Anvi'o backend for 'genome view'

.gitmodules

@@ -37,3 +37,6 @@
 [submodule "anvio/data/interactive/lib/JavaScript-MD5"]
 	path = anvio/data/interactive/lib/JavaScript-MD5
 	url = https://github.com/blueimp/JavaScript-MD5.git
+[submodule "anvio/data/interactive/lib/fabric.js"]
+	path = anvio/data/interactive/lib/fabric
+	url = https://github.com/fabricjs/fabric.js.git

anvio/__init__.py

@@ -166,6 +166,12 @@ def TABULATE(table, header, numalign="right", max_width=0):
              'required': True,
              'help': "Anvi'o structure database."}
                 ),
+    'genome-view-db': (
+            ['-V', '--genome-view-db'],
+            {'metavar': "GENOME_VIEW_DB",
+             'required': True,
+             'help': "Anvi'o genome view database."}
+                ),
     'only-if-structure': (
             ['--only-if-structure'],
             {'default': False,
@@ -3560,7 +3566,8 @@ def set_version():
            t.genomes_storage_vesion, \
            t.structure_db_version, \
            t.metabolic_modules_db_version, \
-           t.trnaseq_db_version
+           t.trnaseq_db_version, \
+           t.genome_view_db_version
 
 
 def get_version_tuples():
@@ -3573,7 +3580,8 @@ def get_version_tuples():
             ("Genome data storage version", __genomes_storage_version__),
             ("Structure DB version", __structure__version__),
             ("KEGG Modules DB version", __kegg_modules_version__),
-            ("tRNA-seq DB version", __trnaseq__version__)]
+            ("tRNA-seq DB version", __trnaseq__version__),
+            ("Genome view DB version", __genome_view_db__version__)]
 
 
 def print_version():
@@ -3585,7 +3593,8 @@ def print_version():
     run.info("Auxiliary data storage", __auxiliary_data_version__)
     run.info("Structure database", __structure__version__)
     run.info("Metabolic modules database", __kegg_modules_version__)
-    run.info("tRNA-seq database", __trnaseq__version__, nl_after=1)
+    run.info("tRNA-seq database", __trnaseq__version__)
+    run.info("Genome view database", __genome_view_db__version__, nl_after=1)
 
 
 __version__, \
@@ -3598,7 +3607,8 @@ def print_version():
 __genomes_storage_version__ , \
 __structure__version__, \
 __kegg_modules_version__, \
-__trnaseq__version__ = set_version()
+__trnaseq__version__, \
+__genome_view_db__version__ = set_version()
 
 
 if '-v' in sys.argv or '--version' in sys.argv:

anvio/bottleroutes.py

@@ -188,6 +188,8 @@ def register_routes(self):
         self.route('/data/reroot_tree',                        callback=self.reroot_tree, method='POST')
         self.route('/data/save_tree',                          callback=self.save_tree, method='POST')
         self.route('/data/check_homogeneity_info',             callback=self.check_homogeneity_info, method='POST')
+        self.route('/data/get_genome_view_data',               callback=self.get_genome_view_data, method='POST')
+        self.route('/data/get_genome_view_adl',                callback=self.get_genome_view_continuous_data_layers, method='POST')
         self.route('/data/search_items',                       callback=self.search_items_by_name, method='POST')
         self.route('/data/get_taxonomy',                       callback=self.get_taxonomy, method='POST')
         self.route('/data/get_functions_for_gene_clusters',    callback=self.get_functions_for_gene_clusters, method='POST')
@@ -264,6 +266,8 @@ def redirect_to_app(self):
             homepage = 'metabolism.html'
         elif self.interactive.mode == 'inspect':
             redirect('/app/charts.html?id=%s&show_snvs=true&rand=%s' % (self.interactive.inspect_split_name, self.random_hash(8)))
+        elif self.interactive.mode == 'genome-view':
+            homepage = 'genomeview.html'
 
         redirect('/app/%s?rand=%s' % (homepage, self.random_hash(8)))
 
@@ -469,9 +473,13 @@ def save_state(self, state_name):
 
     def get_state(self, state_name):
         if state_name in self.interactive.states_table.states:
+
             state = self.interactive.states_table.states[state_name]
             state_dict = json.loads(state['content'])
 
+            if self.interactive.mode == 'genome-view':
+                return json.dumps({'content' : state_dict})
+
             if self.interactive.mode == 'structure':
                 return json.dumps({'content': state['content']})
             else:
@@ -1361,6 +1369,24 @@ def get_initial_data(self):
         return json.dumps(self.interactive.get_initial_data())
 
 
+    def get_genome_view_data(self):
+        try:
+            return json.dumps({'genomes': self.interactive.genomes,
+                               'gene_associations': self.interactive.gene_associations})
+        except Exception as e:
+            return json.dumps({'error': f"Something went wrong at the backend :( Here is the error message: '{e}'"})
+
+
+    def get_genome_view_continuous_data_layers(self):
+        """populate continuous data layers, and send them back to the frontend"""
+
+        try:
+            self.interactive.populate_genome_continuous_data_layers()
+            return json.dumps(self.interactive.continuous_data_layers)
+        except Exception as e:
+            return json.dumps({'error': f"Something went wrong at the backend :( Here is the error message: '{e}'"})
+
+
     def get_column_info(self):
         gene_callers_id = int(request.forms.get('gene_callers_id'))
         engine = request.forms.get('engine')
@@ -1481,7 +1507,7 @@ def get_functions_for_gene_clusters(self):
                 message = (f"At least one of the gene clusters in your list (e.g., {gene_cluster_name}) is missing in "
                            f"the functions summary dict :/")
                 return json.dumps({'status': 1, 'message': message})
-                
+
             d[gene_cluster_name] = self.interactive.gene_clusters_functions_summary_dict[gene_cluster_name]
 
         return json.dumps({'functions': d, 'sources': list(self.interactive.gene_clusters_function_sources)})