From 0d6c9ab0b34199e94aaf262f7a7eb7f6e0f77b72 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 29 Apr 2019 11:12:48 -0500
Subject: Started API readme file

---
 api_readme.md | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 api_readme.md

diff --git a/api_readme.md b/api_readme.md
new file mode 100644
index 00000000..eef0b2d7
--- /dev/null
+++ b/api_readme.md
@@ -0,0 +1,62 @@
+# API Command Documentation #
+
+## Fetch Species List ##
+
+To get a list of species with data available in GN (and their associated names and ids):
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/species
+[
+  {
+    "FullName": "Mus musculus", 
+    "Id": 1, 
+    "Name": "mouse", 
+    "TaxonomyId": 10090
+  }, 
+  ...
+  {
+    "FullName": "Populus trichocarpa", 
+    "Id": 10, 
+    "Name": "poplar", 
+    "TaxonomyId": 3689
+  }
+]
+```
+
+Or to get a single species info:
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse
+``` 
+OR 
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json
+```
+
+*For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later*
+
+## Fetch Groups/RISets ##
+
+This query can optionally filter by species:
+
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/groups (for all species)
+```
+OR
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse groups/RISets)
+[ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ]
+```
+
+## Fetch Datasets ##
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd
+```
+OR
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd
+[ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ]
+```
+(I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary)
+
+
+
+
-- 
cgit v1.2.3


From 7daf96560d0b1f945a0a5fd0aed4a9961b718635 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 29 Apr 2019 11:48:51 -0500
Subject: Added the rest of the currently existing commands

---
 api_readme.md | 72 ++++++++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 56 insertions(+), 16 deletions(-)

diff --git a/api_readme.md b/api_readme.md
index eef0b2d7..00ba25d7 100644
--- a/api_readme.md
+++ b/api_readme.md
@@ -1,25 +1,11 @@
-# API Command Documentation #
+# API Query Documentation #
 
 ## Fetch Species List ##
 
 To get a list of species with data available in GN (and their associated names and ids):
 ```
 curl http://gn2-zach.genenetwork.org/api/v_pre1/species
-[
-  {
-    "FullName": "Mus musculus", 
-    "Id": 1, 
-    "Name": "mouse", 
-    "TaxonomyId": 10090
-  }, 
-  ...
-  {
-    "FullName": "Populus trichocarpa", 
-    "Id": 10, 
-    "Name": "poplar", 
-    "TaxonomyId": 3689
-  }
-]
+[ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ]
 ```
 
 Or to get a single species info:
@@ -57,6 +43,60 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd
 ```
 (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary)
 
+## Fetch Individual Dataset Info ##
+### For mRNA Assay/"ProbeSet" ###
 
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P
+```
+OR
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P```
+{ "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 }
+```
+(This also has the option to specify group/riset)
 
+### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ###
+For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example:
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/10001
+{ "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" }
+```
 
+## Fetch Sample Data for Single Trait ##
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at
+[ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ]
+```
+
+## Fetch Trait Info (Name, Description, Location, etc) ##
+### For mRNA Expression/"ProbeSet" ###
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at
+{ "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" }
+```
+
+### For "Phenotypes" ###
+For phenotypes this just gets the  max LRS, its location, and additive effect (as calculated by qtlreaper)
+
+Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001
+{ "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 }
+```
+
+## Calculate Correlation ##
+Currently only Pearson Sample and Tissue correlations are implemented
+
+This query currently takes the following parameters (though more will be added):
+* trait_id (*required*) - ID for trait used for correlation
+* db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets)
+* target_db (*required*) - Target DB name to be correlated against
+* type - Sample or Tissue (default = Sample)
+* return - Number of results to return (default = 500)
+
+Example query:
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100
+[ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ]
+```
-- 
cgit v1.2.3


From c39a7ca68c2584c49a86fac2d05144a1b32ccd56 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 3 May 2019 11:06:47 -0500
Subject: Added examples for fetching sample data & genotypes

---
 api_readme.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/api_readme.md b/api_readme.md
index 00ba25d7..d0102d67 100644
--- a/api_readme.md
+++ b/api_readme.md
@@ -32,6 +32,12 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse gro
 [ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ]
 ```
 
+## Fetch Genotypes for Group/RISet ##
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/genotypes/BXD
+```
+Returns a CSV file with metadata in the first few rows, sample/strain names as columns, and markers as rows. Currently only works for genotypes we have stored in .geno files; I'll add the option to download BIMBAM files soon.
+
 ## Fetch Datasets ##
 ```
 curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd
@@ -43,6 +49,13 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd
 ```
 (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary)
 
+## Fetch Sample Data for Dataset ##
+``` 
+curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv
+```
+
+Returns a CSV file with sample/strain names as the columns and trait IDs as rows
+
 ## Fetch Individual Dataset Info ##
 ### For mRNA Assay/"ProbeSet" ###
 
-- 
cgit v1.2.3


From 7749cec3336f5ecd3233be7f91cf5750a270c37d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 21 May 2019 15:40:29 -0500
Subject: Added mapping and some other changes to readme

---
 api_readme.md | 46 +++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 43 insertions(+), 3 deletions(-)

diff --git a/api_readme.md b/api_readme.md
index d0102d67..96e8b246 100644
--- a/api_readme.md
+++ b/api_readme.md
@@ -1,5 +1,7 @@
 # API Query Documentation #
-
+---
+# Fetching Dataset/Trait info/data #
+---
 ## Fetch Species List ##
 
 To get a list of species with data available in GN (and their associated names and ids):
@@ -98,14 +100,52 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001
 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 }
 ```
 
+---
+
+# Analyses #
+---
+## Mapping ##
+Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper
+
+Each method's query takes the following parameters respectively (more will be added):
+### GEMMA ###
+* trait_id (*required*) - ID for trait being mapped
+* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets)
+* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false)
+* maf - minor allele frequency (default = 0.01)
+
+Example query:
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true
+```
+
+### R/qtl ###
+(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf)
+* trait_id (*required*) - ID for trait being mapped
+* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets)
+* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function.
+* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function
+* num_perm - number of permutations; 0 by default
+* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate
+* interval_mapping - Whether to use interval mapping; "false" by default
+* pair_scan - *NYI*
+
+Example query:
+```
+curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100
+```
+
+Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case)
+
 ## Calculate Correlation ##
-Currently only Pearson Sample and Tissue correlations are implemented
+Currently only Sample and Tissue correlations are implemented
 
 This query currently takes the following parameters (though more will be added):
 * trait_id (*required*) - ID for trait used for correlation
 * db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets)
 * target_db (*required*) - Target DB name to be correlated against
-* type - Sample or Tissue (default = Sample)
+* type - sample (default) | tissue
+* method - pearson (default) | spearman
 * return - Number of results to return (default = 500)
 
 Example query:
-- 
cgit v1.2.3


From 7dd9a3f8d232f3f747167de082eff22c30657ea0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 21 Apr 2020 16:42:22 -0500
Subject: Testing

---
 wqflask/wqflask/templates/base.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ec55ebeb..90be6111 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -4,7 +4,7 @@
 
 <head>
     <meta charset="utf-8">
-    <title>{% block title %}{% endblock %} GeneNetwork</title>
+    <title>{% block title %}{% endblock %} GeneNetwork2</title>
     <meta name="description" content="">
     <meta name="author" content="">
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
-- 
cgit v1.2.3


From 1444f5618361a1c91bd792cfab8c8c53beb3421c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 21 Apr 2020 16:43:11 -0500
Subject: Testing 2

---
 wqflask/wqflask/templates/tutorials.html | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 wqflask/wqflask/templates/tutorials.html

diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html
new file mode 100644
index 00000000..44e6a2c4
--- /dev/null
+++ b/wqflask/wqflask/templates/tutorials.html
@@ -0,0 +1 @@
+Testing123
-- 
cgit v1.2.3


From 657ab53bef4fc767fdc549f004153a7910b45bd0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 10 Sep 2020 14:33:52 -0500
Subject: Fixed several sorting issues and moved orderDataType definitions into
 search_results.js since all the tables that use them import that file (that
 file's name needs to be changed, though) *
 wqflask/wqflask/static/new/javascript/search_results.js - Added the
 dom-checkbox and dom-inner-text order types into this file; they were
 previously duplicated across several template files *
 wqflask/wqflask/templates/gsearch_gene.html - Added dom-inner-text order type
 to relevant columns with hyperlink contents and disabled deferRender since it
 conflicted with use of both pagination and orderDataType for sorting *
 wqflask/wqflask/templates/gsearch_pheno.html - Same as above *
 wqflask/wqflask/templates/mapping_results.html - Added dom-inner-text for a
 few columns that have hyperlink values - still need to modify
 natural-minus-na to also include other "N/A"-equivalent values like "--" *
 wqflask/wqflask/templates/search_result_page.html Removed the dom-checkbox
 and dom-inner-text order types from this file since they were moved to
 search_results.js

---
 wqflask/wqflask/static/new/javascript/search_results.js | 14 ++++++++++++++
 wqflask/wqflask/templates/gsearch_gene.html             | 16 +---------------
 wqflask/wqflask/templates/gsearch_pheno.html            | 17 ++---------------
 wqflask/wqflask/templates/mapping_results.html          | 12 ++++++------
 wqflask/wqflask/templates/search_result_page.html       | 15 ---------------
 5 files changed, 23 insertions(+), 51 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 4e87d67a..b696dc4d 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -281,4 +281,18 @@ $(function() {
     }
   });
 
+  $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
+  {
+      return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+          return $('input', td).prop('checked') ? '1' : '0';
+      } );
+  };
+
+  $.fn.dataTable.ext.order['dom-inner-text'] = function  ( settings, col )
+  {
+      return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+          return $(td).text();
+      } );
+  }
+
 });
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 478d6f5f..d2c78d65 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -59,20 +59,6 @@
     </script>
 
     <script type="text/javascript" charset="utf-8">
-        $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $('input', td).prop('checked') ? '1' : '0';
-            } );
-        };
-
-        $.fn.dataTable.ext.order['dom-inner-text'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $(td).text();
-            } );
-        }
-
         $(document).ready( function () {
             
             $('#trait_table tr').click(function(event) {
@@ -252,7 +238,7 @@
                 'sDom': "pitirp",
                 'autoWidth': true,
                 'iDisplayLength': 500,
-                'deferRender': true,
+                'deferRender': false,
                 'paging': true,
                 'orderClasses': true,
                 'processing': true,
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index eb998d15..c44231f3 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -59,20 +59,6 @@
     </script>
 
     <script type="text/javascript" charset="utf-8">
-        $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $('input', td).prop('checked') ? '1' : '0';
-            } );
-        };
-
-        $.fn.dataTable.ext.order['dom-inner-text'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $(td).text();
-            } );
-        }
-
         $(document).ready( function () {
 
             $('#trait_table tr').click(function(event) {
@@ -172,6 +158,7 @@
                       'title': "Record",
                       'type': "natural",
                       'data': null,
+                      'orderDataType': "dom-inner-text",
                       'render': function(data, type, row, meta) {
                         return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
                       }
@@ -252,7 +239,7 @@
                 'order': [[1, "asc" ]],
                 'sDom': "pitirp",
                 'autoWidth': false,
-                'deferRender': true,
+                'deferRender': false,
                 'iDisplayLength': 500,
                 'paging': true,
                 'orderClasses': true,
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 8edda548..9c170494 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -395,16 +395,16 @@
                   $('td', row).eq(9).attr("align", "right");
                 },
                 "columns": [
-                    { "bSortable": false},
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
+                    { "orderDataType": "dom-checkbox" },
+                    { "type": "natural"},
+                    { "type": "natural" , "orderDataType": "dom-inner-text" },
+                    { "type": "natural" , "orderDataType": "dom-inner-text" },
+                    { "type": "natural" , "orderDataType": "dom-inner-text" },
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
+                    { "type": "natural" , "orderDataType": "dom-inner-text" },
                     { "type": "natural" }
                 ],
                 "columnDefs": [ {
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 53373b41..282e752d 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -174,21 +174,6 @@
     </script>
 
     <script type="text/javascript" charset="utf-8">
-
-        $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $('input', td).prop('checked') ? '1' : '0';
-            } );
-        };
-
-        $.fn.dataTable.ext.order['dom-inner-text'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $(td).text();
-            } );
-        }
-
         $(document).ready( function () {
             
             $('#trait_table tr').click(function(event) {
-- 
cgit v1.2.3


From 03240c4d22e894b977f7a1a2204a32408245c470 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 10 Sep 2020 14:54:57 -0500
Subject: Modified "natural-minus-na" sort function to treat an array of values
 as equivalent to "N/A" (since different tables sometimes include other values
 that imply there's no value) and applied it to some extra columns in the
 Interval Analyst table *
 wqflask/wqflask/static/new/javascript/search_results.js - Modified sort_NAs
 function to take an array of "N/A"-equivalent values instead of just
 comparing against the string "N/A" *
 wqflask/wqflask/templates/mapping_results.html - Applied "natural-minus-na"
 sort method to several columns that include "--" in the Interval Analyst
 table

---
 wqflask/wqflask/static/new/javascript/search_results.js | 8 +++++---
 wqflask/wqflask/templates/mapping_results.html          | 6 +++---
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index b696dc4d..685d6291 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -259,14 +259,16 @@ $(function() {
   let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"]
   let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"]
 
+  let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A
+
   function sort_NAs(a, b, sort_function){
-    if (a === "N/A" && b === "N/A") {
+    if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
       return 0;
     }
-    if (a === "N/A"){
+    if (na_equivalent_vals.includes(a)){
       return 1
     }
-    if (b === "N/A") {
+    if (na_equivalent_vals.includes(b)) {
       return -1;
     }
     return sort_function(a, b)
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 9c170494..4ea7fa07 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -402,9 +402,9 @@
                     { "type": "natural" , "orderDataType": "dom-inner-text" },
                     { "type": "natural" },
                     { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" , "orderDataType": "dom-inner-text" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" , "orderDataType": "dom-inner-text" },
                     { "type": "natural" }
                 ],
                 "columnDefs": [ {
-- 
cgit v1.2.3


From 9f458b92aa28ac2d00b9bf822c516d0545a79bc9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 11 Sep 2020 16:14:02 -0500
Subject: Wrote code and template for reproducing GN1's Info Page (page that
 displays info about a dataset + download links for its data)

* wqflask/wqflask/db_info.py - Python that pulls the info out of the DB
and parses the download links from the ipfs response
* wqflask/wqflask/templates/info_page.html - template for displaying
db info; need to make a lot of changes to its format/aesthetics
---
 wqflask/wqflask/db_info.py               | 127 +++++++++++++++++++++++++++++++
 wqflask/wqflask/templates/info_page.html |  92 ++++++++++++++++++++++
 2 files changed, 219 insertions(+)
 create mode 100644 wqflask/wqflask/db_info.py
 create mode 100644 wqflask/wqflask/templates/info_page.html

diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
new file mode 100644
index 00000000..f04e38bf
--- /dev/null
+++ b/wqflask/wqflask/db_info.py
@@ -0,0 +1,127 @@
+import httplib, urllib2
+import re
+
+from flask import Flask, g
+
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
+class InfoPage(object):
+    def __init__(self, start_vars):
+        self.info = None
+        self.gn_accession_id = None
+        if 'gn_accession_id' in start_vars:
+            self.gn_accession_id = start_vars['gn_accession_id']
+        self.info_page_name = start_vars['info_page_name']
+
+        self.get_info()
+        self.get_datasets_list()
+
+    def get_info(self, create=False):
+        query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +
+                      "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +
+                      "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +
+                      "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +
+                      "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +
+                      "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +
+                      "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +
+                      "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +
+                      "FROM InfoFiles " +
+                      "LEFT JOIN Species USING (SpeciesId) " +
+                      "LEFT JOIN Tissue USING (TissueId) " +
+                      "LEFT JOIN InbredSet USING (InbredSetId) " +
+                      "LEFT JOIN GeneChip USING (GeneChipId) " +
+                      "LEFT JOIN AvgMethod USING (AvgMethodId) " +
+                      "LEFT JOIN Datasets USING (DatasetId) " +
+                      "LEFT JOIN Investigators USING (InvestigatorId) " +
+                      "LEFT JOIN Organizations USING (OrganizationId) " +
+                      "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
+
+        if self.gn_accession_id:
+            final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id)
+            results = g.db.execute(final_query).fetchone()
+            if self.info_page_name and not results:
+				final_query = query_base + "InfoPageName={}".format(self.info_page_name)
+        elif self.info_page_name:
+            final_query = query_base + "InfoPageName={}".format(self.info_page_name)
+            results = g.db.execute(final_query).fetchone()
+        else:
+            raise 'No correct parameter found'
+
+        if results:
+            self.info = process_query_results(results)
+
+        if (not results or len(results) < 1) and self.info_page_name and create:
+            insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name)
+            return self.get_info()
+
+        if not self.gn_accession_id and self.info:
+            self.gn_accession_id = self.info['accession_id']
+        if not self.info_page_name and self.info:
+            self.info_page_name = self.info['info_page_name'] 
+
+    def get_datasets_list(self):
+        self.filelist = []
+        try:
+            response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id)
+            data = response.read()
+
+            matches = re.findall(r"<tr>.+?</tr>", data, re.DOTALL)
+            for i, match in enumerate(matches):
+                if i == 0:
+                    continue
+                cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL)
+                full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip()
+                filename = full_filename.split("/")[-1]
+                filesize = re.search(r">(.+?)<", cells[2]).group(1).strip()
+                filedate = "N/A" #ZS: Since we can't get it for now
+
+                self.filelist.append([filename, filedate, filesize])
+        except Exception, e:
+            pass
+
+def process_query_results(results):
+    info_ob = {
+        'info_page_name': results[0],
+        'accession_id': results[1],
+        'menu_name': results[2],
+        'taxonomy_id': results[3],
+        'tissue_name': results[4],
+        'group_name': results[5],
+        'gene_chip_name': results[6],
+        'geo_platform': results[7],
+        'avg_method_name': results[8],
+        'dataset_name': results[9],
+        'geo_series': results[10],
+        'publication_title': results[11],
+        'dataset_status_name': results[12],
+        'dataset_summary': results[13],
+        'about_cases': results[14],
+        'about_tissue': results[15],
+        'about_data_processing': results[16],
+        'acknowledgement': results[17],
+        'experiment_design': results[18],
+        'contributors': results[19],
+        'citation': results[20],
+        'notes': results[21],
+        'investigator_firstname': results[22],
+        'investigator_lastname': results[23],
+        'investigator_address': results[24],
+        'investigator_city': results[25],
+        'investigator_state': results[26],
+        'investigator_zipcode': results[27],
+        'investigator_country': results[28],
+        'investigator_phone': results[29],
+        'investigator_email': results[30],
+        'investigator_url': results[31],
+        'organization_name': results[32],
+        'investigator_id': results[33],
+        'dataset_id': results[34],
+        'dataset_status_is': results[35],
+        'about_platform': results[36],
+        'info_file_title': results[37],
+        'specifics': results[38]
+    }
+
+    return info_ob
+        
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/info_page.html b/wqflask/wqflask/templates/info_page.html
new file mode 100644
index 00000000..d8b7d74c
--- /dev/null
+++ b/wqflask/wqflask/templates/info_page.html
@@ -0,0 +1,92 @@
+{% extends "base.html" %}
+{% block title %}Policies{% endblock %}
+{% block content %}
+
+<h1 id="parent-fieldname-title">Data Set Group: {{ info.dataset_name }}
+<!--<a href="/infoshare/manager/member-studies-edit.html?DatasetId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>-->
+<span style="color:red;">{{ info.info_page_name }}</span>
+</h1>
+<table border="0" width="100%">
+<tr>
+<td valign="top" width="50%">
+<table name="info_table" cellSpacing=0 cellPadding=5 width=100% border=0>
+    <tr><td><b>Data Set:</b>  {{ info.info_file_title }} <!--<a href="/infoshare/manager/member-infofile-edit.html?GN_AccesionId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>--></td></tr>
+    <tr><td><b>GN Accession:</b> GN{{ gn_accession_id }}</td></tr>
+    <tr><td><b>GEO Series:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_series }}" target="_blank">{{ info.geo_series }}</a></td></tr>
+    <tr><td><b>Title:</b> {{ info.publication_title }}</td></tr>
+    <tr><td><b>Organism:</b> <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id={{ info.taxonomy_id }}" target="_blank">{{ info.menu_name }}</a></td></tr>
+    <tr><td><b>Group:</b> {{ info.group_name }}</td></tr>
+    <tr><td><b>Tissue:</b> {{ info.tissue_name }}</td></tr>
+    <tr><td><b>Dataset Status:</b> {{ info.dataset_status_name }}</td></tr>
+    <tr><td><b>Platforms:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_platform }}" target="_blank">{{ info.gene_chip_name }}</a></td></tr>
+    <tr><td><b>Normalization:</b> {{ info.avg_method_name }}</td></tr>
+</table>
+</td>
+<td valign="top" width="50%">
+<table border="0" width="100%">
+    <tr>
+        <td><b>Contact Information</b></td>
+    </tr>
+    <tr>
+        <td>
+            {{ info.investigator_first_name }} {{ info.inveestigator_last_name }}<br>
+            {{ info.organization_name }} <br>
+            {{ info.investigator_address }}<br>
+            {{ info.investigator_city }}, {{ info.investigator_state }} {{ info.investigator_zipcode }} {{ info.investigator_country }}<br>
+            Tel. {{ info.investigator_phone }}<br>
+            {{ info.investigator_email }}<br>
+            <a href="{{ info.investigator_url }}" target="_blank">Website</a>
+        </td>
+    </tr>
+
+<tr>
+    <td><b>Download datasets and supplementary data files</b></td>
+</tr>
+<tr>
+    <td>
+        <ul style="line-height: 160%">
+            {% for file in filelist %}
+            <li><a href="http://datafiles.genenetwork.org/download/GN{{ gn_accession_id }}/{{ file[0] }}">{{ file[0] }} ({{ file[2] }})</a></li>
+            {% endfor %}
+        </ul>
+    </td>
+</tr>
+
+<tr><td>
+</td></tr>
+
+</table>
+</td>
+</tr>
+</table>
+<HR>
+<p>
+<table name="info_table" width="100%" border="0" cellpadding="5" cellspacing="0">
+<tr><td><span style="font-size:115%%;font-weight:bold;">Specifics of this Data Set:</span></td></tr>
+    <tr><td> {{ info.specifics|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%%;font-weight:bold;">Summary:</span></td></tr>
+    <tr><td> {{ info.dataset_summary|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About the cases used to generate this set of data:</span></td></tr>
+    <tr><td> {{ info.about_cases|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About the tissue used to generate this set of data:</span></td></tr>
+    <tr><td> {{ info.about_tissue|safe }}<br><br></td></tr>
+    <tr><td><span style="font-size:115%; font-weight:bold;">About the array platform:</span></td></tr>
+    <tr><td> {{ info.about_platform|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About data values and data processing:</span></td></tr>
+    <tr><td> {{ info.about_data_processing|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Notes:</span></td></tr>
+    <tr><td> {{ info.notes|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Experiment Type:</span></td></tr>
+    <tr><td> {{ info.experiment_design|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Contributor:</span></td></tr>
+    <tr><td> {{ info.contributors|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Citation:</span></td></tr>
+    <tr><td> {{ info.citation|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Data source acknowledgment:</span></td></tr>
+    <tr><td> {{ info.acknowledgement|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Study Id:</span></td></tr>
+    <tr><td> {{ info.dataset_id }}<br><br></td></tr>
+</table>
+</p>
+ 
+{% endblock %}
\ No newline at end of file
-- 
cgit v1.2.3


From 7d114484fbb77e20f4e60c10dd0cb5b1a7772eda Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sun, 13 Sep 2020 18:23:28 -0500
Subject: Added in-progress info-page to views.py as well as in-progress
 authorization/security guide

* wqflask/wqflask/views.py - Added endpoint for info page and
authorization/security tutorial
---
 wqflask/wqflask/views.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fc9949a8..3d623736 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -37,6 +37,7 @@ from wqflask import gsearch
 from wqflask import update_search_results
 from wqflask import docs
 from wqflask import news
+from wqflask import db_info
 from wqflask.submit_bnw import get_bnw_input
 from base.data_set import create_dataset, DataSet    # Used by YAML in marker_regression
 from wqflask.show_trait import show_trait
@@ -908,12 +909,24 @@ def snp_browser_page():
 
     return render_template("snp_browser.html", **template_vars.__dict__)
 
+@app.route("/db_info", methods=('GET',))
+def db_info_page():
+    template_vars = db_info.InfoPage(request.args)
+
+    return render_template("info_page.html", **template_vars.__dict__)
+
 @app.route("/tutorial/WebQTLTour", methods=('GET',))
 def tutorial_page():
     #ZS: Currently just links to GN1
     logger.info(request.url)
     return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/")
 
+@app.route("/tutorial/security", methods=('GET',))
+def security_tutorial_page():
+    #ZS: Currently just links to GN1
+    logger.info(request.url)
+    return render_template("admin/security_help.html")
+
 @app.route("/submit_bnw", methods=('POST',))
 def submit_bnw():
     logger.info(request.url)
-- 
cgit v1.2.3


From 77d026e042a3eac9e3de4177ee374a37f2e24127 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 15 Sep 2020 20:53:11 +0300
Subject: Fix failing tests

* wqflask/tests/base/test_data_set.py: Update failing tests introduced
by the change in 301bdd2f4.
---
 wqflask/tests/base/test_data_set.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index 94780a5d..dd7f5051 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -66,7 +66,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_key_mrna(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -84,7 +84,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_key_pheno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -93,7 +93,6 @@ class TestDataSetTypes(unittest.TestCase):
             redis_mock.set.assert_called_once_with(
                 "dataset_structure",
                 '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
-            expected_db_call = """"""
             db_mock.db.execute.assert_called_with(
                 ("SELECT InfoFiles.GN_AccesionId " +
                  "FROM InfoFiles, PublishFreeze, InbredSet " +
@@ -105,7 +104,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_other_pheno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -114,7 +113,6 @@ class TestDataSetTypes(unittest.TestCase):
             redis_mock.set.assert_called_once_with(
                 "dataset_structure",
                 '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
-            expected_db_call = """"""
             db_mock.db.execute.assert_called_with(
                 ("SELECT PublishFreeze.Name " +
                  "FROM PublishFreeze, InbredSet " +
@@ -125,7 +123,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_geno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
-- 
cgit v1.2.3


From 6e776e94bdc2cea9923d70ff836ce1c02a1e1af9 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 15 Sep 2020 23:19:30 +0300
Subject: Add tests for authentication tools

Catches bugs in:
-
https://github.com/genenetwork/genenetwork2/pull/422/commits/70dbeeb5832711ed5271434e482c18bc7ea095b8

* wqflask/tests/utility/test_authentication_tools.py: New file. Add
tests for "check_resource_availability".
---
 wqflask/tests/utility/test_authentication_tools.py | 113 +++++++++++++++++++++
 1 file changed, 113 insertions(+)
 create mode 100644 wqflask/tests/utility/test_authentication_tools.py

diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py
new file mode 100644
index 00000000..59c53879
--- /dev/null
+++ b/wqflask/tests/utility/test_authentication_tools.py
@@ -0,0 +1,113 @@
+"""Tests for authentication tools"""
+import unittest
+import mock
+
+from utility.authentication_tools import check_resource_availability
+
+
+class TestResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return '["foo"]'
+
+
+class TestUser:
+    """Mock user"""
+    @property
+    def user_id(self):
+        """Mockes user id. Used in Flask.g.user_session.user_id"""
+        return "Jane"
+
+
+class TestUserSession:
+    """Mock user session"""
+    @property
+    def user_session(self):
+        """Mock user session. Mocks Flask.g.user_session object"""
+        return TestUser()
+
+
+class TestCheckResourceAvailability(unittest.TestCase):
+    """Test methods related to checking the resource availability"""
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g')
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_default_mask(
+            self,
+            resource_id_mock,
+            g_mock,
+            redis_mock,
+            add_new_resource_mock):
+        """Test the resource availability with default mask"""
+        resource_id_mock.return_value = 1
+        g_mock.return_value = mock.Mock()
+        redis_mock.smembers.return_value = []
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        self.assertEqual(check_resource_availability(test_dataset), 2)
+
+    @mock.patch('utility.authentication_tools.requests.get')
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g')
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_non_default_mask(
+            self,
+            resource_id_mock,
+            g_mock,
+            redis_mock,
+            add_new_resource_mock,
+            requests_mock):
+        """Test the resource availability with default mask"""
+        resource_id_mock.return_value = 1
+        g_mock.return_value = mock.Mock()
+        redis_mock.smembers.return_value = []
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        requests_mock.return_value = TestResponse()
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         ['foo'])
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
+                "SUPERUSER")
+    @mock.patch('utility.authentication_tools.requests.get')
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g', TestUserSession())
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_of_super_user(
+            self,
+            resource_id_mock,
+            redis_mock,
+            add_new_resource_mock,
+            requests_mock):
+        """Test the resource availability if the user is the super user"""
+        resource_id_mock.return_value = 1
+        redis_mock.smembers.return_value = ["Jane"]
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        requests_mock.return_value = TestResponse()
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         "SUPERUSER")
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    def test_check_resource_availability_string_dataset(self):
+        """Test the resource availability if the dataset is a string"""
+        self.assertEqual(check_resource_availability("Test"),
+                         "John Doe")
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    def test_check_resource_availability_temp(self):
+        """Test the resource availability if the dataset is a string"""
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Temp")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         "John Doe")
-- 
cgit v1.2.3


From af0ca059da29391db9b1dfca0fe96883ce95f72f Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 15 Sep 2020 23:43:09 +0300
Subject: Remove unnecessary if branch

* wqflask/utility/authentication_tools.py
(check_resource_availability): Combine if statements into one boolean
check in one if branch.
---
 wqflask/utility/authentication_tools.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 3553b92b..954f55fc 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -17,9 +17,7 @@ logger = logging.getLogger(__name__ )
 def check_resource_availability(dataset, trait_id=None):
 
     #At least for now assume temporary entered traits are accessible
-    if type(dataset) == str:
-        return webqtlConfig.DEFAULT_PRIVILEGES
-    if dataset.type == "Temp":
+    if type(dataset) == str or dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
 
     resource_id = get_resource_id(dataset, trait_id)
-- 
cgit v1.2.3


From cad9d0e4c913eba5ae3c74912b59051885833f90 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 16 Sep 2020 00:03:28 +0300
Subject: Add tests for "add_new_resource" method

* wqflask/tests/utility/test_authentication_tools.py: Add them.
---
 wqflask/tests/utility/test_authentication_tools.py | 80 ++++++++++++++++++++++
 1 file changed, 80 insertions(+)

diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py
index 59c53879..99c74245 100644
--- a/wqflask/tests/utility/test_authentication_tools.py
+++ b/wqflask/tests/utility/test_authentication_tools.py
@@ -3,6 +3,7 @@ import unittest
 import mock
 
 from utility.authentication_tools import check_resource_availability
+from utility.authentication_tools import add_new_resource
 
 
 class TestResponse:
@@ -29,6 +30,10 @@ class TestUserSession:
         return TestUser()
 
 
+def mock_add_resource(resource_ob, update=False):
+    return resource_ob
+
+
 class TestCheckResourceAvailability(unittest.TestCase):
     """Test methods related to checking the resource availability"""
     @mock.patch('utility.authentication_tools.add_new_resource')
@@ -111,3 +116,78 @@ class TestCheckResourceAvailability(unittest.TestCase):
         type(test_dataset).type = mock.PropertyMock(return_value="Temp")
         self.assertEqual(check_resource_availability(test_dataset),
                          "John Doe")
+
+
+class TestAddNewResource(unittest.TestCase):
+    """Test cases for add_new_resource method"""
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_publish_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is 'publish'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Publish")
+        type(test_dataset).id = mock.PropertyMock(return_value=10)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Test_None",
+            "data": {
+                "dataset": 10,
+                "trait": None
+            },
+            "type": "dataset-publish"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_geno_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is 'geno'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).type = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).id = mock.PropertyMock(return_value=20)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Geno",
+            "data": {
+                "dataset": 20,
+            },
+            "type": "dataset-geno"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_other_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is not 'geno' or 'publish'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).type = mock.PropertyMock(return_value="other")
+        type(test_dataset).id = mock.PropertyMock(return_value=20)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Geno",
+            "data": {
+                "dataset": 20,
+            },
+            "type": "dataset-probeset"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
-- 
cgit v1.2.3


From 23521ad683beaaff200743cb37dec68cd19cc2d5 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 16 Sep 2020 00:06:04 +0300
Subject: Apply pep8

* wqflask/utility/authentication_tools.py: Apply pep8 formatting to
file.
---
 wqflask/utility/authentication_tools.py | 37 ++++++++++++++++++++-------------
 1 file changed, 23 insertions(+), 14 deletions(-)

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 954f55fc..239b08e3 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,4 +1,6 @@
 from __future__ import absolute_import, print_function, division
+import logging
+from flask import Flask, g, redirect, url_for
 
 import json
 import requests
@@ -9,31 +11,31 @@ from utility import hmac
 from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
 Redis = get_redis_conn()
 
-from flask import Flask, g, redirect, url_for
 
-import logging
-logger = logging.getLogger(__name__ )
+logger = logging.getLogger(__name__)
+
 
 def check_resource_availability(dataset, trait_id=None):
 
-    #At least for now assume temporary entered traits are accessible
+    # At least for now assume temporary entered traits are accessible
     if type(dataset) == str or dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
 
     resource_id = get_resource_id(dataset, trait_id)
 
-    if resource_id: #ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
+    if resource_id:  # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
         resource_info = get_resource_info(resource_id)
-        if not resource_info: #ZS: If resource isn't already in redis, add it with default privileges
+        if not resource_info:  # ZS: If resource isn't already in redis, add it with default privileges
             resource_info = add_new_resource(dataset, trait_id)
 
-    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+    # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
     if g.user_session.user_id in Redis.smembers("super_users"):
-       return webqtlConfig.SUPER_PRIVILEGES
+        return webqtlConfig.SUPER_PRIVILEGES
 
     response = None
 
-    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(
+        resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)
     except:
@@ -41,18 +43,19 @@ def check_resource_availability(dataset, trait_id=None):
 
     return response
 
+
 def add_new_resource(dataset, trait_id=None):
     resource_ob = {
-        'owner_id'    : "none", # webqtlConfig.DEFAULT_OWNER_ID,
+        'owner_id': "none",  # webqtlConfig.DEFAULT_OWNER_ID,
         'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
-        'group_masks' : {}
+        'group_masks': {}
     }
 
     if dataset.type == "Publish":
         resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id)
         resource_ob['data'] = {
             'dataset': dataset.id,
-            'trait'  : trait_id
+            'trait': trait_id
         }
         resource_ob['type'] = 'dataset-publish'
     elif dataset.type == "Geno":
@@ -72,15 +75,19 @@ def add_new_resource(dataset, trait_id=None):
 
     return resource_info
 
+
 def get_group_code(dataset):
-    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
+    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(
+        dataset.group.name)).fetchone()
     if results[0]:
         return results[0]
     else:
         return ""
 
+
 def check_admin(resource_id=None):
-    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(
+        resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)['admin']
     except:
@@ -94,6 +101,7 @@ def check_admin(resource_id=None):
     else:
         return "not-admin"
 
+
 def check_owner(dataset=None, trait_id=None, resource_id=None):
     if resource_id:
         resource_info = get_resource_info(resource_id)
@@ -108,6 +116,7 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
 
     return False
 
+
 def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
     if not resource_id:
         if dataset.type == "Temp":
-- 
cgit v1.2.3


From 32f434e9f49583b731f1393328a3ff645c2f9af7 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 16 Sep 2020 03:11:01 +0300
Subject: Add new tests for "base/trait.py"

* wqflask/tests/base/test_trait.py: New tests.
---
 wqflask/tests/base/test_trait.py | 101 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 wqflask/tests/base/test_trait.py

diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
new file mode 100644
index 00000000..53b0d440
--- /dev/null
+++ b/wqflask/tests/base/test_trait.py
@@ -0,0 +1,101 @@
+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import unittest
+import mock
+
+from base.trait import GeneralTrait
+from base.trait import retrieve_trait_info
+
+
+class TestResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return "[1, 2, 3, 4]"
+
+
+class TestNilResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return "{}"
+
+
+class MockTrait(GeneralTrait):
+    @property
+    def wikidata_alias_fmt(self):
+        return "Mock alias"
+
+
+class TestRetrieveTraitInfo(unittest.TestCase):
+    """Tests for 'retrieve_trait_info'"""
+    def test_retrieve_trait_info_with_empty_dataset(self):
+        """Test that an exception is raised when dataset is empty"""
+        with self.assertRaises(AssertionError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset={})
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    def test_retrieve_trait_info_with_empty_trait_info(self,
+                                                       g_mock,
+                                                       requests_mock):
+        """Empty trait info"""
+        requests_mock.return_value = TestNilResponse()
+        with self.assertRaises(KeyError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset=mock.MagicMock())
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    def test_retrieve_trait_info_with_non_empty_trait_info(self,
+                                                           g_mock,
+                                                           requests_mock):
+        """Test that attributes are set"""
+        mock_dataset = mock.MagicMock()
+        requests_mock.return_value = TestResponse()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        test_trait = retrieve_trait_info(trait=MockTrait(dataset=mock_dataset),
+                                         dataset=mock_dataset)
+        self.assertEqual(test_trait.a, 1)
+        self.assertEqual(test_trait.b, 2)
+        self.assertEqual(test_trait.c, 3)
+        self.assertEqual(test_trait.d, 4)
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    def test_retrieve_trait_info_utf8_parsing(self,
+                                              g_mock,
+                                              requests_mock):
+        """Test that utf-8 strings are parsed correctly"""
+        utf_8_string = "test_string"
+        mock_dataset = mock.MagicMock()
+        requests_mock.return_value = TestResponse()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = 'Publish'
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description=utf_8_string
+        )
+        trait_attrs = {
+            "group_code": "test_code",
+            "pre_publication_description": "test_pre_pub",
+            "pre_publication_abbreviation": "ファイルを画面毎に見て行くには、次のコマンドを使います。",
+            "post_publication_description": None,
+            "pubmed_id": None,
+            'year': "2020",
+            "authors": "Jane Doe かいと",
+        }
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset)
+        self.assertEqual(test_trait.abbreviation,
+                         "ファイルを画面毎に見て行くには、次のコマンドを使います。")
+        self.assertEqual(test_trait.authors,
+                         "Jane Doe かいと")
-- 
cgit v1.2.3


From b13ca26da67855f9d32f3209176af052ed46617f Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 17 Sep 2020 15:55:05 +0300
Subject: Add tests for hmac utility

* wqflask/tests/utility/test_hmac.py: New tests.
---
 wqflask/tests/utility/test_hmac.py | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 wqflask/tests/utility/test_hmac.py

diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py
new file mode 100644
index 00000000..c7927685
--- /dev/null
+++ b/wqflask/tests/utility/test_hmac.py
@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+"""Test hmac utility functions"""
+
+import unittest
+import mock
+
+from utility.hmac import data_hmac
+from utility.hmac import url_for_hmac
+from utility.hmac import hmac_creation
+
+
+class TestHmacUtil(unittest.TestCase):
+    """Test Utility method for hmac creation"""
+
+    def test_hmac_creation(self):
+        """Test hmac creation with a utf-8 string"""
+        self.assertEqual(hmac_creation("ファイ"), "21fa1d935bbbb07a7875")
+
+    def test_data_hmac(self):
+        """Test data_hmac fn with a utf-8 string"""
+        self.assertEqual(data_hmac("ファイ"), "ファイ:21fa1d935bbbb07a7875")
+
+    @mock.patch("utility.hmac.url_for")
+    def test_url_for_hmac_with_plain_url(self, mock_url):
+        """Test url_for_hmac without params"""
+        mock_url.return_value = "https://mock_url.com/ファイ/"
+        self.assertEqual(url_for_hmac("ファイ"),
+                         "https://mock_url.com/ファイ/?hm=a62896a50d9ffcff7deb")
+
+    @mock.patch("utility.hmac.url_for")
+    def test_url_for_hmac_with_param_in_url(self, mock_url):
+        """Test url_for_hmac with params"""
+        mock_url.return_value = "https://mock_url.com/?ファイ=1"
+        self.assertEqual(url_for_hmac("ファイ"),
+                         "https://mock_url.com/?ファイ=1&hm=b2128fb28bc32da3b5b7")
-- 
cgit v1.2.3


From 225c360d0a5c57957fe2bc3299108e9b39f12929 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 17 Sep 2020 15:55:35 +0300
Subject: Apply pep8

* wqflask/utility/hmac.py: Apply pep8 and fix typo.
---
 wqflask/utility/hmac.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index b08be97e..fd75803e 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -7,11 +7,11 @@ from flask import url_for
 
 from wqflask import app
 
+
 def hmac_creation(stringy):
     """Helper function to create the actual hmac"""
 
     secret = app.config['SECRET_HMAC_CODE']
-
     hmaced = hmac.new(secret, stringy, hashlib.sha1)
     hm = hmaced.hexdigest()
     # ZS: Leaving the below comment here to ask Pjotr about
@@ -20,10 +20,12 @@ def hmac_creation(stringy):
     hm = hm[:20]
     return hm
 
+
 def data_hmac(stringy):
-    """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
+    """Takes arbitrary data string and appends :hmac so we know data hasn't been tampered with"""
     return stringy + ":" + hmac_creation(stringy)
 
+
 def url_for_hmac(endpoint, **values):
     """Like url_for but adds an hmac at the end to insure the url hasn't been tampered with"""
 
@@ -36,5 +38,6 @@ def url_for_hmac(endpoint, **values):
         combiner = "?"
     return url + combiner + "hm=" + hm
 
+
 app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
-                             data_hmac=data_hmac)
\ No newline at end of file
+                             data_hmac=data_hmac)
-- 
cgit v1.2.3


From 0fd23995fa21c32c2a6005b2fd70b0bd99d13214 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 17 Sep 2020 18:05:54 +0300
Subject: Mock "SECRET_HMAC_CODE"

* wqflask/tests/utility/test_hmac.py: Mock app.config's
"SECRET_HMAC_CODE" value.
---
 wqflask/tests/utility/test_hmac.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py
index c7927685..16b50771 100644
--- a/wqflask/tests/utility/test_hmac.py
+++ b/wqflask/tests/utility/test_hmac.py
@@ -12,24 +12,28 @@ from utility.hmac import hmac_creation
 class TestHmacUtil(unittest.TestCase):
     """Test Utility method for hmac creation"""
 
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
     def test_hmac_creation(self):
         """Test hmac creation with a utf-8 string"""
-        self.assertEqual(hmac_creation("ファイ"), "21fa1d935bbbb07a7875")
+        self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
 
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
     def test_data_hmac(self):
         """Test data_hmac fn with a utf-8 string"""
-        self.assertEqual(data_hmac("ファイ"), "ファイ:21fa1d935bbbb07a7875")
+        self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
 
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
     @mock.patch("utility.hmac.url_for")
     def test_url_for_hmac_with_plain_url(self, mock_url):
         """Test url_for_hmac without params"""
         mock_url.return_value = "https://mock_url.com/ファイ/"
         self.assertEqual(url_for_hmac("ファイ"),
-                         "https://mock_url.com/ファイ/?hm=a62896a50d9ffcff7deb")
+                         "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
 
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
     @mock.patch("utility.hmac.url_for")
     def test_url_for_hmac_with_param_in_url(self, mock_url):
         """Test url_for_hmac with params"""
         mock_url.return_value = "https://mock_url.com/?ファイ=1"
         self.assertEqual(url_for_hmac("ファイ"),
-                         "https://mock_url.com/?ファイ=1&hm=b2128fb28bc32da3b5b7")
+                         "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79")
-- 
cgit v1.2.3


From 75fe1adb2cfaf542bd22f33e8985938ca988661d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 18 Sep 2020 02:45:26 +0300
Subject: Apply pep8 formatting

---
 wqflask/utility/redis_tools.py | 120 ++++++++++++++++++++++++++++-------------
 1 file changed, 84 insertions(+), 36 deletions(-)

diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 81ba04ea..ef02268e 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -4,23 +4,21 @@ import uuid
 import simplejson as json
 import datetime
 
-import redis # used for collections
-
-import logging
-
-from flask import (render_template, flash)
-
-from utility import hmac
+import redis  # used for collections
 
+from utility.hmac import hmac_creation
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 def get_redis_conn():
     Redis = redis.StrictRedis(port=6379)
     return Redis
 
+
 Redis = get_redis_conn()
 
+
 def is_redis_available():
     try:
         Redis.ping()
@@ -28,6 +26,7 @@ def is_redis_available():
         return False
     return True
 
+
 def get_user_id(column_name, column_value):
     user_list = Redis.hgetall("users")
     key_list = []
@@ -38,6 +37,7 @@ def get_user_id(column_name, column_value):
 
     return None
 
+
 def get_user_by_unique_column(column_name, column_value):
     item_details = None
 
@@ -52,9 +52,11 @@ def get_user_by_unique_column(column_name, column_value):
 
     return item_details
 
+
 def get_users_like_unique_column(column_name, column_value):
-    """
-    Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+    """Like previous function, but this only checks if the input is a
+    subset of a field and can return multiple results
+
     """
     matched_users = []
 
@@ -74,7 +76,6 @@ def get_users_like_unique_column(column_name, column_value):
 
     return matched_users
 
-# def search_users_by_unique_column(column_name, column_value):
 
 def set_user_attribute(user_id, column_name, column_value):
     user_info = json.loads(Redis.hget("users", user_id))
@@ -82,6 +83,7 @@ def set_user_attribute(user_id, column_name, column_value):
 
     Redis.hset("users", user_id, json.dumps(user_info))
 
+
 def get_user_collections(user_id):
     collections = None
     collections = Redis.hget("collections", user_id)
@@ -91,22 +93,27 @@ def get_user_collections(user_id):
     else:
         return []
 
+
 def save_user(user, user_id):
     Redis.hset("users", user_id, json.dumps(user))
 
+
 def save_collections(user_id, collections_ob):
     Redis.hset("collections", user_id, collections_ob)
 
+
 def save_verification_code(user_email, code):
     Redis.hset("verification_codes", code, user_email)
 
+
 def check_verification_code(code):
     email_address = None
     user_details = None
     email_address = Redis.hget("verification_codes", code)
 
     if email_address:
-        user_details = get_user_by_unique_column('email_address', email_address)
+        user_details = get_user_by_unique_column(
+            'email_address', email_address)
         if user_details:
             return user_details
         else:
@@ -114,10 +121,12 @@ def check_verification_code(code):
     else:
         return None
 
+
 def get_user_groups(user_id):
-    #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups
-    admin_group_ids = []  #ZS: Group IDs where user is an admin
-    user_group_ids = []   #ZS: Group IDs where user is a regular user
+    # ZS: Get the groups where a user is an admin or a member and
+    # return lists corresponding to those two sets of groups
+    admin_group_ids = []  # ZS: Group IDs where user is an admin
+    user_group_ids = []  # ZS: Group IDs where user is a regular user
     groups_list = Redis.hgetall("groups")
     for key in groups_list:
         try:
@@ -142,6 +151,7 @@ def get_user_groups(user_id):
 
     return admin_groups, user_groups
 
+
 def get_group_info(group_id):
     group_json = Redis.hget("groups", group_id)
     group_info = None
@@ -150,6 +160,7 @@ def get_group_info(group_id):
 
     return group_info
 
+
 def get_group_by_unique_column(column_name, column_value):
     """ Get group by column; not sure if there's a faster way to do this """
 
@@ -158,7 +169,8 @@ def get_group_by_unique_column(column_name, column_value):
     all_group_list = Redis.hgetall("groups")
     for key in all_group_list:
         group_info = json.loads(all_group_list[key])
-        if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+        # ZS: Since these fields are lists, search in the list
+        if column_name == "admins" or column_name == "members":
             if column_value in group_info[column_name]:
                 matched_groups.append(group_info)
         else:
@@ -167,9 +179,11 @@ def get_group_by_unique_column(column_name, column_value):
 
     return matched_groups
 
+
 def get_groups_like_unique_column(column_name, column_value):
-    """
-    Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+    """Like previous function, but this only checks if the input is a
+    subset of a field and can return multiple results
+
     """
     matched_groups = []
 
@@ -178,7 +192,8 @@ def get_groups_like_unique_column(column_name, column_value):
         if column_name != "group_id":
             for key in group_list:
                 group_info = json.loads(group_list[key])
-                if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+                # ZS: Since these fields are lists, search in the list
+                if column_name == "admins" or column_name == "members":
                     if column_value in group_info[column_name]:
                         matched_groups.append(group_info)
                 else:
@@ -190,13 +205,15 @@ def get_groups_like_unique_column(column_name, column_value):
 
     return matched_groups
 
-def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"):
+
+def create_group(admin_user_ids, member_user_ids=[],
+                 group_name="Default Group Name"):
     group_id = str(uuid.uuid4())
     new_group = {
-        "id"    : group_id,
+        "id": group_id,
         "admins": admin_user_ids,
-        "members" : member_user_ids,
-        "name"  : group_name,
+        "members": member_user_ids,
+        "name": group_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')
     }
@@ -205,8 +222,9 @@ def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Gro
 
     return new_group
 
+
 def delete_group(user_id, group_id):
-    #ZS: If user is an admin of a group, remove it from the groups hash
+    # ZS: If user is an admin of a group, remove it from the groups hash
     group_info = get_group_info(group_id)
     if user_id in group_info["admins"]:
         Redis.hdel("groups", group_id)
@@ -214,9 +232,15 @@ def delete_group(user_id, group_id):
     else:
         None
 
-def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS "admins" is just to indicate whether the users should be added to the groups admins or regular users set
+
+# ZS "admins" is just to indicate whether the users should be added to
+# the groups admins or regular users set
+def add_users_to_group(user_id, group_id, user_emails=[], admins=False):
     group_info = get_group_info(group_id)
-    if user_id in group_info["admins"]: #ZS: Just to make sure that the user is an admin for the group, even though they shouldn't be able to reach this point unless they are
+    # ZS: Just to make sure that the user is an admin for the group,
+    # even though they shouldn't be able to reach this point unless
+    # they are
+    if user_id in group_info["admins"]:
         if admins:
             group_users = set(group_info["admins"])
         else:
@@ -231,25 +255,36 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
         else:
             group_info["members"] = list(group_users)
 
-        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime(
+            '%b %d %Y %I:%M%p')
         Redis.hset("groups", group_id, json.dumps(group_info))
         return group_info
     else:
         return None
 
-def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins
+
+# ZS: User type is because I assume admins can remove other admins
+def remove_users_from_group(user_id,
+                            users_to_remove_ids,
+                            group_id,
+                            user_type="members"):
     group_info = get_group_info(group_id)
 
     if user_id in group_info["admins"]:
         users_to_remove_set = set(users_to_remove_ids)
-        if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less
+        # ZS: Make sure an admin can't remove themselves from a group,
+        # since I imagine we don't want groups to be able to become
+        # admin-less
+        if user_type == "admins" and user_id in users_to_remove_set:
             users_to_remove_set.remove(user_id)
         group_users = set(group_info[user_type])
         group_users -= users_to_remove_set
         group_info[user_type] = list(group_users)
-        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime(
+            '%b %d %Y %I:%M%p')
         Redis.hset("groups", group_id, json.dumps(group_info))
 
+
 def change_group_name(user_id, group_id, new_name):
     group_info = get_group_info(group_id)
     if user_id in group_info["admins"]:
@@ -259,22 +294,28 @@ def change_group_name(user_id, group_id, new_name):
     else:
         return None
 
+
 def get_resources():
     resource_list = Redis.hgetall("resources")
     return resource_list
 
+
 def get_resource_id(dataset, trait_id=None):
     resource_id = False
     if dataset.type == "Publish":
         if trait_id:
-            resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
+            resource_id = hmac_creation("{}:{}:{}".format(
+                'dataset-publish', dataset.id, trait_id))
     elif dataset.type == "ProbeSet":
-        resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
+        resource_id = hmac_creation(
+            "{}:{}".format('dataset-probeset', dataset.id))
     elif dataset.type == "Geno":
-        resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
+        resource_id = hmac_creation(
+            "{}:{}".format('dataset-geno', dataset.id))
 
     return resource_id
 
+
 def get_resource_info(resource_id):
     resource_info = Redis.hget("resources", resource_id)
     if resource_info:
@@ -282,17 +323,23 @@ def get_resource_info(resource_id):
     else:
         return None
 
+
 def add_resource(resource_info, update=True):
     if 'trait' in resource_info['data']:
-        resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
+        resource_id = hmac_creation('{}:{}:{}'.format(
+            str(resource_info['type']), str(
+                resource_info['data']['dataset']),
+            str(resource_info['data']['trait'])))
     else:
-        resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset'])))
+        resource_id = hmac_creation('{}:{}'.format(
+            str(resource_info['type']), str(resource_info['data']['dataset'])))
 
     if update or not Redis.hexists("resources", resource_id):
         Redis.hset("resources", resource_id, json.dumps(resource_info))
 
     return resource_info
 
+
 def add_access_mask(resource_id, group_id, access_mask):
     the_resource = get_resource_info(resource_id)
     the_resource['group_masks'][group_id] = access_mask
@@ -301,9 +348,10 @@ def add_access_mask(resource_id, group_id, access_mask):
 
     return the_resource
 
+
 def change_resource_owner(resource_id, new_owner_id):
-    the_resource= get_resource_info(resource_id)
+    the_resource = get_resource_info(resource_id)
     the_resource['owner_id'] = new_owner_id
 
     Redis.delete("resource")
-    Redis.hset("resources", resource_id, json.dumps(the_resource))
\ No newline at end of file
+    Redis.hset("resources", resource_id, json.dumps(the_resource))
-- 
cgit v1.2.3


From 957a465d8a91f9100fc23f285d6f01bc6b087323 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 22 Sep 2020 03:19:29 +0300
Subject: Update bug_report template

* .github/ISSUE_TEMPLATE/bug_report.md: Update environment setup
section
---
 .github/ISSUE_TEMPLATE/bug_report.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index 789d6a57..7d7e34a5 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -26,7 +26,8 @@ If applicable, add screenshots to help explain your problem.
 **Environment setup (please complete the following information):**
 
 - OS: [e.g. Linux]
-- Racket Version [e.g. v7.6]
+- Guix Version (optional)
+- [Anything else you think is relevant]
 
 **Additional context**
 
-- 
cgit v1.2.3


From 125c75b724350dd750b8633410d4b9b3841ce984 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 22 Sep 2020 03:43:50 +0300
Subject: Update Mechanical Rob

* test/requests/main_web_functionality.py (check_search_page):
Breaking change introduced by updating text in search page. See:
9f76abc95
---
 test/requests/main_web_functionality.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py
index d070dab9..d4c3b1ad 100644
--- a/test/requests/main_web_functionality.py
+++ b/test/requests/main_web_functionality.py
@@ -20,7 +20,7 @@ def check_search_page(host):
         , search_terms_or=""
         , search_terms_and="MEAN=(15 16) LRS=(23 46)")
     result = requests.get(host+"/search", params=data)
-    found = result.text.find("records are shown below")
+    found = result.text.find("records were found")
     assert(found >= 0)
     assert(result.status_code == 200)
     print("OK")
-- 
cgit v1.2.3


From f184e2b4762d1ec5608d600dcb87406679212e39 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 22 Sep 2020 04:27:43 +0300
Subject: Add unittesting github action

* .github/workflows/main.yml: Add it.
---
 .github/workflows/main.yml | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 .github/workflows/main.yml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 00000000..4c8db1c4
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,31 @@
+name: tests
+
+# Run actions when pushing to the testing branch or when you create a
+# PR against it
+on:
+  push:
+    branches: [ testing ]
+  pull_request:
+    branches: [ testing ]
+
+jobs:
+  unittest:
+    runs-on: ubuntu-latest
+    container: bonfacekilz/python2-genenetwork2:latest
+
+    steps:
+    # Use v1 of checkout since v2 fails
+    - name: Checkout Project
+      uses: actions/checkout@v1
+
+    # Redis is required by some of the tests
+    - name: Start Redis
+      run: |
+        redis-server --daemonize yes
+
+    - name: Run the unit tests
+      run: |
+        mkdir -p /genotype_files/genotype/json
+        env GN2_PROFILE=/usr/gn2-profile TMPDIR=/tmp SERVER_PORT=5004 \
+        GENENETWORK_FILES=/genotype_files/ bash bin/genenetwork2 \
+        etc/default_settings.py -c -m unittest discover -v
-- 
cgit v1.2.3


From 9f49e2dbdf4e06fcb39ed5146560937f228682a7 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 22 Sep 2020 04:31:05 +0300
Subject: Update documentation on testing and CI

* README.md: Update section on testing.
* doc/docker-container.org: Add it.
---
 README.md                | 10 +++++-
 doc/docker-container.org | 86 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 95 insertions(+), 1 deletion(-)
 create mode 100644 doc/docker-container.org

diff --git a/README.md b/README.md
index 46264252..f1decb3c 100644
--- a/README.md
+++ b/README.md
@@ -42,9 +42,17 @@ Also mariadb and redis need to be running, see
 ## Testing
 
 To have tests pass, the redis and mariadb instance should be running, because of
-asserts sprinkled in the code base(these will be removed in due time).
+asserts sprinkled in the code base.
+
+Right now, the only tests running in CI are unittests. Please make
+sure the existing unittests are green when submitting a PR.
+
+See
+[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/doc/docker-container.org)
+for more details.
 
 #### Mechanical Rob
+
 We are building 'Mechanical Rob' automated testing using Python
 [requests](https://github.com/genenetwork/genenetwork2/tree/testing/test/requests)
 which can be run with:
diff --git a/doc/docker-container.org b/doc/docker-container.org
new file mode 100644
index 00000000..3c9864c5
--- /dev/null
+++ b/doc/docker-container.org
@@ -0,0 +1,86 @@
+#+TITLE: Genenetwork2 Dockerized
+
+* Table of Contents                                                     :TOC:
+- [[#introduction][Introduction]]
+- [[#creating-the-docker-images][Creating the Docker Images]]
+- [[#pushing-to-dockerhub][Pushing to DockerHub]]
+
+* Introduction
+
+The CI(Continuous Integration) system for Genenetwork2 uses [[https://github.com/features/actions][Github
+Actions]]. As such, it's important to have a way to run tests using
+facilities provided by GUIX in a reproducible way. This project
+leverages GUIX to generate a docker container from which the unittests
+are ran from.
+
+Find instructions on how to set docker up inside GUIX [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker][here]]. This
+document will not get into that. It's assumed that you have a working
+dockec setup.
+
+The rest of this document outlines how the docker container used in
+the CI builds were created.
+
+* Creating the Docker Images
+
+First create the image by running:
+
+#+begin_src sh
+# For the Python 2 version:
+env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \
+    ./pre-inst-env guix pack -f docker --no-grafts \
+    -S /usr/bin=/bin -S /etc/profile=/etc/profile \
+    -S /share/genenetwork2=/share/genenetwork2 \
+    -S /share/javascript=/share/javascript \
+    -S /lib=/lib \
+    -S /usr/gn2-profile=/ \
+    coreutils bash genenetwork2
+
+# For the Python 3 version:
+env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \
+    ./pre-inst-env guix pack -f docker --no-grafts \
+    -S /usr/bin=/bin -S /etc/profile=/etc/profile \
+    -S /share/genenetwork2=/share/genenetwork2 \
+    -S /share/javascript=/share/javascript \
+    -S /lib=/lib \
+    -S /usr/gn2-profile=/ \
+    coreutils bash python3-genenetwork2
+  #+end_src
+
+The output will look something similar to:
+
+: /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz
+
+Load the docker image by running:
+
+: docker load --input /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz
+
+Results look something similar to:
+
+#+begin_export ascii
+a93f52b7f565: Loading layer  3.174GB/3.174GB
+Loaded image: coreutils-genenetwork2:latest
+#+end_export
+
+Assuming you have a docker instance running, you could always run
+commands in it e.g:
+
+: docker run "coreutils-genenetwork2:latest" python --version 
+
+
+* Pushing to DockerHub
+
+We use DockerHub to store the docker images from which we use on our
+CI environment using Github Actions.
+
+To push to dockerhub, first get the image name by running =docker
+images=. Push to dockerhub using a command similar to:
+
+: docker push bonfacekilz/python2-genenetwork2:latest
+
+Right now, we have 2 images on DockerHub:
+
+- https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2:
+  Contains the python2 version of gn2. Don't use this. Please use the
+  python3 image!
+- https://hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2:
+  Contains the python3 version of gn2.
-- 
cgit v1.2.3


From 564b235bdc518a3ed91ca506ad2ac93d5bc91eef Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 22 Sep 2020 04:32:00 +0300
Subject: Add testing badge on README

* README.md: Badge becomes green on successful runs.
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index f1decb3c..cd35defb 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
 [![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2) [![JOSS](http://joss.theoj.org/papers/10.21105/joss.00025/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00025)
+[![Actions Status](https://github.com/genenetwork/genenetwork2/workflows/tests/badge.svg)](https://github.com/genenetwork/genenetwork2/actions)
 
 # GeneNetwork
 
-- 
cgit v1.2.3


From de3ffeea12ad38222eab3e1f4a179b67025fffd0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 22 Sep 2020 16:11:20 -0500
Subject: Replaced Chr and Mb/cM columns with a single position column in
 mapping results and also changes the -log(p) to use an endash instead

* wqflask/wqflask/marker_regression/run_mapping.py - added "display_pos"
to each marker object that is a combination of Chr and Mb/cM
* wqflask/wqflask/templates/mapping_results.html - Included
"display_pos" in results table and replaced -log(p) with using an endash
---
 wqflask/wqflask/marker_regression/run_mapping.py |  10 +-
 wqflask/wqflask/templates/mapping_results.html   | 118 +++++++++++------------
 2 files changed, 61 insertions(+), 67 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 9bde343c..8bc91b47 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -401,9 +401,7 @@ class RunMapping(object):
                           rs  = marker['name'],
                           pos  = this_ps
                       )
-                  #if 'p_value' in marker:
-                  #    logger.debug("P EXISTS:", marker['p_value'])
-                  #else:
+
                   if 'lrs_value' in marker and marker['lrs_value'] > 0:
                       browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61)
                   elif 'lod_score' in marker and marker['lod_score'] > 0:
@@ -417,6 +415,12 @@ class RunMapping(object):
                       if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
                           highest_chr = marker['chr']
                       if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
+                          if 'Mb' in marker.keys():
+                              marker['display_pos'] = str(marker['chr']) + "{.3f}".format(marker['Mb'])
+                          elif 'cM' in marker.keys():
+                              marker['display_pos'] = str(marker['chr']) + "{.3f}".format(marker['Mb'])
+                          else:
+                              marker['display_pos'] = "N/A"
                           self.qtl_results.append(marker)
 
               with Bench("Exporting Results"):
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 4ea7fa07..657731b1 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -229,70 +229,60 @@
         <br />
         <br />
           <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}500{% else %}470{% endif %}px;">
-          <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
-            <thead>
-              <tr>
-                <th></th>
-                <th>Row</th>
-                <th>Marker</th>
-                <th>{{ LRS_LOD }}</th>
-                <th>Chr</th>
-                {% if plotScale != "physic" %}
-                <th>cM</th>
-                {% else %}
-                <th align="right">Mb</th>
-                {% endif %}
-                {% if 'additive' in trimmed_markers[0] %}
-                <th>Add Eff</th>
-                {% endif %}
-                {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
-                <th>Dom Eff</th>
-                {% endif %}
-              </tr>
-            </thead>
-            <tbody>
-              {% for marker in trimmed_markers %}
-              <tr>
-                <td align="center" style="padding: 1px 0px 1px 0px;">
-                  <input type="checkbox" name="selectCheck"
-                         class="checkbox trait_checkbox"
-                         value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}">
-                </td>
-                <td align="right">{{ loop.index }}</td>
-                <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
-                {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
-                {% if 'lod_score' in marker %}
-                <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
-                {% else %}
-                <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
-                {% endif %}
-                {% else %}
-                {% if 'lod_score' in marker %}
-                <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
-                {% else %}
-                <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
-                {% endif %}
-                {% endif %}
-                <td align="right">{{marker.chr}}</td>
-                {% if plotScale != "physic" %}
-                {% if 'cM' in marker %}
-                <td align="right">{{ '%0.3f' | format(marker.cM|float) }}</td>
-                {% else %}
-                <td align="right">{{ '%0.3f' | format(marker.Mb|float) }}</td>
-                {% endif %}
-                {% else %}
-                <td align="right">{{ '%0.6f' | format(marker.Mb|float) }}</td>
-                {% endif %}
-                {% if 'additive' in marker %}
-                <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
-                {% endif %}
-                {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
-                <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
-                {% endif %}
-              </tr>
-              {% endfor %}
-            </tbody>
-          </table>
+            <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
+              <thead>
+                <tr>
+                  <th></th>
+                  <th>Row</th>
+                  <th>Marker</th>
+                  {% LRS_LOD == "-log(p)" %}
+                  <th>–log(p)</th>
+                  {% else %}
+                  <th>{{ LRS_LOD }}</th>
+                  {% endif %}
+                  <th>Position</th>
+                  {% if 'additive' in trimmed_markers[0] %}
+                  <th>Add Eff</th>
+                  {% endif %}
+                  {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
+                  <th>Dom Eff</th>
+                  {% endif %}
+                </tr>
+              </thead>
+              <tbody>
+                {% for marker in trimmed_markers %}
+                <tr>
+                  <td align="center" style="padding: 1px 0px 1px 0px;">
+                    <input type="checkbox" name="selectCheck"
+                           class="checkbox trait_checkbox"
+                           value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}">
+                  </td>
+                  <td align="right">{{ loop.index }}</td>
+                  <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
+                  {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
+                  {% if 'lod_score' in marker %}
+                  <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
+                  {% else %}
+                  <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
+                  {% endif %}
+                  {% else %}
+                  {% if 'lod_score' in marker %}
+                  <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
+                  {% else %}
+                  <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
+                  {% endif %}
+                  {% endif %}
+                  <td align="right">{{ marker.display_pos }}/td>
+                  {% if 'additive' in marker %}
+                  <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
+                  {% endif %}
+                  {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
+                  <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
+                  {% endif %}
+                </tr>
+                {% endfor %}
+              </tbody>
+            </table>
           </div>
         </div>
         {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %}
-- 
cgit v1.2.3


From 3687a5882ea94385d49b7bc91b01d5c9025ea40f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 22 Sep 2020 16:44:03 -0500
Subject: Fixed a couple mistakes in the previous commit and changed the
 position header on the mapping results page to include the mapping scale

* wqflask/wqflask/marker_regression/run_mapping.py - changed how
"display_pos" is defined for marker obs
* wqflask/wqflask/templates/mapping_results.html - Fixed issues with
last commit and changed position header name to include mapping scale
---
 wqflask/wqflask/marker_regression/run_mapping.py |  4 ++--
 wqflask/wqflask/templates/mapping_results.html   | 11 +++++------
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 8bc91b47..8a44b3fd 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -416,9 +416,9 @@ class RunMapping(object):
                           highest_chr = marker['chr']
                       if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
                           if 'Mb' in marker.keys():
-                              marker['display_pos'] = str(marker['chr']) + "{.3f}".format(marker['Mb'])
+                              marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['Mb'])
                           elif 'cM' in marker.keys():
-                              marker['display_pos'] = str(marker['chr']) + "{.3f}".format(marker['Mb'])
+                              marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM'])
                           else:
                               marker['display_pos'] = "N/A"
                           self.qtl_results.append(marker)
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 657731b1..41d760c0 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -228,19 +228,19 @@
         <button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
         <br />
         <br />
-          <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}500{% else %}470{% endif %}px;">
+          <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
             <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
               <thead>
                 <tr>
                   <th></th>
                   <th>Row</th>
                   <th>Marker</th>
-                  {% LRS_LOD == "-log(p)" %}
+                  {% if LRS_LOD == "-log(p)" %}
                   <th>–log(p)</th>
                   {% else %}
                   <th>{{ LRS_LOD }}</th>
                   {% endif %}
-                  <th>Position</th>
+                  <th>Position ({% if plotScale == "physic" %}Mb{% else %}cM{% endif %})</th>
                   {% if 'additive' in trimmed_markers[0] %}
                   <th>Add Eff</th>
                   {% endif %}
@@ -272,7 +272,7 @@
                   <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
                   {% endif %}
                   {% endif %}
-                  <td align="right">{{ marker.display_pos }}/td>
+                  <td align="right">{{ marker.display_pos }}</td>
                   {% if 'additive' in marker %}
                   <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
                   {% endif %}
@@ -352,8 +352,7 @@
                 "columns": [
                     { "type": "natural", "width": "5%" },
                     { "type": "natural", "width": "8%" },
-                    { "type": "natural", "width": "25%" },
-                    { "type": "natural" },
+                    { "type": "natural", "width": "20%" },
                     { "type": "natural" },
                     { "type": "natural" }{% if 'additive' in qtlresults[0] %},
                     { "type": "natural" }{% endif %}{% if 'dominance' in qtlresults[0] and dataset.group.genetic_type != "riset" %},
-- 
cgit v1.2.3


From f887ee8ca60d5c18c394b04a9bc5a9341da95327 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 22 Sep 2020 16:46:16 -0500
Subject: Added something to the mapping result page CSS to change the
 highlight color to match the high color in other tables

* wqflask/wqflask/static/new/css/marker_regression.css - changed
background color when selecting a row (i.e. "highlight color")
---
 wqflask/wqflask/static/new/css/marker_regression.css | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index f1a26a83..e0a5ceea 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -62,6 +62,10 @@ table.dataTable tbody td {
   padding: 4px 20px 2px 10px;
 }
 
+table.dataTable tbody tr.selected {
+  background-color: #ffee99;
+}
+
 table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
   border-top: 1px solid #ccc;
   border-right: 1px solid #ccc;
-- 
cgit v1.2.3


From 00cefa3d42c3e2b6633573eb124e1bcf68cea7ab Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 22 Sep 2020 16:47:24 -0500
Subject: Fixed a pretty big mistake where user accounts would be saved even
 when there was some mistake/error during registration

* wqflask/wqflask/user_login.py - Previously it would still save a user
even if there was some problem like their e-mail already being
associated with an account. It would display the error, but still run
save_user. I fixed this so that it no longer saves the user if there are
any errors
---
 wqflask/wqflask/user_login.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 9331f369..077a799b 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -453,7 +453,9 @@ def register_user(params):
         user_details['confirmed'] = 1
 
         user_details['registration_info'] = basic_info()
-        save_user(user_details, user_details['user_id'])
+
+        if len(errors) == 0:
+            save_user(user_details, user_details['user_id'])
 
         return errors
 
-- 
cgit v1.2.3


From fd151ade1d9f12157bc0ae25570e982122be0c7d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 23 Sep 2020 02:23:02 +0300
Subject: Fix failing tests

* wqflask/tests/base/test_trait.py: In python2 it's necessary to
decode the utf-8 string.
---
 wqflask/tests/base/test_trait.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
index 53b0d440..960f2c81 100644
--- a/wqflask/tests/base/test_trait.py
+++ b/wqflask/tests/base/test_trait.py
@@ -96,6 +96,6 @@ class TestRetrieveTraitInfo(unittest.TestCase):
         test_trait = retrieve_trait_info(trait=mock_trait,
                                          dataset=mock_dataset)
         self.assertEqual(test_trait.abbreviation,
-                         "ファイルを画面毎に見て行くには、次のコマンドを使います。")
+                         "ファイルを画面毎に見て行くには、次のコマンドを使います。".decode('utf-8'))
         self.assertEqual(test_trait.authors,
-                         "Jane Doe かいと")
+                         "Jane Doe かいと".decode('utf-8'))
-- 
cgit v1.2.3


From d9853ade5a70843c47792e8327301b7b3d5d4a6b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 23 Sep 2020 03:01:35 +0300
Subject: Fix failing builds

* wqflask/wqflask/__init__.py: Move imports from views.py to
"__init__.py". Fixes failing build.
* wqflask/wqflask/views.py: Ditto.
---
 wqflask/wqflask/__init__.py | 21 +++++++++++++-----
 wqflask/wqflask/views.py    | 53 ++++++++++++++++++++-------------------------
 2 files changed, 40 insertions(+), 34 deletions(-)

diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index d729aef5..7ed9c7b8 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -12,13 +12,24 @@ logging.basicConfig(level=logging.INFO)
 
 app = Flask(__name__)
 
-app.config.from_envvar('GN2_SETTINGS')       # See http://flask.pocoo.org/docs/config/#configuring-from-files
+# See http://flask.pocoo.org/docs/config/#configuring-from-files
 # Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
-
+app.config.from_envvar('GN2_SETTINGS')
 app.jinja_env.globals.update(
-    undefined = jinja2.StrictUndefined,
-    numify = formatting.numify
-)
+    undefined=jinja2.StrictUndefined,
+    numify=formatting.numify)
 
 from wqflask.api import router
+from wqflask import group_manager
+from wqflask import resource_manager
+from wqflask import search_results
+from wqflask import export_traits
+from wqflask import gsearch
+from wqflask import update_search_results
+from wqflask import docs
+from wqflask import news
+from wqflask import db_info
+from wqflask import user_login
+from wqflask import user_session
+
 import wqflask.views
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3d623736..42a10c7a 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -29,15 +29,7 @@ import array
 import sqlalchemy
 from wqflask import app
 from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
-from wqflask import group_manager
-from wqflask import resource_manager
-from wqflask import search_results
-from wqflask import export_traits
-from wqflask import gsearch
-from wqflask import update_search_results
-from wqflask import docs
-from wqflask import news
-from wqflask import db_info
+
 from wqflask.submit_bnw import get_bnw_input
 from base.data_set import create_dataset, DataSet    # Used by YAML in marker_regression
 from wqflask.show_trait import show_trait
@@ -54,6 +46,12 @@ from wqflask.correlation import corr_scatter_plot
 from wqflask.wgcna import wgcna_analysis
 from wqflask.ctl import ctl_analysis
 from wqflask.snp_browser import snp_browser
+from wqflask.search_results import SearchResultPage
+from wqflask.export_traits import export_search_results_csv
+from wqflask.gsearch import GSearch
+from wqflask.update_search_results import GSearch as UpdateGSearch
+from wqflask.docs import Docs
+from wqflask.db_info import InfoPage
 
 from utility import temp_data
 from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
@@ -67,9 +65,6 @@ from utility.benchmark import Bench
 
 from pprint import pformat as pf
 
-from wqflask import user_login
-from wqflask import user_session
-
 from wqflask import collect
 from wqflask.database import db_session
 
@@ -216,7 +211,7 @@ def search_page():
         logger.info("Skipping Redis cache (USE_REDIS=False)")
 
     logger.info("request.args is", request.args)
-    the_search = search_results.SearchResultPage(request.args)
+    the_search = SearchResultPage(request.args)
     result = the_search.__dict__
     valid_search = result['search_term_exists']
 
@@ -234,7 +229,7 @@ def search_page():
 @app.route("/gsearch", methods=('GET',))
 def gsearchact():
     logger.info(request.url)
-    result = gsearch.GSearch(request.args).__dict__
+    result = GSearch(request.args).__dict__
     type = request.args['type']
     if type == "gene":
         return render_template("gsearch_gene.html", **result)
@@ -245,7 +240,7 @@ def gsearchact():
 def gsearch_updating():
     logger.info("REQUEST ARGS:", request.values)
     logger.info(request.url)
-    result = update_search_results.GSearch(request.args).__dict__
+    result = UpdateGSearch(request.args).__dict__
     return result['results']
     # type = request.args['type']
     # if type == "gene":
@@ -258,7 +253,7 @@ def docedit():
     logger.info(request.url)
     try:
         if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com":
-            doc = docs.Docs(request.args['entry'], request.args)
+            doc = Docs(request.args['entry'], request.args)
             return render_template("docedit.html", **doc.__dict__)
         else:
             return "You shouldn't be here!"
@@ -274,7 +269,7 @@ def generated_file(filename):
 @app.route("/help")
 def help():
     logger.info(request.url)
-    doc = docs.Docs("help", request.args)
+    doc = Docs("help", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/wgcna_setup", methods=('POST',))
@@ -309,54 +304,54 @@ def ctl_results():
 
 @app.route("/news")
 def news():
-    doc = docs.Docs("news", request.args)
+    doc = Docs("news", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/references")
 def references():
-    doc = docs.Docs("references", request.args)
+    doc = Docs("references", request.args)
     return render_template("docs.html", **doc.__dict__)
     #return render_template("reference.html")
 
 @app.route("/intro")
 def intro():
-    doc = docs.Docs("intro", request.args)
+    doc = Docs("intro", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/policies")
 def policies():
-    doc = docs.Docs("policies", request.args)
+    doc = Docs("policies", request.args)
     #return render_template("policies.html")
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/links")
 def links():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("links.html")
 
 @app.route("/tutorials")
 def tutorials():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("tutorials.html")
 
 @app.route("/credits")
 def credits():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("credits.html")
 
 @app.route("/environments")
 def environments():
-    doc = docs.Docs("environments", request.args)
+    doc = Docs("environments", request.args)
     return render_template("docs.html", **doc.__dict__)
     #return render_template("environments.html", **doc.__dict__)
 
 @app.route("/update_text", methods=('POST',))
 def update_page():
     docs.update_text(request.form)
-    doc = docs.Docs(request.form['entry_type'], request.form)
+    doc = Docs(request.form['entry_type'], request.form)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/submit_trait")
@@ -371,7 +366,7 @@ def create_temp_trait():
 
     #template_vars = submit_trait.SubmitTrait(request.form)
 
-    doc = docs.Docs("links")
+    doc = Docs("links")
     return render_template("links.html", **doc.__dict__)
     #return render_template("show_trait.html", **template_vars.__dict__)
 
@@ -426,7 +421,7 @@ def export_traits_csv():
     logger.info("In export_traits_csv")
     logger.info("request.form:", request.form)
     logger.info(request.url)
-    file_list = export_traits.export_search_results_csv(request.form)
+    file_list = export_search_results_csv(request.form)
 
     if len(file_list) > 1:
         now = datetime.datetime.now()
@@ -911,7 +906,7 @@ def snp_browser_page():
 
 @app.route("/db_info", methods=('GET',))
 def db_info_page():
-    template_vars = db_info.InfoPage(request.args)
+    template_vars = InfoPage(request.args)
 
     return render_template("info_page.html", **template_vars.__dict__)
 
-- 
cgit v1.2.3


From 855558084a538ebdfec0bd43f829ba8d0d314a21 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 23 Sep 2020 03:05:42 +0300
Subject: Update github action to include mariadb service

* .github/workflows/main.yml: Add mariadb service. This makes the
build pass because somewhere(because of cyclic imports), a connection
to mariadb is required.
---
 .github/workflows/main.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4c8db1c4..94b0db75 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,6 +13,19 @@ jobs:
     runs-on: ubuntu-latest
     container: bonfacekilz/python2-genenetwork2:latest
 
+    services:
+      mariadb:
+        image: mariadb:latest
+        ports:
+          - 3306:3306
+        env:
+          MYSQL_USER: gn2
+          MYSQL_PASSWORD: mysql_password
+          MYSQL_ALLOW_EMPTY_PASSWORD: yes
+          MYSQL_DATABASE: db_webqtl_s
+          MYSQL_ROOT_PASSWORD: mysql_password
+        options: --health-cmd="mysqladmin ping" --health-interval=5s --health-timeout=2s --health-retries=3
+
     steps:
     # Use v1 of checkout since v2 fails
     - name: Checkout Project
-- 
cgit v1.2.3


From 1907457a00f0f7a9f7e74d8955265c8635f03bce Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 25 Sep 2020 03:55:33 +0300
Subject: Update github action

* .github/workflows/main.yml: Set up a mariadb and redis within the GH
action.
(services): Remove mariadb service.
---
 .github/workflows/main.yml | 40 ++++++++++++++++++++++------------------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 94b0db75..2fd9a886 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,32 +13,36 @@ jobs:
     runs-on: ubuntu-latest
     container: bonfacekilz/python2-genenetwork2:latest
 
-    services:
-      mariadb:
-        image: mariadb:latest
-        ports:
-          - 3306:3306
-        env:
-          MYSQL_USER: gn2
-          MYSQL_PASSWORD: mysql_password
-          MYSQL_ALLOW_EMPTY_PASSWORD: yes
-          MYSQL_DATABASE: db_webqtl_s
-          MYSQL_ROOT_PASSWORD: mysql_password
-        options: --health-cmd="mysqladmin ping" --health-interval=5s --health-timeout=2s --health-retries=3
-
     steps:
+    # First start with mariadb set then checkout. The checkout gives
+    # the mysqld enough time to start
+    - name: Set up mariadb
+      run: |
+        mysql_install_db --user=mysql --datadir=/usr/local/mysql
+        # Wait for the mysqld_safe process to start
+        mysqld_safe --user=mysql --datadir=/usr/local/mysql &
+
     # Use v1 of checkout since v2 fails
     - name: Checkout Project
       uses: actions/checkout@v1
 
-    # Redis is required by some of the tests
+    # Redis is required by some of the tests 6379
     - name: Start Redis
       run: |
-        redis-server --daemonize yes
+        /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server
+
+    # Redis is required by some of the tests 6379
+    - name: Bootstrap tables
+      run: |
+        mysql -u root -e "SHOW DATABASES;"
+        mysql -u root -e "CREATE DATABASE db_webqtl_s;"
+        mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';"
+        mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;"
 
     - name: Run the unit tests
       run: |
-        mkdir -p /genotype_files/genotype/json
-        env GN2_PROFILE=/usr/gn2-profile TMPDIR=/tmp SERVER_PORT=5004 \
-        GENENETWORK_FILES=/genotype_files/ bash bin/genenetwork2 \
+        env GN2_PROFILE=/gn2-profile \
+        TMPDIR=/tmp SERVER_PORT=5004 \
+        WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
+        GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
         etc/default_settings.py -c -m unittest discover -v
-- 
cgit v1.2.3


From 3ec4eb6b831eaa5adcf32a9fca8a60ea229cc1c4 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 25 Sep 2020 04:09:35 +0300
Subject: Update docs on CI setup with docker

* doc/docker-container.org: Update it.
---
 doc/docker-container.org | 61 +++++++++++++++++++++++++-----------------------
 1 file changed, 32 insertions(+), 29 deletions(-)

diff --git a/doc/docker-container.org b/doc/docker-container.org
index 3c9864c5..ec91824a 100644
--- a/doc/docker-container.org
+++ b/doc/docker-container.org
@@ -15,57 +15,60 @@ are ran from.
 
 Find instructions on how to set docker up inside GUIX [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker][here]]. This
 document will not get into that. It's assumed that you have a working
-dockec setup.
+docker setup.
 
 The rest of this document outlines how the docker container used in
-the CI builds were created.
+the CI builds was created.
 
 * Creating the Docker Images
 
-First create the image by running:
+The general idea is that GUIX is used to generate a set of binaries,
+which will be added to a base mariaDB image.
+
+First create the gn2 tar archive by running:
 
 #+begin_src sh
 # For the Python 2 version:
-env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \
-    ./pre-inst-env guix pack -f docker --no-grafts \
-    -S /usr/bin=/bin -S /etc/profile=/etc/profile \
-    -S /share/genenetwork2=/share/genenetwork2 \
-    -S /share/javascript=/share/javascript \
-    -S /lib=/lib \
-    -S /usr/gn2-profile=/ \
-    coreutils bash genenetwork2
+env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
+    ./pre-inst-env guix pack --no-grafts\
+    -S /gn2-profile=/ \
+    screen genenetwork2
 
 # For the Python 3 version:
-env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \
-    ./pre-inst-env guix pack -f docker --no-grafts \
-    -S /usr/bin=/bin -S /etc/profile=/etc/profile \
-    -S /share/genenetwork2=/share/genenetwork2 \
-    -S /share/javascript=/share/javascript \
-    -S /lib=/lib \
-    -S /usr/gn2-profile=/ \
-    coreutils bash python3-genenetwork2
+env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
+    ./pre-inst-env guix pack --no-grafts\
+    -S /gn2-profile=/ \
+    screen python3-genenetwork2
   #+end_src
 
 The output will look something similar to:
 
-: /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz
+: /gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz
+
+Now create a folder from which will host the following dockerfile. You
+can name this file Dockerfile. Note that mariadb is the base image
+since it already has mariadb installed for us.
+
+#+begin_src conf :mkdirp yes :tangle ~/docker/Dockerfile
+FROM mariadb:latest
 
-Load the docker image by running:
+COPY ./gn2.tar.gz /tmp/gn2.tar.gz
+RUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \
+    mkdir -p /usr/local/mysql /genotype_files/genotype/json
+#+end_src
 
-: docker load --input /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz
+Build the image(Note the fullstop at the end):
 
-Results look something similar to:
+: sudo docker build -t python2-genenetwork2:latest -f Dockerfile .
 
-#+begin_export ascii
-a93f52b7f565: Loading layer  3.174GB/3.174GB
-Loaded image: coreutils-genenetwork2:latest
-#+end_export
+To load the image interactively you've just created:
+
+: docker run -ti "python2-genenetwork2:latest" bash
 
 Assuming you have a docker instance running, you could always run
 commands in it e.g:
 
-: docker run "coreutils-genenetwork2:latest" python --version 
-
+: docker run "python2-genenetwork2:latest" python --version 
 
 * Pushing to DockerHub
 
-- 
cgit v1.2.3


From e247f43bf9bc31164948760694ff796bb469ae4c Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 28 Sep 2020 02:25:58 +0300
Subject: Update trait tests

* wqflask/tests/base/test_trait.py
(test_retrieve_trait_info_with_non_empty_lrs): Check
trait.LRS_score_repr is set correctly if trait.lrs is None.
(test_retrieve_trait_info_with_empty_lrs_field): Check
trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly
if trait.lrs is None.
(test_retrieve_trait_info_with_empty_chr_field): Check
test_trait.LRS_score_repr and test_trait.LRS_location_repr is set
correctly if trait.locus is None.
---
 wqflask/tests/base/test_trait.py | 134 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 134 insertions(+)

diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
index 960f2c81..1a3820f2 100644
--- a/wqflask/tests/base/test_trait.py
+++ b/wqflask/tests/base/test_trait.py
@@ -99,3 +99,137 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                          "ファイルを画面毎に見て行くには、次のコマンドを使います。".decode('utf-8'))
         self.assertEqual(test_trait.authors,
                          "Jane Doe かいと".decode('utf-8'))
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_non_empty_lrs(self,
+                                                    resource_id_mock,
+                                                    g_mock,
+                                                    requests_mock):
+        """Test """
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, 2.37, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2.7333, 2.1204]  # trait_info = g.db.execute(query).fetchone()
+        ]
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "2.4")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_lrs_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty lrs field"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, None, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2, 3]  # trait_info = g.db.execute(query).fetchone()
+        ]
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "Chr2: 3.000000")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_chr_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty chr field"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, 2, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [None, 3]  # trait_info = g.db.execute(query).fetchone()
+        ]
+
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "N/A")
-- 
cgit v1.2.3


From 312835014d8d243c72f3520bb116eb3c36cd6b85 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 28 Sep 2020 02:33:09 +0300
Subject: Convert None to "" in if statement

* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork
error: float argument required, not NoneType)"
---
 wqflask/base/trait.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7666348e..bdd9c3d6 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -599,12 +599,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                         trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
                 else:
                     trait.locus = trait.lrs = trait.additive = ""
-
-            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
+            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "":
                 trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
-                if trait.lrs != "":
+                if str(trait.lrs or "") != "":
                     trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
     else:
         raise KeyError, `trait.name`+' information is not found in the database.'
         
-    return trait
\ No newline at end of file
+    return trait
-- 
cgit v1.2.3


From d34258bed3ef13350499414100401df3bf08a105 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 28 Sep 2020 18:08:34 +0300
Subject: Fix casting error

* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
---
 wqflask/base/trait.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index bdd9c3d6..8f8b5b70 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -507,13 +507,14 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
             target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
-            if len(description_string) > 1 and description_string != 'None':
+            if str(description_string or "") != "" and description_string != 'None':
                 description_display = description_string
             else:
                 description_display = trait.symbol
 
-            if (len(description_display) > 1 and description_display != 'N/A' and
-                    len(target_string) > 1 and target_string != 'None'):
+            if (str(description_display or "") != "" and
+                description_display != 'N/A' and
+                str(target_string or "") != "" and target_string != 'None'):
                 description_display = description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
-- 
cgit v1.2.3


From a7316acfe9110ee8b7c1482d3eae613aa5d75d1a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Sep 2020 13:37:35 -0500
Subject: Changed add to collection to open the collection in a new tab/page so
 the results on the initial page aren't lost

* wqflask/wqflask/static/new/javascript/search_results.js - Changed the
add to collection method name to "add_to_collection" because it was
previously "add" which is a terrible method name

* wqflask/wqflask/templates/collections/add.html - Added target="_blank"
to the add to collection form so it will open in a new tab/window
---
 wqflask/wqflask/static/new/javascript/search_results.js | 4 ++--
 wqflask/wqflask/templates/collections/add.html          | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 685d6291..61134a88 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -93,7 +93,7 @@ $(function() {
 
   });
 
-  add = function() {
+  add_to_collection = function() {
     var traits;
     traits = $("#trait_table input:checked").map(function() {
       return $(this).val();
@@ -250,7 +250,7 @@ $(function() {
   $("#select_all").click(select_all);
   $("#deselect_all").click(deselect_all);
   $("#invert").click(invert);
-  $("#add").click(add);
+  $("#add").click(add_to_collection);
   $("#submit_bnw").click(submit_bnw);
   $("#export_traits").click(export_traits);
   $('.trait_checkbox, .btn').click(change_buttons);
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 825dfb84..62b6abb5 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -5,7 +5,7 @@
         or add to an existing collection.</p>
     </div>
     <div class="modal-body" style="margin-left: 20px;">
-        <form action="/collections/new" data-validate="parsley" id="add_form">
+        <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form">
             {% if traits is defined %}
             <input type="hidden" name="traits" value="{{ traits }}" />
             {% else %}
-- 
cgit v1.2.3


From 5ec0a7b0aa543203ade7920389fdf922865f59a0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Sep 2020 13:46:10 -0500
Subject: Changed the DataTables column sort arrows to a different color by
 changing the image they're referencing

* wqflask/wqflask/templates/base.html - Added CSS changing the table
sort arrow image directly into
base.html because it requires using url_for to reference the images in
the GUIX profile (so it needs to be in the template and can't just be
added to a CSS file)
---
 wqflask/wqflask/templates/base.html | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index e6802cc4..b44538cf 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -21,6 +21,14 @@
     {% block css %}
     {% endblock %}
 
+    <style>
+        table.dataTable thead .sorting_asc {
+            background-image: url({{ url_for("js", filename="DataTables/images/sort_asc_disabled.png") }});
+        }
+        table.dataTable thead .sorting_desc {
+            background-image: url({{ url_for("js", filename="DataTables/images/sort_desc_disabled.png") }});
+        }
+    </style>
 </head>
 
 <body style="width: 100%">
-- 
cgit v1.2.3


From 12a350c1185978602eaa91025c5ea5e7dd7bfbff Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Sep 2020 13:50:01 -0500
Subject: Changed Add (to collection) button color to match other Add buttons
 and changed the text for the GN1 link button

* wqflask/wqflask/templates/show_trait_details.html - Changed Add button
class to btn-success (to make it green like the other Add buttons) and
changed text from "View in GN1" to "Go to GN1"
---
 wqflask/wqflask/templates/show_trait_details.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 8b3e4907..2284ca99 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -216,7 +216,7 @@
 <div style="margin-bottom:15px;" class="btn-toolbar">
     <div class="btn-group">
         <a href="#redirect">
-        <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
+        <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button>
         </a>
         {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
         {% if this_trait.symbol != None %}
@@ -246,7 +246,7 @@
         {% endif %}
         {% endif %}
         <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
-        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">Go to GN1</button>
         </a>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
         <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
-- 
cgit v1.2.3


From 2637872ed32be6223eb464a76370a4e38850b5cd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Sep 2020 14:42:33 -0500
Subject: Fixed issue where negative additive effect values weren't being
 displayed in the "view collection" page

* wqflask/wqflask/templates/collections/view.html - Apparently the
correct way to check if a value can be cast to a float in Jinja2 is to
say "value != 0"; it previous said "value > 0" which exlcuded all
negative values
---
 wqflask/wqflask/templates/collections/view.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index dce814dd..13d45d62 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -144,7 +144,7 @@
                             <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">N/A</TD>
                             {% endif %}
                             <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD>
-                            {% if this_trait.additive|float > 0 %}
+                            {% if this_trait.additive|float != 0 %}
                             <TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD>
                             {% else %}
                             <TD data-export="{{ this_trait.additive }}" align="right">N/A</TD>
-- 
cgit v1.2.3


From 1320283cb1374365777dbe61e9c4ec6d42cba40d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Sep 2020 16:10:07 -0500
Subject: Made a variety of changes to table pages

* wqflask/wqflask/static/new/css/show_trait.css - Adding position
relative and a 2px offset for glyphicons to make them better align with
button text
* wqflask/wqflask/templates/collections/view.html - Added glyphicon to
Download button, changed a couple head names (Peak Location and Effect
Size), made Location and Peak Location columns the same width, and made
the "?" glossary links a little larger and red
* wqflask/wqflask/templates/search_result_page.html - same as above
* wqflask/wqflask/templates/show_trait_edit_data.html - Added glyphicon
to Export button
---
 wqflask/wqflask/static/new/css/show_trait.css       |  5 +++++
 wqflask/wqflask/templates/collections/view.html     | 10 ++++------
 wqflask/wqflask/templates/search_result_page.html   | 20 ++++++++++----------
 wqflask/wqflask/templates/show_trait_edit_data.html |  2 +-
 4 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 338302af..92deab20 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -46,4 +46,9 @@ table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
 table.dataTable.cell-border tbody tr th:first-child,
 table.dataTable.cell-border tbody tr td:first-child {
   border-left: 1px solid #ccc;
+}
+
+.glyphicon {
+  position: relative;
+  top: 2px;
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 13d45d62..ca8aece3 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -16,8 +16,6 @@
         </h1>
         <h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3>
 
-        <!--<hr style="height: 1px; background-color: #A9A9A9;">-->
-
         <div>
           <form id="collection_form" action="/delete" method="post">
             <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
@@ -77,7 +75,7 @@
             <input type="hidden" name="database_name" id="database_name" value="None">
             <input type="hidden" name="export_data" id="export_data" value="">
             <input type="hidden" name="file_name" id="file_name" value="collection_table">
-            <button class="btn btn-default" id="export_traits">Download CSV</button>
+            <button class="btn btn-default" id="export_traits">Download</button>
             <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ...">
             <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
             <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -99,9 +97,9 @@
                             <th data-export="Description">Description</th>
                             <th data-export="Location">Location</th>
                             <th data-export="Mean">Mean</th>
-                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup>?</sup></a></th>
-                            <th data-export="Max LRS Location">Max LRS Location</th>
-                            <th data-export="Add. Eff.">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th>
+                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
+                            <th data-export="Peak Location">Peak Location</th>
+                            <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                         </tr>
                     </thead>
 
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 282e752d..487c6980 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -127,7 +127,7 @@
               <input type="hidden" name="export_data" id="export_data" value="">
               <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button>
               <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
-              <button class="btn btn-default" id="export_traits">Download CSV</button>
+              <button class="btn btn-default" id="export_traits">Download <span class="glyphicon glyphicon-download"></span></button>
               <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
               <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
               <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -315,20 +315,20 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "80px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS Location",
+                      'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "150px",
+                      'width': "120px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "additive",
                       'width': "120px",
@@ -390,20 +390,20 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "80px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS Location",
+                      'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "150px",
+                      'width': "120px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'width': "120px",
                       'data': "additive",
@@ -412,7 +412,7 @@
                     {
                       'title': "Location",
                       'type': "natural-minus-na",
-                      'width': "140px",
+                      'width': "120px",
                       'data': "location"
                     }{% endif %}
                 ],
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 05a2be73..a8ed91b1 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -5,7 +5,7 @@
           <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control" style="width: 200px; display: inline; float: left; vertical-align: top;" placeholder="Search This Table For ...">
         </div>
         <div style="padding-left: 10px; display: inline;">
-          <input type="button" class="btn btn-default export" value="Export">
+          <button class="btn btn-default export">Export <span class="glyphicon glyphicon-download-alt"></span></button>
           <select class="select optional span2 export_format">
             <option value="excel">Excel</option>
             <option value="csv">CSV</option>
-- 
cgit v1.2.3


From 556ae146be4b2a7220e1f7634ca02bab587cbc7e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Sep 2020 16:23:39 -0500
Subject: Removed "Color By Trait" button from the Bar Chart, because it was
 meant to work with the figure we used before switching to Plotly. This
 feature will need to be redone to work with Plotly

* wqflask/wqflask/templates/show_trait_statistics.html - commented out
Color By Trait button until it's reimplemented
---
 wqflask/wqflask/templates/show_trait_statistics.html | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 974081d3..7bdb3ef9 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -76,11 +76,13 @@
                             <i class="icon-signal"></i> Sort By Value
                             </button>
                         </div>
+                        <!--
                         <div class="btn-group">
-                            <button type="button" class="btn btn-default" id="color_by_trait">
+                            <button type="button" class="btn btn-default" id="color_by_trait" style="margin-bottom: 5px;">
                                 <i class="icon-tint"></i> Color by Trait
                             </button>
                         </div>
+                        -->
                         <div id="bar_chart_container">
                             <div id="bar_chart"></div>
                         </div>
-- 
cgit v1.2.3


From 5a5dd3daf638cd95358bf102fd8d8c2023d44aae Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Sep 2020 16:41:29 -0500
Subject: Trait page link-out buttons were previously inside <a> tags, but this
 caused there to be a small line between buttons when hovering over them
 (because the <a> tags were wider than the button itself); this was changed to
 instead just be an "onclick" on the button (which is also a bit more concise)

* wqflask/wqflask/templates/show_trait_details.html - Replaced <a> tags
with onclick for trait page link-out buttons
---
 wqflask/wqflask/templates/show_trait_details.html | 30 ++++++-----------------
 1 file changed, 7 insertions(+), 23 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 2284ca99..4aced50c 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -215,43 +215,27 @@
 
 <div style="margin-bottom:15px;" class="btn-toolbar">
     <div class="btn-group">
-        <a href="#redirect">
         <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button>
-        </a>
         {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
         {% if this_trait.symbol != None %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
-        <button type="button" class="btn btn-default" title="Find similar expression data">Find</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}', '_blank')">Find</button>
         {% endif %}
         {% if UCSC_BLAT_URL != "" %}
-        <a target="_blank" href="{{ UCSC_BLAT_URL }}">
-        <button type="button" class="btn btn-default" title="Check probe locations at UCSC">Verify</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button>
         {% endif %}
         {% if this_trait.symbol != None %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}">
-        <button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">GeneWiki</button>
         {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
-        <a href="/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on">
-        <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button>
-        </a>
+        <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button>
         {% endif %}
         {% endif %}
         {% if show_probes == "True" %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON">
-        <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button>
         {% endif %}
         {% endif %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
-        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">Go to GN1</button>
-        </a>
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
-        <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
-            <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
-        </a>
+            <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit</button>
         {% endif %}
     </div>
 </div>
-- 
cgit v1.2.3


From 4bd5534658fe7ed2a9ffd50c137be81d7a7b190b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 30 Sep 2020 13:32:54 -0500
Subject: Removed unused code from TempDataSet class

* wqflask/base/data_set.py - TempDataSet class contained some code
referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore
---
 wqflask/base/data_set.py | 34 ----------------------------------
 1 file changed, 34 deletions(-)

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index afffe780..e0ef559c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1173,40 +1173,6 @@ class TempDataSet(DataSet):
         self.fullname = 'Temporary Storage'
         self.shortname = 'Temp'
 
-    @staticmethod
-    def handle_pca(desc):
-        if 'PCA' in desc:
-            # Todo: Modernize below lines
-            desc = desc[desc.rindex(':')+1:].strip()
-        else:
-            desc = desc[:desc.index('entered')].strip()
-        return desc
-
-    def get_desc(self):
-        query = 'SELECT description FROM Temp WHERE Name=%s' % self.name
-        logger.sql(query)
-        g.db.execute(query)
-        desc = g.db.fetchone()[0]
-        desc = self.handle_pca(desc)
-        return desc
-
-    def retrieve_sample_data(self, trait):
-        query = """
-                SELECT
-                        Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
-                FROM
-                        TempData, Temp, Strain
-                WHERE
-                        TempData.StrainId = Strain.Id AND
-                        TempData.Id = Temp.DataId AND
-                        Temp.name = '%s'
-                Order BY
-                        Strain.Name
-                """ % escape(trait.name)
-
-        logger.sql(query)
-        results = g.db.execute(query).fetchall()
-
 
 def geno_mrna_confidentiality(ob):
     dataset_table = ob.type + "Freeze"
-- 
cgit v1.2.3


From c291a82b0127048d3aa969f82d42d29acb142ea2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 30 Sep 2020 14:59:30 -0500
Subject: Fixed issue where columns sorted by inner text (text inside link
 tags) didn't sort all rows when a table is paginated and has more than one
 page

* wqflask/wqflask/static/new/javascript/search_results.js - Added
"extract_inner_text" function for getting the inner text from a string
containing HTML in order to avoid using DataTables' orderDataType (which
can only fetch values directly from the DOM, which is why sorting wasn't
working with multiple pages), and also included this function in the
"natural-minus-na" data type (so columns can be sorted that contain both
HTML/links and N/A values)
* wqflask/wqflask/templates/collections/view.html - Changed record column
to use "natural-minus-na" sort method in order to fix the inner-text
sorting issue + added sorting to the checkbox column (in the same way as
it already works in the search result page)
* wqflask/wqflask/templates/search_results_page.html - Replaced the
columns that used orderDataType with using the updated
"natural-minus-na" data type
* wqflask/wqflask/templates/correlation_page.html - Fixed issue where
N/As in the Year column (for phenotype correlations) were still displayed as links
---
 wqflask/wqflask/static/new/javascript/search_results.js | 10 ++++++++--
 wqflask/wqflask/templates/collections/view.html         | 14 +++++++-------
 wqflask/wqflask/templates/correlation_page.html         |  4 ++++
 wqflask/wqflask/templates/search_result_page.html       |  9 +--------
 4 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 61134a88..86660126 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -261,6 +261,12 @@ $(function() {
 
   let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A
 
+  function extract_inner_text(the_string){
+    var span = document.createElement('span');
+    span.innerHTML = the_string;
+    return span.textContent || span.innerText;
+  }
+
   function sort_NAs(a, b, sort_function){
     if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
       return 0;
@@ -276,10 +282,10 @@ $(function() {
 
   $.extend( $.fn.dataTableExt.oSort, {
     "natural-minus-na-asc": function (a, b) {
-      return sort_NAs(a, b, naturalAsc)
+      return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalAsc)
     },
     "natural-minus-na-desc": function (a, b) {
-      return sort_NAs(a, b, naturalDesc)
+      return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalDesc)
     }
   });
 
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index ca8aece3..bc487a59 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -164,13 +164,13 @@
 {% block js %}
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
-    <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
+    <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
 
 
     <script language="javascript" type="text/javascript">
@@ -185,10 +185,14 @@
             console.time("Creating table");
             $('#trait_table').dataTable( {
                 "columns": [
-                    { "type": "natural", "width": 10 },
+                    {
+                        "orderDataType": "dom-checkbox",
+                        "orderSequence": [ "desc", "asc"],
+                        "width": 10
+                    },
                     { "type": "natural", "width": 50 },
                     { "type": "natural" },
-                    { "type": "natural", "width": 120 },
+                    { 'type': "natural-minus-na", "width": 120 },
                     { "type": "natural" },
                     { "type": "natural"  },
                     { "type": "natural", "width": 130 },
@@ -197,10 +201,6 @@
                     { "type": "natural", "width": 130 },
                     { "type": "natural" }
                 ],
-                "columnDefs": [ {
-                    "targets": 0,
-                    "orderable": false
-                } ],
                 "order": [[1, "asc" ]],
                 buttons: [
                     {
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index e597bea9..03d93f14 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -175,9 +175,13 @@
                         <TD data-export="N/A">N/A</TD>
                         {% endif %}
                         <td data-export="{{ trait.pubmed_text }}">
+                            {% if trait.pubmed_text != "N/A" %}
                             <a href="{{ trait.pubmed_link }}">
                                 {{ trait.pubmed_text }}
                             </a>
+                            {% else %}
+                            {{ trait.pubmed_text }}
+                            {% endif %}
                         </td>
                         <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 487c6980..e2e1aa46 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -274,10 +274,9 @@
                     },
                     {
                       'title': "Record",
-                      'type': "natural",
+                      'type': "natural-minus-na",
                       'data': null,
                       'width': "60px",
-                      'orderDataType': "dom-inner-text",
                       'render': function(data, type, row, meta) {
                         return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
                       }
@@ -367,17 +366,11 @@
                           author_string = data.authors
                         }
                         return author_string
-                        // try {
-                        //   return decodeURIComponent(escape(author_string))
-                        // } catch(err){
-                        //   return author_string
-                        // }
                       }
                     },
                     {
                       'title': "Year",
                       'type': "natural-minus-na",
-                      'orderDataType': "dom-inner-text",
                       'data': null,
                       'width': "80px",
                       'render': function(data, type, row, meta) {
-- 
cgit v1.2.3


From 692f3b7c4ac608b5d71f1249a0596ccb1f781e76 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 30 Sep 2020 15:19:10 -0500
Subject: Added "natural-minus-na" sorting for relevant columns in the
 correlation page

* wqflask/wqflask/templates/correlation_page.html - Added
natural-minus-na type to columns that can contain N/A values, since I
apparently forgot to add it to this table before
---
 wqflask/wqflask/templates/correlation_page.html | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 03d93f14..bb2a697f 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -369,9 +369,9 @@
                     { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
                     { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
                     { "type": "scientific" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" }
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" }
                 ],
                 "createdRow": function ( row, data, index ) {
                     $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
@@ -423,13 +423,13 @@
                     { "type": "natural" },
                     { "type": "natural", "width": "20%" },
                     { "type": "natural", "width": "12%" },
-                    { "orderDataType": "dom-innertext" },
+                    { "type": "natural-minus-na" },
                     { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
                     { "type": "natural" },
                     { "type": "scientific" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" }
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" }
                 ],
                 "order": [[9, "asc" ]],
                 "sDom": "Btir",
@@ -465,7 +465,7 @@
                     { "type": "natural" },
                     { "type": "natural" },
                     { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
-                    { "type": "natural" },
+                    { "type": "natural-minus-na" },
                     { "type": "scientific" }
                 ],
                 "order": [[6, "asc" ]],
-- 
cgit v1.2.3


From 8a01dca227aa03e794ced5f99513355f2a035f2f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 30 Sep 2020 15:37:10 -0500
Subject: Changed the logic for adding 0 to the PCA results to do so when the
 shared samples are < 2 instead of 0; this fixed the error when running the
 correlation matrix, but results in the PCA traits having no values

* wqflask/wqflask/correlation_matrx/show_corr_matrix.py - changed
"if num_overlap == 0" to "if num_overlap < 2" because correlations can't
be run if there are fewer than 2 shared samples (and previously would
throw an error if there was exactly 1 shared sample)
---
 wqflask/wqflask/correlation_matrix/show_corr_matrix.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 0ac94139..3beee84f 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -147,7 +147,7 @@ class CorrelationMatrix(object):
 
                     if num_overlap < self.lowest_overlap:
                         self.lowest_overlap = num_overlap
-                    if num_overlap == 0:
+                    if num_overlap < 2:
                         corr_result_row.append([target_trait, 0, num_overlap])
                         pca_corr_result_row.append(0)
                     else:
-- 
cgit v1.2.3


From 8c0ab33592e29bf6bae14ba4831dde8a53a27363 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 2 Oct 2020 14:54:09 -0500
Subject: Checked if owner_id is "none" to avoid an error when trying to access
 the resource manager page with newly added datasets

* wqflask/wqflask/resource_manager.py - Only get owner user info conditional on owner_id not being "none" (which it will be by default for newly added datasets). Previously it would throw an error due to "owner_info" being None
---
 wqflask/wqflask/resource_manager.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 39a07310..14ff2183 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -25,16 +25,16 @@ def manage_resource():
         group_masks_with_names = get_group_names(group_masks)
         default_mask = resource_info['default_mask']['data']
         owner_id = resource_info['owner_id']
-        owner_info = get_user_by_unique_column("user_id", owner_id)
-
-        if 'name' in owner_info:
-            owner_display_name = owner_info['full_name']
-        elif 'user_name' in owner_info:
-            owner_display_name = owner_info['user_name']
-        elif 'email_address' in owner_info:
-            owner_display_name = owner_info['email_address']
-        else:
-            owner_display_name = None
+
+        owner_display_name = None
+        if owner_id != "none":
+            owner_info = get_user_by_unique_column("user_id", owner_id)
+            if 'name' in owner_info:
+                owner_display_name = owner_info['full_name']
+            elif 'user_name' in owner_info:
+                owner_display_name = owner_info['user_name']
+            elif 'email_address' in owner_info:
+                owner_display_name = owner_info['email_address']
 
         return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
 
-- 
cgit v1.2.3


From 17fe50912ee358dbacaaa402a55e1fcfa14f7e85 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 6 Oct 2020 14:19:21 -0500
Subject: Fixed issue where drop-down arrows and textarea corners couldn't be
 clicked with certain window widths

* wqflask/wqflask/templates/index_page_orig.html - Changed the left/right div's padding to prevent them from overlapping and changed the textareas' styles to make them only expandable vertically
---
 wqflask/wqflask/templates/index_page_orig.html | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 06b71f53..6b3bec9a 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -17,13 +17,13 @@
     </header>
 -->
 
-    <div class="container-fluid" style="min-width: 1200px;">
+    <div class="container-fluid" style="min-width: 1210px;">
 
         {{ flash_me() }}
 
         <div class="row" style="width: 100%;">
 
-            <div class="col-xs-5" style="min-width: 530px; max-width: 550px;">
+            <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;">
                 <section id="search">
                     <div>
                         <h1>Select and search</h1>
@@ -84,7 +84,7 @@
                                     <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
                                     <div class="col-xs-10 controls" style="padding-left: 20px;">
                                         <div class="col-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
+                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -105,7 +105,7 @@
                                     <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
                                     <div class="col-xs-10 controls" style="padding-left: 20px;">
                                         <div class="col-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -184,7 +184,7 @@
                 </section>
             </div>
 
-            <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;">
+            <div class="col-xs-4" style="width: 600px !important;">
 	        <section id="affiliates">
 	            <div class="page-header">
                         <h1>Affiliates</h1>
-- 
cgit v1.2.3


From 2583c3347f0f5a655df6c095a5162dc8d49c4fde Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 6 Oct 2020 15:35:07 -0500
Subject: Made change that should fix error when trying to change page text
 using ckeditor

* wqflask/wqflask/docs.py - Changed query to include casting as binary to deal with certain unicode characters in ckeditor pages
* wqflask/wqflask/views.py - Imported update_text from Docs since it previously wasn't updated, causing an error when attempting to update text
---
 wqflask/wqflask/docs.py  | 4 ++--
 wqflask/wqflask/views.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 78407e22..9fad1cf1 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -11,7 +11,7 @@ class Docs(object):
 
     def __init__(self, entry, start_vars={}):
         sql = """
-            SELECT Docs.title, Docs.content
+            SELECT Docs.title, CAST(Docs.content AS BINARY)
             FROM Docs
             WHERE Docs.entry LIKE %s
             """
@@ -22,7 +22,7 @@ class Docs(object):
             self.content = ""
         else:
             self.title = result[0]
-            self.content = result[1].encode("latin1")
+            self.content = result[1]
 
         self.editable = "false"
         # ZS: Removing option to edit to see if text still gets vandalized
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 42a10c7a..94ec7137 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -50,7 +50,7 @@ from wqflask.search_results import SearchResultPage
 from wqflask.export_traits import export_search_results_csv
 from wqflask.gsearch import GSearch
 from wqflask.update_search_results import GSearch as UpdateGSearch
-from wqflask.docs import Docs
+from wqflask.docs import Docs, update_text
 from wqflask.db_info import InfoPage
 
 from utility import temp_data
@@ -350,7 +350,7 @@ def environments():
 
 @app.route("/update_text", methods=('POST',))
 def update_page():
-    docs.update_text(request.form)
+    update_text(request.form)
     doc = Docs(request.form['entry_type'], request.form)
     return render_template("docs.html", **doc.__dict__)
 
-- 
cgit v1.2.3


From b09fc33754dd8f250332180eefa988e77a6f898c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 13:21:27 -0500
Subject: When generating links to correlation scatterplots (in corr results
 and corr matrix), append the group name to Temp dataset names so temp traits
 can be used in scatterplot

* wqflask/wqflask/correlation/corr_scatter_plot.py - Create the dataset object using the group name included with Temp dataset names (which take the form "Temp_(group_name)")
* wqflask/wqflask/templates/correlation_matrix.html - Change scatterplot links to include the group name if the dataset name is "Temp"
* wqflask/wqflask/templates/correlation_page.html - Change scatterplot links to include the group name if the dataset name is "Temp" + a couple minor style changes
---
 wqflask/wqflask/correlation/corr_scatter_plot.py  | 11 +++++++++--
 wqflask/wqflask/templates/correlation_matrix.html |  2 +-
 wqflask/wqflask/templates/correlation_page.html   | 12 ++++++------
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 819836b1..0f3d455c 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -17,8 +17,15 @@ class CorrScatterPlot(object):
     """Page that displays a correlation scatterplot with a line fitted to it"""
 
     def __init__(self, params):
-        self.dataset_1 = data_set.create_dataset(params['dataset_1'])
-        self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+        if "Temp" in params['dataset_1']:
+            self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1])
+        else:
+            self.dataset_1 = data_set.create_dataset(params['dataset_1'])
+        if "Temp" in params['dataset_2']:
+            self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1])
+        else:
+            self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+
         #self.dataset_3 = data_set.create_dataset(params['dataset_3'])
         self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1)
         self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 9b96de1c..d556f31a 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -51,7 +51,7 @@
       {% if result[0].name == trait.name and result[0].dataset == trait.dataset %}
       <td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td>
       {% else %}
-      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
+      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
       {% endif %}
       {% endfor %}
     </tr>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index bb2a697f..fb218e29 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -144,7 +144,7 @@
                         <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD>
                         <td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td>
                         <td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                         {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
@@ -164,15 +164,15 @@
                         <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Publish" %}
                         {% if trait.abbreviation %}
-                        <TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD>
+                        <td title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</td>
                         {% else %}
-                        <TD data-export="N/A">N/A</TD>
+                        <td data-export="N/A">N/A</td>
                         {% endif %}
                         <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
                         {% if trait.authors %}
                         <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
                         {% else %}
-                        <TD data-export="N/A">N/A</TD>
+                        <td data-export="N/A">N/A</td>
                         {% endif %}
                         <td data-export="{{ trait.pubmed_text }}">
                             {% if trait.pubmed_text != "N/A" %}
@@ -183,7 +183,7 @@
                             {{ trait.pubmed_text }}
                             {% endif %}
                         </td>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                         <td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td>
@@ -191,7 +191,7 @@
                         <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Geno" %}
                         <td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</TD>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                       {% endif %}
-- 
cgit v1.2.3


From cfb45c4e6980e9f37b12ac4f4c2016ac8a37efe2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 14:52:49 -0500
Subject: Changed the min-width of trait page main div in order to allow trait
 descriptions to shrink to a smaller width (but not too small)

* wqflask/wqflask/templates/show_trait.html - Changed width of main container div to 700px
---
 wqflask/wqflask/templates/show_trait.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 56df2049..ea881917 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -37,7 +37,7 @@
         <input type="hidden" name="covariates" value="">
         <input type="hidden" name="transform" value="">
 
-        <div class="container" style="min-width: 1450px;">
+        <div class="container" style="min-width: 700px;">
             <div class="panel-group" id="accordion">
                 <div class="panel panel-default">
                     <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true">
-- 
cgit v1.2.3


From a79e099d6ce428459affd44afc8f795dd7561fae Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 14:54:02 -0500
Subject: Adjusted some widths/classes to allow correlation description text to
 expand/shrink with screen size and make drop-downs a better width

* wqflask/wqflask/templates/show_trait_calculate_correlations.html - Adjusted widths of drop-down divs and removed the col-width class from the description div (the right side) so it can shrink wqwith screen size
---
 .../wqflask/templates/show_trait_calculate_correlations.html | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 1378b91b..9420c9c6 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,5 +1,5 @@
 <div>
-  <div class="col-xs-7">
+  <div class="col-xs-6" style="min-width: 800px;">
     <div style="padding: 20px" class="form-horizontal">
         
         <div class="form-group">
@@ -39,7 +39,7 @@
         
         <div class="form-group">
             <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_return_results" class="form-control">
                     {% for return_result in corr_tools.return_results_menu %}
                         <option value="{{ return_result }}" 
@@ -55,7 +55,7 @@
         
         <div class="form-group">
             <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_samples_group" class="form-control">
                     {% for group, pretty_group in sample_group_types.items() %}
                         <option value="{{ group }}">{{ pretty_group }}</option>
@@ -66,7 +66,7 @@
             
         <div id="corr_sample_method" class="form-group">
             <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_sample_method" class="form-control">
                     <option value="pearson">Pearson</option>
                     <option value="spearman">Spearman Rank</option>
@@ -77,7 +77,7 @@
         {% if dataset.type != "Publish" %}
         <div class="form-group">
             <label class="col-xs-2 control-label">Min Expr</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <input name="min_expr" value="" type="text" class="form-control" style="width: 70px;">
             </div>
         </div>
@@ -114,7 +114,7 @@
         </div>
     </div>
   </div>
-  <div class="col-xs-5">
+  <div>
     <span id="sample_r_desc" class="correlation_desc fs12">
         The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
         is computed
-- 
cgit v1.2.3


From 205f2277493fca1d7b8a0520438767296a9c20d4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 14:55:54 -0500
Subject: Allowed mapping method description text to shrink with screen size

* wqflask/wqflask/templates/show_trait_mapping_tools.html - Removed the "col-xs-_" class to allow the div containing mapping description text to shrink with screen size
---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 27040045..94388b2f 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -397,8 +397,8 @@
             </div>
         </div>
     </div>
-    <div class="col-xs-7">
-        <dl style="width: 500px;">
+    <div>
+        <dl>
              {% for mapping_method in dataset.group.mapping_names %}
              {% if mapping_method == "GEMMA" %}
              <dt style="padding-top: 20px;">GEMMA</dt>
-- 
cgit v1.2.3


From 217f527e873d5197c7efcaec627e1df5afadefa4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 15:32:18 -0500
Subject: Fixed issue where new phenotype groups wouldn't be saved to the
 self.datasets property because the group name was used as the key (instead of
 the group name + "Publish", which is the full dataset name for phenotypes)

* wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets
---
 wqflask/base/data_set.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index e0ef559c..aeafc027 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -150,10 +150,11 @@ Publish or ProbeSet. E.g.
             "geno": "Geno",
         }
 
+        group_name = name
         if t in ['pheno', 'other_pheno']:
-            name = name.replace("Publish", "")
+            group_name = name.replace("Publish", "")
 
-        if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())):
+        if bool(len(g.db.execute(sql_query_mapping[t].format(group_name)).fetchone())):
             self.datasets[name] = dataset_name_mapping[t]
             self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
             return True
-- 
cgit v1.2.3


From 3d444c29ab975e313534dd7c57747b3e79f06c26 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 8 Oct 2020 15:40:18 -0500
Subject: Fixed remaining issue that applies to all dataset types

* wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results
---
 wqflask/base/data_set.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index aeafc027..2f1549ae 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -154,7 +154,8 @@ Publish or ProbeSet. E.g.
         if t in ['pheno', 'other_pheno']:
             group_name = name.replace("Publish", "")
 
-        if bool(len(g.db.execute(sql_query_mapping[t].format(group_name)).fetchone())):
+        results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone()
+        if results:
             self.datasets[name] = dataset_name_mapping[t]
             self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
             return True
-- 
cgit v1.2.3


From 4d16656304b9702c124721e82ea0dcda3c40ae44 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 29 Sep 2020 15:57:01 +0300
Subject: Add test for process_traits from collections.py

* wqflask/tests/wqflask/test_collect.py: Add it.
---
 wqflask/tests/wqflask/test_collect.py | 57 +++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 wqflask/tests/wqflask/test_collect.py

diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/wqflask/test_collect.py
new file mode 100644
index 00000000..6b8d7931
--- /dev/null
+++ b/wqflask/tests/wqflask/test_collect.py
@@ -0,0 +1,57 @@
+"""Test cases for some methods in collect.py"""
+
+import unittest
+import mock
+
+from flask import Flask
+from wqflask.collect import process_traits
+
+app = Flask(__name__)
+
+
+class MockSession:
+    """Helper class for mocking wqflask.collect.g.user_session.logged_in"""
+    def __init__(self, is_logged_in=False):
+        self.is_logged_in = is_logged_in
+
+    @property
+    def logged_in(self):
+        return self.is_logged_in
+
+
+class MockFlaskG:
+    """Helper class for mocking wqflask.collect.g.user_session"""
+    def __init__(self, is_logged_in=False):
+        self.is_logged_in = is_logged_in
+
+    @property
+    def user_session(self):
+        if self.is_logged_in:
+            return MockSession(is_logged_in=True)
+        return MockSession()
+
+
+class TestCollect(unittest.TestCase):
+
+    def setUp(self):
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    @mock.patch("wqflask.collect.g", MockFlaskG())
+    def test_process_traits_when_user_is_logged_out(self):
+        """
+        Test that the correct traits are returned when the user is logged
+        out
+        """
+        self.assertEqual(process_traits(
+            b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,'
+            b'1452447_at:HC_M2_0606_P:eeece8fceb67072debea,'
+            b'1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,'
+            b'1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'),
+            set(['1429252_at:HC_M2_0606_P',
+                 '1451401_a_at:HC_M2_0606_P',
+                 '1452447_at:HC_M2_0606_P',
+                 '1452452_at:HC_M2_0606_P']))
-- 
cgit v1.2.3


From eae4f1e6fad57a77063a637f0b03c171b6437565 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 29 Sep 2020 14:57:25 +0300
Subject: Apply PEP 8 to buffer

* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8
* wqflask/wqflask/collect.py: Ditto
* wqflask/base/trait.py: Ditto
---
 wqflask/base/trait.py                   | 194 +++++++++++++++++++-------------
 wqflask/wqflask/collect.py              |  37 +++---
 wqflask/wqflask/wgcna/wgcna_analysis.py | 181 +++++++++++++++++------------
 3 files changed, 238 insertions(+), 174 deletions(-)

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 8f8b5b70..7ebbc4bb 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,4 +1,10 @@
 from __future__ import absolute_import, division, print_function
+from utility.logger import getLogger
+from flask import Flask, g, request, url_for, redirect, make_response, render_template
+from pprint import pformat as pf
+from MySQLdb import escape_string as escape
+import simplejson as json
+from wqflask import app
 
 import os
 import string
@@ -16,22 +22,19 @@ from utility import webqtlUtil
 from utility import hmac
 from utility.authentication_tools import check_resource_availability
 from utility.tools import GN2_BASE_URL, GN_VERSION
-from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info
-Redis = get_redis_conn()
+from utility.redis_tools import get_redis_conn
+from utility.redis_tools import get_resource_id
+from utility.redis_tools import get_resource_info
 
-from wqflask import app
+Redis = get_redis_conn()
 
-import simplejson as json
-from MySQLdb import escape_string as escape
-from pprint import pformat as pf
 
-from flask import Flask, g, request, url_for, redirect, make_response, render_template
+logger = getLogger(__name__)
 
-from utility.logger import getLogger
-logger = getLogger(__name__ )
 
 def create_trait(**kw):
-    assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
+    assert bool(kw.get('dataset')) != bool(
+        kw.get('dataset_name')), "Needs dataset ob. or name"
 
     permitted = True
     if kw.get('name'):
@@ -43,18 +46,21 @@ def create_trait(**kw):
 
         if kw.get('dataset_name') != "Temp":
             if dataset.type == 'Publish':
-                permissions = check_resource_availability(dataset, kw.get('name'))
+                permissions = check_resource_availability(
+                    dataset, kw.get('name'))
             else:
                 permissions = check_resource_availability(dataset)
 
     if "view" in permissions['data']:
         the_trait = GeneralTrait(**kw)
         if the_trait.dataset.type != "Temp":
-            the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
+            the_trait = retrieve_trait_info(
+                the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
         return the_trait
     else:
         return None
 
+
 class GeneralTrait(object):
     """
     Trait class defines a trait in webqtl, can be either Microarray,
@@ -64,12 +70,15 @@ class GeneralTrait(object):
 
     def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
         # xor assertion
-        assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
-        self.name = kw.get('name')                 # Trait ID, ProbeSet ID, Published ID, etc.
+        assert bool(kw.get('dataset')) != bool(
+            kw.get('dataset_name')), "Needs dataset ob. or name"
+        # Trait ID, ProbeSet ID, Published ID, etc.
+        self.name = kw.get('name')
         if kw.get('dataset_name'):
             if kw.get('dataset_name') == "Temp":
                 temp_group = self.name.split("_")[2]
-                self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+                self.dataset = create_dataset(
+                    dataset_name="Temp", dataset_type="Temp", group_name=temp_group)
             else:
                 self.dataset = create_dataset(kw.get('dataset_name'))
         else:
@@ -77,7 +86,8 @@ class GeneralTrait(object):
         self.cellid = kw.get('cellid')
         self.identification = kw.get('identification', 'un-named trait')
         self.haveinfo = kw.get('haveinfo', False)
-        self.sequence = kw.get('sequence')         # Blat sequence, available for ProbeSet
+        # Blat sequence, available for ProbeSet
+        self.sequence = kw.get('sequence')
         self.data = kw.get('data', {})
         self.view = True
 
@@ -125,11 +135,11 @@ class GeneralTrait(object):
                     vals.append(sample_data.value)
                     the_vars.append(sample_data.variance)
                     sample_aliases.append(sample_data.name2)
-        return  samples, vals, the_vars, sample_aliases
+        return samples, vals, the_vars, sample_aliases
 
     @property
     def description_fmt(self):
-        '''Return a text formated description'''
+        """Return a text formated description"""
         if self.dataset.type == 'ProbeSet':
             if self.description:
                 formatted = self.description
@@ -149,7 +159,7 @@ class GeneralTrait(object):
 
     @property
     def alias_fmt(self):
-        '''Return a text formatted alias'''
+        """Return a text formatted alias"""
 
         alias = 'Not available'
         if getattr(self, "alias", None):
@@ -160,16 +170,20 @@ class GeneralTrait(object):
 
     @property
     def wikidata_alias_fmt(self):
-        '''Return a text formatted alias'''
+        """Return a text formatted alias"""
 
         alias = 'Not available'
         if self.symbol:
-            human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
-            mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
-            other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
+            human_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
+            mouse_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
+            other_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
 
             if human_response and mouse_response and other_response:
-                alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content)
+                alias_list = json.loads(human_response.content) + json.loads(
+                    mouse_response.content) + json.loads(other_response.content)
 
                 filtered_aliases = []
                 seen = set()
@@ -183,31 +197,31 @@ class GeneralTrait(object):
 
         return alias
 
-
     @property
     def location_fmt(self):
-        '''Return a text formatted location
+        """Return a text formatted location
 
         While we're at it we set self.location in case we need it later (do we?)
 
-        '''
+        """
 
         if self.chr and self.mb:
-            self.location = 'Chr %s @ %s Mb'  % (self.chr,self.mb)
+            self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb)
         elif self.chr:
             self.location = 'Chr %s @ Unknown position' % (self.chr)
         else:
             self.location = 'Not available'
 
         fmt = self.location
-        ##XZ: deal with direction
+        # XZ: deal with direction
         if self.strand_probe == '+':
             fmt += (' on the plus strand ')
         elif self.strand_probe == '-':
             fmt += (' on the minus strand ')
 
         return fmt
-        
+
+
 def retrieve_sample_data(trait, dataset, samplelist=None):
     if samplelist == None:
         samplelist = []
@@ -225,16 +239,19 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
             all_samples_ordered = dataset.group.all_samples_ordered()
             for i, item in enumerate(results):
                 try:
-                    trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
+                    trait.data[all_samples_ordered[i]] = webqtlCaseData(
+                        all_samples_ordered[i], float(item))
                 except:
                     pass
         else:
             for item in results:
                 name, value, variance, num_cases, name2 = item
                 if not samplelist or (samplelist and name in samplelist):
-                    trait.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
+                    # name, value, variance, num_cases)
+                    trait.data[name] = webqtlCaseData(*item)
     return trait
 
+
 @app.route("/trait/get_sample_data")
 def get_sample_data():
     params = request.args
@@ -250,7 +267,8 @@ def get_sample_data():
         trait_dict['group'] = trait_ob.dataset.group.name
         trait_dict['tissue'] = trait_ob.dataset.tissue
         trait_dict['species'] = trait_ob.dataset.group.species
-        trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
+        trait_dict['url'] = url_for(
+            'show_trait_page', trait_id=trait, dataset=dataset)
         trait_dict['description'] = trait_ob.description_display
         if trait_ob.dataset.type == "ProbeSet":
             trait_dict['symbol'] = trait_ob.symbol
@@ -260,22 +278,24 @@ def get_sample_data():
                 trait_dict['pubmed_link'] = trait_ob.pubmed_link
             trait_dict['pubmed_text'] = trait_ob.pubmed_text
 
-        return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
+        return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems()}])
     else:
         return None
-    
+
+
 def jsonable(trait):
     """Return a dict suitable for using as json
 
     Actual turning into json doesn't happen here though"""
 
-    dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
-    
+    dataset = create_dataset(dataset_name=trait.dataset.name,
+                             dataset_type=trait.dataset.type, group_name=trait.dataset.group.name)
+
     if dataset.type == "ProbeSet":
         return dict(name=trait.name,
                     symbol=trait.symbol,
                     dataset=dataset.name,
-                    dataset_name = dataset.shortname,
+                    dataset_name=dataset.shortname,
                     description=trait.description_display,
                     mean=trait.mean,
                     location=trait.location_repr,
@@ -287,7 +307,7 @@ def jsonable(trait):
         if trait.pubmed_id:
             return dict(name=trait.name,
                         dataset=dataset.name,
-                        dataset_name = dataset.shortname,
+                        dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
@@ -300,7 +320,7 @@ def jsonable(trait):
         else:
             return dict(name=trait.name,
                         dataset=dataset.name,
-                        dataset_name = dataset.shortname,
+                        dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
@@ -312,19 +332,20 @@ def jsonable(trait):
     elif dataset.type == "Geno":
         return dict(name=trait.name,
                     dataset=dataset.name,
-                    dataset_name = dataset.shortname,
+                    dataset_name=dataset.shortname,
                     location=trait.location_repr
                     )
     else:
         return dict()
 
+
 def jsonable_table_row(trait, dataset_name, index):
     """Return a list suitable for json and intended to be displayed in a table
 
     Actual turning into json doesn't happen here though"""
 
     dataset = create_dataset(dataset_name)
-    
+
     if dataset.type == "ProbeSet":
         if trait.mean == "":
             mean = "N/A"
@@ -336,11 +357,13 @@ def jsonable_table_row(trait, dataset_name, index):
             additive = "%.3f" % round(float(trait.additive), 2)
         return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                 index,
-                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                '<a href="/show_trait?trait_id=' +
+                str(trait.name)+'&dataset='+dataset.name +
+                '">'+str(trait.name)+'</a>',
                 trait.symbol,
                 trait.description_display,
                 trait.location_repr,
-                mean, 
+                mean,
                 trait.LRS_score_repr,
                 trait.LRS_location_repr,
                 additive]
@@ -352,7 +375,9 @@ def jsonable_table_row(trait, dataset_name, index):
         if trait.pubmed_id:
             return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                     index,
-                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                    '<a href="/show_trait?trait_id=' +
+                    str(trait.name)+'&dataset='+dataset.name +
+                    '">'+str(trait.name)+'</a>',
                     trait.description_display,
                     trait.authors,
                     '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>',
@@ -362,7 +387,9 @@ def jsonable_table_row(trait, dataset_name, index):
         else:
             return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                     index,
-                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                    '<a href="/show_trait?trait_id=' +
+                    str(trait.name)+'&dataset='+dataset.name +
+                    '">'+str(trait.name)+'</a>',
                     trait.description_display,
                     trait.authors,
                     trait.pubmed_text,
@@ -372,7 +399,9 @@ def jsonable_table_row(trait, dataset_name, index):
     elif dataset.type == "Geno":
         return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                 index,
-                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                '<a href="/show_trait?trait_id=' +
+                str(trait.name)+'&dataset='+dataset.name +
+                '">'+str(trait.name)+'</a>',
                 trait.location_repr]
     else:
         return dict()
@@ -383,14 +412,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     resource_id = get_resource_id(dataset, trait.name)
     if dataset.type == 'Publish':
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(
+            resource_id, g.user_session.user_id)
     else:
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(
+            resource_id, g.user_session.user_id, trait.name)
 
     try:
         response = requests.get(the_url).content
         trait_info = json.loads(response)
-    except: #ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
+    except:  # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
         if dataset.type == 'Publish':
             query = """
                     SELECT
@@ -419,8 +450,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             logger.sql(query)
             trait_info = g.db.execute(query).fetchone()
 
-        #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
-        #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
+        # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
+        # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
         elif dataset.type == 'ProbeSet':
             display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
             display_fields_string = 'ProbeSet.' + display_fields_string
@@ -433,14 +464,15 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                             ProbeSetFreeze.Name = '%s' AND
                             ProbeSet.Name = '%s'
                     """ % (escape(display_fields_string),
-                        escape(dataset.name),
-                        escape(str(trait.name)))
+                           escape(dataset.name),
+                           escape(str(trait.name)))
             logger.sql(query)
             trait_info = g.db.execute(query).fetchone()
-        #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
+        # XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
         # to avoid the problem of same marker name from different species.
         elif dataset.type == 'Geno':
-            display_fields_string = string.join(dataset.display_fields,',Geno.')
+            display_fields_string = string.join(
+                dataset.display_fields, ',Geno.')
             display_fields_string = 'Geno.' + display_fields_string
             query = """
                     SELECT %s
@@ -451,21 +483,21 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                             GenoFreeze.Name = '%s' AND
                             Geno.Name = '%s'
                     """ % (escape(display_fields_string),
-                        escape(dataset.name),
-                        escape(trait.name))
+                           escape(dataset.name),
+                           escape(trait.name))
             logger.sql(query)
             trait_info = g.db.execute(query).fetchone()
-        else: #Temp type
+        else:  # Temp type
             query = """SELECT %s FROM %s WHERE Name = %s"""
             logger.sql(query)
             trait_info = g.db.execute(query,
-                                    (string.join(dataset.display_fields,','),
-                                                dataset.type, trait.name)).fetchone()
+                                      (string.join(dataset.display_fields, ','),
+                                       dataset.type, trait.name)).fetchone()
 
     if trait_info:
         trait.haveinfo = True
         for i, field in enumerate(dataset.display_fields):
-            holder =  trait_info[i]
+            holder = trait_info[i]
             setattr(trait, field, holder)
 
         if dataset.type == 'Publish':
@@ -478,9 +510,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
             description = trait.post_publication_description
 
-            #If the dataset is confidential and the user has access to confidential
-            #phenotype traits, then display the pre-publication description instead
-            #of the post-publication description
+            # If the dataset is confidential and the user has access to confidential
+            # phenotype traits, then display the pre-publication description instead
+            # of the post-publication description
             if trait.confidential:
                 trait.abbreviation = trait.pre_publication_abbreviation
                 trait.description_display = trait.pre_publication_description
@@ -491,9 +523,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 else:
                     trait.description_display = ""
 
-            trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
-            trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
-            trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
+            trait.abbreviation = unicode(str(trait.abbreviation).strip(
+                codecs.BOM_UTF8), 'utf-8', errors="replace")
+            trait.description_display = unicode(str(trait.description_display).strip(
+                codecs.BOM_UTF8), 'utf-8', errors="replace")
+            trait.authors = unicode(str(trait.authors).strip(
+                codecs.BOM_UTF8), 'utf-8', errors="replace")
 
             if not trait.year.isdigit():
                 trait.pubmed_text = "N/A"
@@ -504,8 +539,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
 
         if dataset.type == 'ProbeSet' and dataset.group:
-            description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
-            target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+            description_string = unicode(
+                str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
+            target_string = unicode(
+                str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
             if str(description_string or "") != "" and description_string != 'None':
                 description_display = description_string
@@ -514,7 +551,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
             if (str(description_display or "") != "" and
                 description_display != 'N/A' and
-                str(target_string or "") != "" and target_string != 'None'):
+                    str(target_string or "") != "" and target_string != 'None'):
                 description_display = description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
@@ -522,15 +559,17 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
             trait.location_repr = 'N/A'
             if trait.chr and trait.mb:
-                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+                trait.location_repr = 'Chr%s: %.6f' % (
+                    trait.chr, float(trait.mb))
 
         elif dataset.type == "Geno":
             trait.location_repr = 'N/A'
             if trait.chr and trait.mb:
-                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+                trait.location_repr = 'Chr%s: %.6f' % (
+                    trait.chr, float(trait.mb))
 
         if get_qtl_info:
-            #LRS and its location
+            # LRS and its location
             trait.LRS_score_repr = "N/A"
             trait.LRS_location_repr = "N/A"
             trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
@@ -601,10 +640,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 else:
                     trait.locus = trait.lrs = trait.additive = ""
             if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "":
-                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
+                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+                    trait.locus_chr, float(trait.locus_mb))
                 if str(trait.lrs or "") != "":
                     trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
     else:
-        raise KeyError, `trait.name`+' information is not found in the database.'
-        
+        raise KeyError, `trait.name`+ ' information is not found in the database.'
+
     return trait
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 42a09fed..4c558bfe 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -1,41 +1,30 @@
 from __future__ import print_function, division, absolute_import
 
-
-import os
-import hashlib
 import datetime
-import time
-
-import uuid
-import hashlib
-import base64
-
-import urlparse
-
 import simplejson as json
 
-from flask import (Flask, g, render_template, url_for, request, make_response,
-                   redirect, flash, jsonify)
+from flask import g
+from flask import render_template
+from flask import url_for
+from flask import request
+from flask import redirect
+from flask import flash
 
 from wqflask import app
-
-from pprint import pformat as pf
-
-from wqflask.database import db_session
-
-from wqflask import model
-
-from utility import Bunch, Struct, hmac
+from utility import hmac
 from utility.formatting import numify
 from utility.redis_tools import get_redis_conn
-Redis = get_redis_conn()
 
-from base.trait import create_trait, retrieve_trait_info, jsonable
+from base.trait import create_trait
+from base.trait import retrieve_trait_info
+from base.trait import jsonable
 from base.data_set import create_dataset
 
-import logging
 from utility.logger import getLogger
+
 logger = getLogger(__name__)
+Redis = get_redis_conn()
+
 
 def process_traits(unprocessed_traits):
     if isinstance(unprocessed_traits, basestring):
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 880a1cb2..70077703 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -1,5 +1,8 @@
-# WGCNA analysis for GN2
-# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+"""
+WGCNA analysis for GN2
+
+Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+"""
 import sys
 from numpy import *
 import scipy as sp                            # SciPy
@@ -17,106 +20,138 @@ from utility import helper_functions
 from rpy2.robjects.packages import importr
 utils = importr("utils")
 
-## Get pointers to some common R functions
-r_library       = ro.r["library"]             # Map the library function
-r_options       = ro.r["options"]             # Map the options function
-r_read_csv      = ro.r["read.csv"]            # Map the read.csv function
-r_dim           = ro.r["dim"]                 # Map the dim function
-r_c             = ro.r["c"]                   # Map the c function
-r_cat           = ro.r["cat"]                 # Map the cat function
-r_paste         = ro.r["paste"]               # Map the paste function
-r_unlist        = ro.r["unlist"]              # Map the unlist function
-r_unique        = ro.r["unique"]              # Map the unique function
-r_length        = ro.r["length"]              # Map the length function
-r_unlist        = ro.r["unlist"]              # Map the unlist function
-r_list          = ro.r.list                   # Map the list function
-r_matrix        = ro.r.matrix                 # Map the matrix function
-r_seq           = ro.r["seq"]                 # Map the seq function
-r_table         = ro.r["table"]               # Map the table function
-r_names         = ro.r["names"]               # Map the names function
-r_sink          = ro.r["sink"]                # Map the sink function
-r_is_NA         = ro.r["is.na"]               # Map the is.na function
-r_file          = ro.r["file"]                # Map the file function
-r_png           = ro.r["png"]                 # Map the png function for plotting
-r_dev_off       = ro.r["dev.off"]             # Map the dev.off function
+# Get pointers to some common R functions
+r_library = ro.r["library"]    # Map the library function
+r_options = ro.r["options"]    # Map the options function
+r_read_csv = ro.r["read.csv"]  # Map the read.csv function
+r_dim = ro.r["dim"]            # Map the dim function
+r_c = ro.r["c"]                # Map the c function
+r_cat = ro.r["cat"]            # Map the cat function
+r_paste = ro.r["paste"]        # Map the paste function
+r_unlist = ro.r["unlist"]      # Map the unlist function
+r_unique = ro.r["unique"]      # Map the unique function
+r_length = ro.r["length"]      # Map the length function
+r_unlist = ro.r["unlist"]      # Map the unlist function
+r_list = ro.r.list             # Map the list function
+r_matrix = ro.r.matrix         # Map the matrix function
+r_seq = ro.r["seq"]            # Map the seq function
+r_table = ro.r["table"]        # Map the table function
+r_names = ro.r["names"]        # Map the names function
+r_sink = ro.r["sink"]          # Map the sink function
+r_is_NA = ro.r["is.na"]        # Map the is.na function
+r_file = ro.r["file"]          # Map the file function
+r_png = ro.r["png"]            # Map the png function for plotting
+r_dev_off = ro.r["dev.off"]    # Map the dev.off function
+
 
 class WGCNA(object):
     def __init__(self):
+        # To log output from stdout/stderr to a file add `r_sink(log)`
         print("Initialization of WGCNA")
-        #log = r_file("/tmp/genenetwork_wcgna.log", open = "wt")
-        #r_sink(log)                                  # Uncomment the r_sink() commands to log output from stdout/stderr to a file
-        #r_sink(log, type = "message")
-        r_library("WGCNA")                            # Load WGCNA - Should only be done once, since it is quite expensive
-        r_options(stringsAsFactors = False)
+
+        # Load WGCNA - Should only be done once, since it is quite expensive
+        r_library("WGCNA")
+        r_options(stringsAsFactors=False)
         print("Initialization of WGCNA done, package loaded in R session")
-        self.r_enableWGCNAThreads    = ro.r["enableWGCNAThreads"]        # Map the enableWGCNAThreads function
-        self.r_pickSoftThreshold     = ro.r["pickSoftThreshold"]         # Map the pickSoftThreshold function
-        self.r_blockwiseModules      = ro.r["blockwiseModules"]          # Map the blockwiseModules function
-        self.r_labels2colors         = ro.r["labels2colors"]             # Map the labels2colors function
-        self.r_plotDendroAndColors   = ro.r["plotDendroAndColors"]       # Map the plotDendroAndColors function
+        # Map the enableWGCNAThreads function
+        self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"]
+        # Map the pickSoftThreshold function
+        self.r_pickSoftThreshold = ro.r["pickSoftThreshold"]
+        # Map the blockwiseModules function
+        self.r_blockwiseModules = ro.r["blockwiseModules"]
+        # Map the labels2colors function
+        self.r_labels2colors = ro.r["labels2colors"]
+        # Map the plotDendroAndColors function
+        self.r_plotDendroAndColors = ro.r["plotDendroAndColors"]
         print("Obtained pointers to WGCNA functions")
 
     def run_analysis(self, requestform):
         print("Starting WGCNA analysis on dataset")
-        self.r_enableWGCNAThreads()                                      # Enable multi threading
-        self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
-        print("Retrieved phenotype data from database", requestform['trait_list'])
+        # Enable multi threading
+        self.r_enableWGCNAThreads()
+        self.trait_db_list = [trait.strip()
+                              for trait in requestform['trait_list'].split(',')]
+        print("Retrieved phenotype data from database",
+              requestform['trait_list'])
         helper_functions.get_trait_db_obs(self, self.trait_db_list)
 
-        self.input = {}           # self.input contains the phenotype values we need to send to R
-        strains = []              # All the strains we have data for (contains duplicates)
-        traits  = []              # All the traits we have data for (should not contain duplicates)
+        # self.input contains the phenotype values we need to send to R
+        self.input = {}
+        # All the strains we have data for (contains duplicates)
+        strains = []
+        # All the traits we have data for (should not contain duplicates)
+        traits = []
         for trait in self.trait_list:
             traits.append(trait[0].name)
             self.input[trait[0].name] = {}
             for strain in trait[0].data:
                 strains.append(strain)
-                self.input[trait[0].name][strain]  = trait[0].data[strain].value
+                self.input[trait[0].name][strain] = trait[0].data[strain].value
 
         # Transfer the load data from python to R
-        uStrainsR = r_unique(ro.Vector(strains))    # Unique strains in R vector
+        # Unique strains in R vector
+        uStrainsR = r_unique(ro.Vector(strains))
         uTraitsR = r_unique(ro.Vector(traits))      # Unique traits in R vector
 
         r_cat("The number of unique strains:", r_length(uStrainsR), "\n")
         r_cat("The number of unique traits:", r_length(uTraitsR), "\n")
 
-        # rM is the datamatrix holding all the data in R /rows = strains columns = traits
-        rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length(uTraitsR), dimnames = r_list(uStrainsR, uTraitsR))
+        # rM is the datamatrix holding all the data in
+        # R /rows = strains columns = traits
+        rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length(
+            uTraitsR), dimnames=r_list(uStrainsR, uTraitsR))
         for t in uTraitsR:
-            trait = t[0]                  # R uses vectors every single element is a vector
+            # R uses vectors every single element is a vector
+            trait = t[0]
             for s in uStrainsR:
-                strain = s[0]             # R uses vectors every single element is a vector
-                #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0])
-                rM.rx[strain, trait] = self.input[trait].get(strain)  # Update the matrix location
+                # R uses vectors every single element is a vector
+                strain = s[0]
+                rM.rx[strain, trait] = self.input[trait].get(
+                    strain)  # Update the matrix location
                 sys.stdout.flush()
 
         self.results = {}
-        self.results['nphe'] = r_length(uTraitsR)[0]          # Number of phenotypes/traits
-        self.results['nstr'] = r_length(uStrainsR)[0]         # Number of strains
+        # Number of phenotypes/traits
+        self.results['nphe'] = r_length(uTraitsR)[0]
+        self.results['nstr'] = r_length(
+            uStrainsR)[0]         # Number of strains
         self.results['phenotypes'] = uTraitsR                 # Traits used
-        self.results['strains'] = uStrainsR                   # Strains used in the analysis
-        self.results['requestform'] = requestform             # Store the user specified parameters for the output page
+        # Strains used in the analysis
+        self.results['strains'] = uStrainsR
+        # Store the user specified parameters for the output page
+        self.results['requestform'] = requestform
 
-        # Calculate soft threshold if the user specified the SoftThreshold variable
+        # Calculate soft threshold if the user specified the
+        # SoftThreshold variable
         if requestform.get('SoftThresholds') is not None:
-          powers = [int(threshold.strip()) for threshold in requestform['SoftThresholds'].rstrip().split(",")]
-          rpow = r_unlist(r_c(powers))
-          print "SoftThresholds: {} == {}".format(powers, rpow)
-          self.sft    = self.r_pickSoftThreshold(rM, powerVector = rpow, verbose = 5)
-
-          print "PowerEstimate: {}".format(self.sft[0])
-          self.results['PowerEstimate'] = self.sft[0]
-          if self.sft[0][0] is ri.NA_Integer:
-            print "No power is suitable for the analysis, just use 1"
-            self.results['Power'] = 1                         # No power could be estimated
-          else:
-            self.results['Power'] = self.sft[0][0]            # Use the estimated power
+            powers = [int(threshold.strip())
+                      for threshold in requestform['SoftThresholds'].rstrip().split(",")]
+            rpow = r_unlist(r_c(powers))
+            print("SoftThresholds: {} == {}".format(powers, rpow))
+            self.sft = self.r_pickSoftThreshold(
+                rM, powerVector=rpow, verbose=5)
+
+            print("PowerEstimate: {}".format(self.sft[0]))
+            self.results['PowerEstimate'] = self.sft[0]
+            if self.sft[0][0] is ri.NA_Integer:
+                print "No power is suitable for the analysis, just use 1"
+                # No power could be estimated
+                self.results['Power'] = 1
+            else:
+                # Use the estimated power
+                self.results['Power'] = self.sft[0][0]
         else:
-          # The user clicked a button, so no soft threshold selection
-          self.results['Power'] = requestform.get('Power')    # Use the power value the user gives
+            # The user clicked a button, so no soft threshold selection
+            # Use the power value the user gives
+            self.results['Power'] = requestform.get('Power')
 
         # Create the block wise modules using WGCNA
-        network = self.r_blockwiseModules(rM, power = self.results['Power'], TOMType = requestform['TOMtype'], minModuleSize = requestform['MinModuleSize'], verbose = 3)
+        network = self.r_blockwiseModules(
+            rM,
+            power=self.results['Power'],
+            TOMType=requestform['TOMtype'],
+            minModuleSize=requestform['MinModuleSize'],
+            verbose=3)
 
         # Save the network for the GUI
         self.results['network'] = network
@@ -130,7 +165,9 @@ class WGCNA(object):
         self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl']
         r_png(self.results['imgloc'], width=1000, height=600, type='cairo-png')
         mergedColors = self.r_labels2colors(network[1])
-        self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", dendroLabels = False, hang = 0.03, addGuide = True, guideHang = 0.05)
+        self.r_plotDendroAndColors(network[5][0], mergedColors,
+                                   "Module colors", dendroLabels=False,
+                                   hang=0.03, addGuide=True, guideHang=0.05)
         r_dev_off()
         sys.stdout.flush()
 
@@ -146,11 +183,9 @@ class WGCNA(object):
         print("Processing WGCNA output")
         template_vars = {}
         template_vars["input"] = self.input
-        template_vars["powers"] = self.sft[1:]                      # Results from the soft threshold analysis
+        # Results from the soft threshold analysis
+        template_vars["powers"] = self.sft[1:]
         template_vars["results"] = self.results
         self.render_image(results)
         sys.stdout.flush()
-        #r_sink(type = "message")                                   # This restores R output to the stdout/stderr
-        #r_sink()                                                   # We should end the Rpy session more or less
         return(dict(template_vars))
-
-- 
cgit v1.2.3


From ef49f885d5f668e50b3b8849012d3fec99483e2b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 9 Oct 2020 13:39:29 -0500
Subject: Change some column and overall table widths for search result table
 and view collections table + changed "Max LRS" column header to "High P"

* wqflask/wqflask/templates/collections/view.html - changed column widths and "Max LRS" header to "High P"
* wqflask/wqflask/templates/search_result_page.html - changed column widths and "Max LRS" header to "High P"
---
 wqflask/wqflask/templates/collections/view.html   | 16 ++++++++--------
 wqflask/wqflask/templates/search_result_page.html | 12 +++++-------
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index bc487a59..d1a97310 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -8,7 +8,7 @@
 {% block content %}
 <!-- Start of body -->
 
-    <div class="container" style="min-width: 2050px;">
+    <div class="container">
         <h1>
             <span id="collection_name">{{ uc.name }}</span>
             <input type="text" name="new_collection_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ uc.name }}"> 
@@ -85,7 +85,7 @@
             <div style="margin-top: 10px; margin-bottom: 5px;">
                 <b>Show/Hide Columns:</b>
             </div>
-            <div>
+            <div style="min-width: 1500px;">
                 <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
                     <thead>
                         <tr>
@@ -97,7 +97,7 @@
                             <th data-export="Description">Description</th>
                             <th data-export="Location">Location</th>
                             <th data-export="Mean">Mean</th>
-                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
+                            <th data-export="Max LRS">High P <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                             <th data-export="Peak Location">Peak Location</th>
                             <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                         </tr>
@@ -195,11 +195,11 @@
                     { 'type': "natural-minus-na", "width": 120 },
                     { "type": "natural" },
                     { "type": "natural"  },
-                    { "type": "natural", "width": 130 },
-                    { "type": "natural", "width": 35 },
-                    { "type": "natural", "width": 35 },
-                    { "type": "natural", "width": 130 },
-                    { "type": "natural" }
+                    { "type": "natural", "width": 125 },
+                    { "type": "natural", "width": 60 },
+                    { "type": "natural", "width": 60 },
+                    { "type": "natural", "width": 125 },
+                    { "type": "natural", "width": 85 }
                 ],
                 "order": [[1, "asc" ]],
                 buttons: [
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index e2e1aa46..2318bfb8 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -140,7 +140,6 @@
             <b>Show/Hide Columns:</b>
           </div>
           {% endif %}
-          <!--<div id="table_container" style="min-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px;">-->
           <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
             <table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};">
                 <tbody>
@@ -290,7 +289,6 @@
                     {
                       'title': "Description",
                       'type': "natural",
-                      'width': "500px",
                       'data': null,
                       'render': function(data, type, row, meta) {
                         try {
@@ -303,7 +301,7 @@
                     {
                       'title': "Location",
                       'type': "natural-minus-na",
-                      'width': "120px",
+                      'width': "125px",
                       'data': "location"
                     },
                     {
@@ -314,23 +312,23 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
+                      'title': "High P<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
-                      'width': "80px",
+                      'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
                       'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "120px",
+                      'width': "125px",
                       'data': "lrs_location"
                     },
                     {
                       'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "additive",
-                      'width': "120px",
+                      'width': "85px",
                       'orderSequence': [ "desc", "asc"]
                     }{% elif dataset.type == 'Publish' %},
                     {
-- 
cgit v1.2.3