Add use_external_help config option

If set, use Manuel's Canto tutorial:
https://pombase.github.io/canto_tutorial/

Refs #2835

Author: kimrutherford

canto.yaml

@@ -48,6 +48,9 @@ strains_mode: 0
 instance_front_path: /docs/instance_front
 canto_front_path: /docs/canto_front
 help_path: /docs/index
+external_help_url: 'https://pombase.github.io/canto_tutorial/'
+
+use_external_help: 0
 
 base_docs_path: docs
 
@@ -1935,6 +1938,7 @@ available_annotation_type_list:
       complexes). As a general rule, molecular functions correspond to
       single step activities performed by individual gene products.
     detailed_help_path: /docs/go_annotation
+    external_help_url: 'https://pombase.github.io/canto_tutorial/go_MF/'
   - name: biological_process
     category: ontology
     abbreviation: P
@@ -1973,6 +1977,7 @@ available_annotation_type_list:
       term request because there is no translation machinery specifically for
       histone H2A.
     detailed_help_path: /docs/go_annotation
+    external_help_url: 'https://pombase.github.io/canto_tutorial/go_BP/'
   - name: cellular_component
     category: ontology
     abbreviation: C
@@ -2004,6 +2009,7 @@ available_annotation_type_list:
       proteins or nucleic acids. Cellular component also does not include
       multicellular anatomical terms.
     detailed_help_path: /docs/go_annotation
+    external_help_url: 'https://pombase.github.io/canto_tutorial/go_CC/'
   - name: host_phenotype
     category: ontology
     namespace: 'host_phenotype'
@@ -2204,6 +2210,7 @@ available_annotation_type_list:
       Alleles may be annotated with multiple phenotype terms,
       including both normal and abnormal phenotypes for one allele.
     detailed_help_path: /docs/fypo_annotation
+    external_help_url: 'https://pombase.github.io/canto_tutorial/phenotypes/'
   - name: post_translational_modification
     category: ontology
     namespace: PSI-MOD
@@ -2221,6 +2228,7 @@ available_annotation_type_list:
     evidence_codes:
       - IDA
     detailed_help_path: /docs/modification_annotation
+    external_help_url: 'https://pombase.github.io/canto_tutorial/protein_modification/'
     clear_extensions_on_feature_change:
       - residue
   - name: wt_rna_expression
@@ -2250,6 +2258,7 @@ available_annotation_type_list:
       - Reporter gene assay
       - RNA-sequencing evidence
     detailed_help_path: /docs/gene_expression
+    external_help_url: 'https://pombase.github.io/canto_tutorial/rna_protein_level/'
   - name: wt_protein_expression
     category: ontology
     ontology_size: small
@@ -2266,6 +2275,7 @@ available_annotation_type_list:
       - Reporter gene assay
       - Western blot
     detailed_help_path: /docs/gene_expression
+    external_help_url: 'https://pombase.github.io/canto_tutorial/rna_protein_level/'
   - name: genotype_interaction
     category: genotype_interaction
     feature_type: genotype
@@ -2306,6 +2316,7 @@ available_annotation_type_list:
         - Synthetic Growth Defect
         - Synthetic Lethality
         - Synthetic Rescue
+    external_help_url: 'https://pombase.github.io/canto_tutorial/genetic_interaction/'
   - name: genetic_interaction
     category: interaction
     display_name: 'legacy genetic interaction'
@@ -2322,6 +2333,7 @@ available_annotation_type_list:
       - Synthetic Lethality
       - Synthetic Rescue
     detailed_help_path: /docs/genetic_interaction_annotation
+    external_help_url: 'https://pombase.github.io/canto_tutorial/genetic_interaction/'
   - name: physical_interaction
     category: interaction
     display_name: 'physical interaction'
@@ -2344,6 +2356,7 @@ available_annotation_type_list:
       - Reconstituted Complex
       - Two-hybrid
     detailed_help_path: /docs/physical_interaction_annotation
+    external_help_url: 'https://pombase.github.io/canto_tutorial/physical_interaction/'
   - name: protein_sequence_feature_or_motif
     category: ontology
     ontology_size: small
@@ -2359,6 +2372,7 @@ available_annotation_type_list:
       peptide_localization_signal
     help_text: >
       A Protein localization signal is a peptide sub-sequence used to target the protein to a specific organelle.
+    external_help_url: 'https://pombase.github.io/canto_tutorial/protein_sequence_feature/'
 
 # restrict the list of annotation types
 enabled_annotation_type_list:
@@ -2438,27 +2452,35 @@ help_text:
   biological_process_definition:
     inline: Annotate a gene product's role in a process.
     docs_path: "go_annotation#process"
+    url: "https://pombase.github.io/canto_tutorial/go_BP/"
   cellular_component_definition:
     inline: Annotate the location in a cell where a gene product acts.
     docs_path: "go_annotation#component"
+    url: 'https://pombase.github.io/canto_tutorial/go_CC/'
   molecular_function_definition:
     inline: Annotate a gene product's molecular activity.
     docs_path: "go_annotation#function"
+    url: 'https://pombase.github.io/canto_tutorial/go_MF/'
   post_translational_modification_definition:
     inline: Annotate the type, position, timing, etc. of covalent protein modifications.
     docs_path: "modification_annotation"
+    url: 'https://pombase.github.io/canto_tutorial/protein_modification/'
   wt_rna_expression_definition:
     inline: Annotate qualitative descriptions for the normal level and timing of RNA expression from a gene.
     docs_path: "gene_expression"
+    url: 'https://pombase.github.io/canto_tutorial/rna_protein_level/'
   wt_protein_expression_definition:
     inline: Annotate qualitative descriptions for the normal level and timing of protein expression from a gene.
     docs_path: "gene_expression"
+    url: 'https://pombase.github.io/canto_tutorial/rna_protein_level/'
   physical_interaction_definition:
     inline: Annotate interacting gene products and supporting evidence.
     docs_path: "physical_interaction_annotation"
+    url: 'https://pombase.github.io/canto_tutorial/protein_sequence_feature/'
   genetic_interaction_definition:
     inline: Annotate interaction type and interacting genes.
     docs_path: "genetic_interaction_annotation"
+    url: 'https://pombase.github.io/canto_tutorial/genetic_interaction/'
   experimental_conditions_definition:
     inline: >
       Conditions are the aspects of the experimental setup that are independent

root/curs/autohandler

@@ -29,6 +29,7 @@ var flybase_mode = <% $flybase_mode ? 'true' : 'false' %>;
 var max_term_name_select_count = <% $max_term_name_select_count %>;
 var show_quick_deletion_buttons = <% $show_quick_deletion_buttons %>;
 var show_quick_wild_type_buttons = <% $show_quick_wild_type_buttons %>;
+var use_external_help = <% $use_external_help ? 'true' : 'false' %>;
 </script>
 
 <div id="disabled-overlay"></div>
@@ -88,4 +89,5 @@ my $flybase_mode = $c->config()->{flybase_mode} || 0;
 my $max_term_name_select_count = $c->config()->{max_term_name_select_count} || 20;
 my $show_quick_deletion_buttons = $c->config()->{show_quick_deletion_buttons} || 0;
 my $show_quick_wild_type_buttons = $c->config()->{show_quick_wild_type_buttons} || 0;
+my $use_external_help = $c->config()->{use_external_help};
 </%init>

root/docs/annotation_type_list.mhtml

@@ -1,10 +1,9 @@
 <ul class="canto-type-list">
 % for my $an_type (@annotation_type_list) {
   <li>
-%   my $annotation_doc_path = $an_type->{detailed_help_path};
-%   if (defined $annotation_doc_path) {
-%     my $an_doc_uri = $c->uri_for($annotation_doc_path);
-    <span class="canto-type-list-name"><a href="<% $an_doc_uri %>"><% $an_type->{display_name} %></a></span>:
+%   my $annotation_doc_url = get_doc_uri($an_type);
+%   if (defined $annotation_doc_url) {
+    <span class="canto-type-list-name"><a href="<% $annotation_doc_url %>"><% $an_type->{display_name} %></a></span>:
 %   } else {
     <span class="canto-type-list-name"><% $an_type->{display_name} %></span>:
 %   }
@@ -16,4 +15,19 @@
 <%init>
 my $config = $c->config();
 my @annotation_type_list = @{$config->{annotation_type_list}};
+
+sub get_doc_uri
+{
+  my $an_type = shift;
+
+  if ($c->config()->{use_external_help}) {
+    my $external_help_url = $an_type->{external_help_url};
+    if (defined $external_help_url) {
+      return $external_help_url;
+    }
+  }
+
+  return $an_type->{detailed_help_path};
+}
+
 </%init>

root/menu.mhtml

@@ -28,7 +28,7 @@
 % }
       </ul>
     </span>
-    <a class="btn btn-default" href="<% $c->uri_for($c->config()->{help_path}) %>">Help</a>
+    <a class="btn btn-default" target="_blank" href="<% $help_url %>">Help</a>
   </span>
 </div>
 
@@ -37,4 +37,12 @@
 my $local_path = $c->req()->path();
 my $return_path_uri = $c->req()->uri();
 my $login_url = $c->uri_for('/do_oauth', { return_path => $return_path_uri });
+
+my $help_url;
+
+if ($c->config()->{use_external_help}) {
+  $help_url = $c->config()->{external_help_url};
+} else {
+  $help_url = $c->uri_for($c->config()->{help_path})
+}
 </%init>

root/static/js/canto-modules.js

@@ -886,6 +886,7 @@ canto.service('CantoGlobals', function ($window) {
   this.hostsWithNoGenes = $window.hostsWithNoGenes;
   this.annotationFigureField = $window.annotation_figure_field;
   this.allele_qc_api_url = $window.allele_qc_api_url;
+  this.use_external_help = $window.use_external_help;
 });
 
 canto.service('CantoService', function ($http) {
@@ -1291,8 +1292,18 @@ var helpIcon = function (CantoGlobals, CantoConfig) {
 
       CantoConfig.get('help_text').then(function (results) {
         if (results[$scope.key]) {
-          if (results[$scope.key].docs_path) {
-            $scope.url = CantoGlobals.application_root + '/docs/' + results[$scope.key].docs_path;
+          if (CantoGlobals.use_external_help) {
+            if (results[$scope.key].url) {
+              $scope.url = results[$scope.key].url;
+            } else {
+              $scope.url = CantoGlobals.application_root + '/docs/' + results[$scope.key].docs_path;
+            }
+          } else {
+            if (results[$scope.key].docs_path) {
+              $scope.url = CantoGlobals.application_root + '/docs/' + results[$scope.key].docs_path;
+            } else {
+              $scope.url = results[$scope.key].url;
+            }
           }
           if (results[$scope.key].inline) {
             $scope.helpText = results[$scope.key].inline;