Added change to automatically update datasets list using rest api instead of json file

Removed option to edit certain html pages, like news, policies, etc

7 files changed, 53 insertions, 29 deletions

diff --git a/etc/default_settings.py b/etc/default_settings.py
index a1fe81e5..a16ac3ad 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -91,4 +91,5 @@ JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript"
 # ---- GN2 Executables (overwrite for testing only)
 # PLINK_COMMAND = str.strip(os.popen("which plink2").read())
 # GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
+REAPER_COMMAND = HOME + "/gn2-zach/rust-qtlreaper/target/release/qtlreaper"
 # GEMMA_WRAPPER_COMMAND = str.strip(os.popen("which gemma-wrapper").read())
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d766e284..41de8492 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -46,6 +46,8 @@ from utility import chunks
 from utility import gen_geno_ob
 from utility.tools import locate, locate_ignore_error, flat_files
 
+from wqflask.api import gen_menu
+
 from maintenance import get_group_samplelists
 
 from MySQLdb import escape_string as escape
@@ -92,7 +94,7 @@ Publish or ProbeSet. E.g.
         """
         self.datasets = {}
         if USE_GN_SERVER:
-            data = menu_main()
+            data = gen_menu.gen_dropdown_json()
         else:
             file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
             with open(file_name, 'r') as fh:
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 8b2260f5..31ab2046 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -107,6 +107,9 @@ def js_path(module=None):
         return try_guix
     raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
 
+def reaper_command(guess=None):
+    return get_setting("REAPER_COMMAND",guess)
+
 def gemma_command(guess=None):
     return assert_bin(get_setting("GEMMA_COMMAND",guess))
 
@@ -274,6 +277,7 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT')
 SMTP_USERNAME = get_setting('SMTP_USERNAME')
 SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
 
+REAPER_COMMAND     = app_set("REAPER_COMMAND",reaper_command())
 GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
 assert(GEMMA_COMMAND is not None)
 PLINK_COMMAND      = app_set("PLINK_COMMAND",plink_command())
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 3bcd613f..d9601405 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1790,7 +1790,6 @@ class DisplayMappingResults(object):
             m = 0
             thisLRSColor = self.colorCollection[0]
             if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
-
                 if self.manhattan_plot != True:
                     canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
 
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 2bde2b53..6e9fe85c 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -36,7 +36,7 @@ from utility import helper_functions
 from utility import Plot, Bunch
 from utility import temp_data
 from utility.benchmark import Bench
-from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
+from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping, rust_reaper_mapping
 
 from utility.tools import locate, locate_ignore_error, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
 from utility.external import shell
@@ -242,7 +242,8 @@ class RunMapping(object):
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
             logger.info("Running qtlreaper")
-            results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
+
+            results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = rust_reaper_mapping.run_reaper(self.this_trait,
                                                                                                                                                         self.dataset,
                                                                                                                                                         self.samples,
                                                                                                                                                         self.vals,
@@ -253,6 +254,18 @@ class RunMapping(object):
                                                                                                                                                         self.do_control,
                                                                                                                                                         self.control_marker,
                                                                                                                                                         self.manhattan_plot)
+
+            # results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
+            #                                                                                                                                             self.dataset,
+            #                                                                                                                                             self.samples,
+            #                                                                                                                                             self.vals,
+            #                                                                                                                                             self.json_data,
+            #                                                                                                                                             self.num_perm,
+            #                                                                                                                                             self.bootCheck,
+            #                                                                                                                                             self.num_bootstrap,
+            #                                                                                                                                             self.do_control,
+            #                                                                                                                                             self.control_marker,
+            #                                                                                                                                             self.manhattan_plot)
         elif self.mapping_method == "plink":
             self.score_type = "-log(p)"
             self.manhattan_plot = True
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 0d73213d..6531f5a0 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1440,7 +1440,7 @@
                [
                   "None",
                   "HSBPublish",
-                  "HSB Phenotypes"
+                  "HSB Published Phenotypes"
                ]
             ],
             "Posterior Inferior Parietal Cortex mRNA": [
@@ -1721,7 +1721,7 @@
                [
                   "None",
                   "B6D2Publish",
-                  "B6D2 Phenotypes"
+                  "UTHSC-Glaucoma-Aged-Retina Phenotypes"
                ]
             ]
          },
@@ -2248,6 +2248,11 @@
                   "Eye M430v2 WT Gpnmb (Sep08) RMA"
                ],
                [
+                  "382",
+                  "Eye_M2_0908_WTWT",
+                  "Eye M430v2 WT WT (Sep08) RMA"
+               ],
+               [
                   "279",
                   "Eye_M2_0908_R_WT",
                   "Eye M430v2 WT Tyrp1 (Sep08) RMA"
@@ -2258,11 +2263,6 @@
                   "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
                ],
                [
-                  "382",
-                  "Eye_M2_0908_WTWT",
-                  "Eye M430v2 WT WT (Sep08) RMA"
-               ],
-               [
                   "400",
                   "DBA2J-ONH-1212",
                   "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA"
@@ -2500,6 +2500,11 @@
                   "245",
                   "UT_ILM_BXD_hipp_RSE_0909",
                   "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv"
+               ],
+               [
+                  "711",
+                  "UTHSC_BXD_AgeHipp0515",
+                  "UTHSC BXD Aged Hippocampus Affy MoGene1.0 ST (May15) RMA Gene Level"
                ]
             ],
             "Hypothalamus mRNA": [
@@ -3029,16 +3034,6 @@
             ],
             "Striatum mRNA": [
                [
-                  "376",
-                  "DevStriatum_ILM6.2P3RInv_1111",
-                  "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv"
-               ],
-               [
-                  "377",
-                  "DevStriatum_ILM6.2P14RInv_1111",
-                  "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv"
-               ],
-               [
                   "399",
                   "Striatum_Exon_1212",
                   "HQF Striatum Affy Mouse Exon 1.0ST Gene Level (Dec09) RMA"
@@ -3049,6 +3044,16 @@
                   "HQF Striatum Affy Mouse Exon 1.0ST Exon Level (Dec09) RMA"
                ],
                [
+                  "376",
+                  "DevStriatum_ILM6.2P3RInv_1111",
+                  "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv"
+               ],
+               [
+                  "377",
+                  "DevStriatum_ILM6.2P14RInv_1111",
+                  "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv"
+               ],
+               [
                   "285",
                   "UTHSC_Striatum_RankInv_1210",
                   "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv"
@@ -3555,6 +3560,11 @@
             ],
             "Hippocampus mRNA": [
                [
+                  "211",
+                  "Illum_LXS_Hipp_RSS_1008",
+                  "Hippocampus Illumina RSS (Oct08) RankInv beta"
+               ],
+               [
                   "213",
                   "Illum_LXS_Hipp_NOS_1008",
                   "Hippocampus Illumina NOS (Oct08) RankInv beta"
@@ -3575,11 +3585,6 @@
                   "Hippocampus Illumina NOE (Oct08) RankInv beta"
                ],
                [
-                  "211",
-                  "Illum_LXS_Hipp_RSS_1008",
-                  "Hippocampus Illumina RSS (Oct08) RankInv beta"
-               ],
-               [
                   "143",
                   "Illum_LXS_Hipp_loess0807",
                   "Hippocampus Illumina (Aug07) LOESS"
@@ -3835,7 +3840,7 @@
                [
                   "None",
                   "HSNIH-RGSMCPublish",
-                  "HSNIH-RGSMC Phenotypes"
+                  "HSNIH Published Phenotypes"
                ]
             ]
          },
diff --git a/wqflask/wqflask/templates/docs.html b/wqflask/wqflask/templates/docs.html
index c485f757..1a241ce7 100644
--- a/wqflask/wqflask/templates/docs.html
+++ b/wqflask/wqflask/templates/docs.html
@@ -6,9 +6,9 @@
 <div class="container">
 	<h3>{{title}}</h3>
 	<div style="text-align: right;">
-		<a href="docedit?entry={{entry}}">
+		<!--<a href="docedit?entry={{entry}}">-->
 			<img style="width: 16px;" src="/static/new/images/edit.gif">
-		</a>
+		<!--</a>-->
 	</div>
 	{{content|safe}}
 </div>