Fixed appearance of several tables (search, mapping results, sample data)

Temporarily removed second sample table for CFW traits

Fixed location of global search bar to work with wider screens

2 files changed, 120 insertions, 105 deletions

diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 06586372..ad4d9419 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -117,14 +117,14 @@
                   "Barley1 Leaf MAS 5.0 SCRI (Dec06)"
                ],
                [
-                  "126",
-                  "B30_K_1206_Rn",
-                  "Barley1 Leaf gcRMAn SCRI (Dec06)"
-               ],
-               [
                   "125",
                   "B30_K_1206_R",
                   "Barley1 Leaf gcRMA SCRI (Dec06)"
+               ],
+               [
+                  "126",
+                  "B30_K_1206_Rn",
+                  "Barley1 Leaf gcRMAn SCRI (Dec06)"
                ]
             ],
             "Phenotypes": [
@@ -1340,14 +1340,14 @@
                   "GSE9588 Human Liver Normal (Mar11) Both Sexes"
                ],
                [
-                  "383",
-                  "HLCM_0311",
-                  "GSE9588 Human Liver Normal (Mar11) Males"
-               ],
-               [
                   "384",
                   "HLCF_0311",
                   "GSE9588 Human Liver Normal (Mar11) Females"
+               ],
+               [
+                  "383",
+                  "HLCM_0311",
+                  "GSE9588 Human Liver Normal (Mar11) Males"
                ]
             ],
             "Phenotypes": [
@@ -1526,14 +1526,14 @@
                   "NCI Mammary LMT miRNA v2 (Apr09) RMA"
                ],
                [
-                  "37",
-                  "MA_M_0704_R",
-                  "NCI Mammary mRNA M430 (July04) RMA"
-               ],
-               [
                   "36",
                   "MA_M_0704_M",
                   "NCI Mammary mRNA M430 (July04) MAS5"
+               ],
+               [
+                  "37",
+                  "MA_M_0704_R",
+                  "NCI Mammary mRNA M430 (July04) RMA"
                ]
             ]
          },
@@ -1591,14 +1591,14 @@
             ],
             "Liver mRNA": [
                [
-                  "39",
-                  "LVF2_M_0704_R",
-                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
-               ],
-               [
                   "38",
                   "LVF2_M_0704_M",
                   "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
+               ],
+               [
+                  "39",
+                  "LVF2_M_0704_R",
+                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
                ]
             ],
             "Phenotypes": [
@@ -1621,11 +1621,6 @@
          "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"
@@ -1636,19 +1631,24 @@
                   "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"
                ],
                [
-                  "32",
-                  "BRF2_M_0304_R",
-                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
-               ],
-               [
                   "31",
                   "BRF2_M_0304_M",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
+               ],
+               [
+                  "32",
+                  "BRF2_M_0304_R",
+                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
                ]
             ],
             "Genotypes": [
@@ -1727,11 +1727,6 @@
             ],
             "Striatum mRNA": [
                [
-                  "84",
-                  "SA_M2_0905_R",
-                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
-               ],
-               [
                   "83",
                   "SA_M2_0905_M",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
@@ -1740,22 +1735,27 @@
                   "85",
                   "SA_M2_0905_P",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
+               ],
+               [
+                  "84",
+                  "SA_M2_0905_R",
+                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
                ]
             ]
          },
          "BHF2": {
             "Adipose mRNA": [
                [
-                  "196",
-                  "UCLA_BHF2_ADIPOSE_MALE",
-                  "UCLA BHF2 Adipose Male mlratio"
-               ],
-               [
                   "197",
                   "UCLA_BHF2_ADIPOSE_FEMALE",
                   "UCLA BHF2 Adipose Female mlratio"
                ],
                [
+                  "196",
+                  "UCLA_BHF2_ADIPOSE_MALE",
+                  "UCLA BHF2 Adipose Male mlratio"
+               ],
+               [
                   "165",
                   "UCLA_BHF2_ADIPOSE_0605",
                   "UCLA BHF2 Adipose (June05) mlratio"
@@ -1763,16 +1763,16 @@
             ],
             "Brain mRNA": [
                [
-                  "198",
-                  "UCLA_BHF2_BRAIN_MALE",
-                  "UCLA BHF2 Brain Male mlratio"
-               ],
-               [
                   "199",
                   "UCLA_BHF2_BRAIN_FEMALE",
                   "UCLA BHF2 Brain Female mlratio"
                ],
                [
+                  "198",
+                  "UCLA_BHF2_BRAIN_MALE",
+                  "UCLA BHF2 Brain Male mlratio"
+               ],
+               [
                   "166",
                   "UCLA_BHF2_BRAIN_0605",
                   "UCLA BHF2 Brain (June05) mlratio"
@@ -1787,16 +1787,16 @@
             ],
             "Liver mRNA": [
                [
-                  "200",
-                  "UCLA_BHF2_LIVER_MALE",
-                  "UCLA BHF2 Liver Male mlratio"
-               ],
-               [
                   "201",
                   "UCLA_BHF2_LIVER_FEMALE",
                   "UCLA BHF2 Liver Female mlratio"
                ],
                [
+                  "200",
+                  "UCLA_BHF2_LIVER_MALE",
+                  "UCLA BHF2 Liver Male mlratio"
+               ],
+               [
                   "167",
                   "UCLA_BHF2_LIVER_0605",
                   "UCLA BHF2 Liver (June05) mlratio"
@@ -2000,6 +2000,11 @@
                   "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"
@@ -2010,11 +2015,6 @@
                   "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"
@@ -2081,11 +2081,6 @@
                   "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"
@@ -2096,6 +2091,11 @@
                   "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"
@@ -2352,14 +2352,14 @@
                   "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN"
                ],
                [
-                  "116",
-                  "MA_M2_0706_P",
-                  "Mouse Kidney M430v2 (Jul06) PDNN"
-               ],
-               [
                   "115",
                   "MA_M2_0706_R",
                   "Mouse Kidney M430v2 (Jul06) RMA"
+               ],
+               [
+                  "116",
+                  "MA_M2_0706_P",
+                  "Mouse Kidney M430v2 (Jul06) PDNN"
                ]
             ],
             "Liver Metabolome": [
@@ -2521,16 +2521,16 @@
             ],
             "Neocortex mRNA": [
                [
-                  "375",
-                  "DevNeocortex_ILM6.2P14RInv_1111",
-                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
-               ],
-               [
                   "374",
                   "DevNeocortex_ILM6.2P3RInv_1111",
                   "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
                ],
                [
+                  "375",
+                  "DevNeocortex_ILM6.2P14RInv_1111",
+                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
+               ],
+               [
                   "284",
                   "HQFNeoc_1210v2_RankInv",
                   "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
@@ -2546,14 +2546,14 @@
                   "HQF BXD Neocortex ILM6v1.1 (Feb08) 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"
+               ],
+               [
+                  "274",
+                  "DevNeocortex_ILM6.2P3RInv_1110",
+                  "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
                ]
             ],
             "Nucleus Accumbens mRNA": [
@@ -2761,11 +2761,6 @@
             ],
             "Ventral Tegmental Area mRNA": [
                [
-                  "229",
-                  "VCUEtOH_0609_R",
-                  "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
-               ],
-               [
                   "228",
                   "VCUSal_0609_R",
                   "VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
@@ -2774,6 +2769,11 @@
                   "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"
                ]
             ]
          },
@@ -2852,6 +2852,11 @@
          "CFW": {
             "Hippocampus mRNA": [
                [
+                  "811",
+                  "UCSD_CFW_HIP_RNA-Seq_log2_0117",
+                  "UCSD CFW Hippocampus (Jan17) RNA-Seq Log2 Z-score"
+               ],
+               [
                   "808",
                   "UCSD_CFW_HIP_RNA-Seq_0117",
                   "UCSD CFW Hippocampus (Jan17) RNA-Seq"
@@ -2866,6 +2871,11 @@
             ],
             "Prefrontal Cortex mRNA": [
                [
+                  "813",
+                  "UCSD_CFW_PFC_RNA-Seq_log2_0117",
+                  "UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq Log2 Z-score"
+               ],
+               [
                   "810",
                   "UCSD_CFW_PFC_RNA-Seq_0117",
                   "UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq"
@@ -2873,6 +2883,11 @@
             ],
             "Striatum mRNA": [
                [
+                  "812",
+                  "UCSD_CFW_STR_RNA-Seq_log2_0117",
+                  "UCSD CFW Striatum (Jan17) RNA-Seq Log2 Z-score"
+               ],
+               [
                   "809",
                   "UCSD_CFW_SPL_RNA-Seq_0117",
                   "UCSD CFW Striatum (Jan17) RNA-Seq"
@@ -3008,14 +3023,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "100",
-                  "HC_M2CB_1205_R",
-                  "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
-               ],
-               [
                   "99",
                   "HC_M2CB_1205_P",
                   "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
+               ],
+               [
+                  "100",
+                  "HC_M2CB_1205_R",
+                  "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
                ]
             ],
             "Phenotypes": [
@@ -3082,16 +3097,6 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "219",
-                  "Illum_LXS_Hipp_NON_1008",
-                  "Hippocampus Illumina NON (Oct08) RankInv beta"
-               ],
-               [
-                  "212",
-                  "Illum_LXS_Hipp_RSE_1008",
-                  "Hippocampus Illumina RSE (Oct08) RankInv beta"
-               ],
-               [
                   "214",
                   "Illum_LXS_Hipp_NOE_1008",
                   "Hippocampus Illumina NOE (Oct08) RankInv beta"
@@ -3107,6 +3112,16 @@
                   "Hippocampus Illumina NOS (Oct08) RankInv beta"
                ],
                [
+                  "219",
+                  "Illum_LXS_Hipp_NON_1008",
+                  "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"
@@ -3197,14 +3212,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "273",
-                  "UMUTAffyExon_0209_RMA_MDP",
-                  "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
-               ],
-               [
                   "272",
                   "HC_M2_0606_MDP",
                   "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
+               ],
+               [
+                  "273",
+                  "UMUTAffyExon_0209_RMA_MDP",
+                  "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
                ]
             ],
             "Liver mRNA": [
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index c1c25a58..d6cd8134 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -166,7 +166,7 @@
     return function() {
       var form_data, url;
       //$("#progress_bar_container").modal();
-      url = "/marker_regression";
+      url = "/loading";
       $('input[name=method]').val("pylmm");
       $('input[name=genofile]').val($('#genofile_pylmm').val());
       $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
@@ -182,7 +182,7 @@
     return function() {
       var form_data, url;
       //$("#progress_bar_container").modal();
-      url = "/marker_regression";
+      url = "/loading";
       $('input[name=method]').val("rqtl_geno");
       $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
       $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
@@ -212,7 +212,7 @@
     return function() {
       var form_data, url;
       //$("#static_progress_bar_container").modal();
-      url = "/marker_regression";
+      url = "/loading";
       $('input[name=method]').val("plink");
       $('input[name=maf]').val($('input[name=maf_plink]').val());
       form_data = $('#trait_data_form').serialize();
@@ -227,7 +227,7 @@
       var form_data, url;
       console.log("RUNNING GEMMA");
       //$("#static_progress_bar_container").modal();
-      url = "/marker_regression";
+      url = "/loading";
       $('input[name=method]').val("gemma");
       $('input[name=maf]').val($('input[name=maf_gemma]').val());
       form_data = $('#trait_data_form').serialize();
@@ -242,7 +242,7 @@
       var form_data, url;
       console.log("In interval mapping");
       //$("#progress_bar_container").modal();
-      url = "/marker_regression";
+      url = "/loading";
       $('input[name=method]').val("reaper");
       $('input[name=genofile]').val($('#genofile_reaper').val());
       $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());