hippocampus mRNA": [
[
+ "212",
+ "Illum_LXS_Hipp_RSE_1008",
+ "Hippocampus Illumina RSE (Oct08) RankInv beta"
+ ],
+ [
"214",
"Illum_LXS_Hipp_NOE_1008",
"Hippocampus Illumina NOE (Oct08) RankInv beta"
@@ -2962,11 +3026,6 @@
"Hippocampus Illumina NON (Oct08) RankInv beta"
],
[
- "212",
- "Illum_LXS_Hipp_RSE_1008",
- "Hippocampus Illumina RSE (Oct08) RankInv beta"
- ],
- [
"143",
"Illum_LXS_Hipp_loess0807",
"Hippocampus Illumina (Aug07) LOESS"
@@ -3130,16 +3189,32 @@
"Scripps-2013": {}
},
"rat": {
- "HSNIH": {
+ "HSNIH-Palmer": {
"Phenotypes": [
[
- "619",
- "HSNIHPublish",
- "HSNIH Published Phenotypes"
+ "None",
+ "HSNIH-PalmerPublish",
+ "HSNIH-Palmer Published Phenotypes"
+ ]
+ ]
+ },
+ "HSNIH-RGSMC": {
+ "Phenotypes": [
+ [
+ "None",
+ "HSNIH-RGSMCPublish",
+ "HSNIH-RGSMC Published Phenotypes"
]
]
},
"HXBBXH": {
+ "Adipose mRNA": [
+ [
+ "799",
+ "FGUCAS_BAdip0516",
+ "FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST (May16) log2 **"
+ ]
+ ],
"Adrenal Gland mRNA": [
[
"220",
@@ -3460,8 +3535,12 @@
],
"rat": [
[
- "HSNIH",
- "NIH Heterogeneous Stock"
+ "HSNIH-Palmer",
+ "NIH Heterogeneous Stock (Palmer)"
+ ],
+ [
+ "HSNIH-RGSMC",
+ "NIH Heterogeneous Stock (RGSMC 2013)"
],
[
"HXBBXH",
@@ -4351,6 +4430,10 @@
"Adipose mRNA"
],
[
+ "Adipose Proteome",
+ "Adipose Proteome"
+ ],
+ [
"Adrenal Gland mRNA",
"Adrenal Gland mRNA"
],
@@ -4465,6 +4548,10 @@
[
"T Cell (regulatory) mRNA",
"T Cell (regulatory) mRNA"
+ ],
+ [
+ "Ventral Tegmental Area mRNA",
+ "Ventral Tegmental Area mRNA"
]
],
"BXH": [
@@ -4656,7 +4743,13 @@
"Scripps-2013": []
},
"rat": {
- "HSNIH": [
+ "HSNIH-Palmer": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ]
+ ],
+ "HSNIH-RGSMC": [
[
"Phenotypes",
"Phenotypes"
@@ -4672,6 +4765,10 @@
"Genotypes"
],
[
+ "Adipose mRNA",
+ "Adipose mRNA"
+ ],
+ [
"Adrenal Gland mRNA",
"Adrenal Gland mRNA"
],
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 13:24:41 +0000