Adding supported genomes to species page, returning None from Require…

…dYieldQ30._get_yield if no yield found

etc/example_reporting.yaml

@@ -51,7 +51,7 @@ rest_app:
         username: user
         password: pass
 
-    available_coverages: [1, 2, 5, 10, 20]
+    available_coverages: [1, 2, 4, 5, 10, 20]
     available_yields:  # keys are required yields, and values are associated required yield q30s
         5: 4
         10: 8

reporting_app/__init__.py

@@ -489,6 +489,12 @@ def species_page(species):
                 util.construct_url('species', where={'name': species}),
                 minimal=True
             ),
+            util.datatable_cfg(
+                'Supported genomes',
+                'genomes',
+                util.construct_url('genomes', where={'species': species}, max_results=1000),
+                minimal=True
+            ),
             util.datatable_cfg(
                 'Yield requirements',
                 'yields',

rest_api/aggregation/database_hooks.py

@@ -156,7 +156,8 @@ def _get_yield(self, genome_size, required_coverage):
         into a required yield q30.
         """
         required_yield = super()._get_yield(genome_size, required_coverage)
-        return self.quantised_yields[required_yield]
+        if required_yield:
+            return self.quantised_yields[required_yield]
 
 
 class MostRecent(Calculation):  # TODO: Should replace server_side.MostRecent

tests/test_reporting_app.py

@@ -333,3 +333,4 @@ def test_project_status_report(self):
 
     def test_genome_page(self):
         self._test_render_template('/species')
+        self._test_render_template('/species/a_species')

tests/test_rest_api/test_aggregation/test_database_hooks.py

@@ -480,21 +480,23 @@ def test_nb_unique_mutable_elements():
 
 def test_required_yield():
     e = database_hooks.RequiredYield('approximate_genome_size')
-    assert e.evaluate({'approximate_genome_size': 1990.6}) == {
+    assert e.evaluate({'approximate_genome_size': 2100.6}) == {
         '1X': 5,
         '2X': 5,
-        '5X': 10,
-        '10X': 20,
-        '20X': 40
+        '4X': 10,
+        '5X': 20,
+        '10X': 40,
+        '20X': None
     }
 
 
 def test_yield_for_quoted_coverage():
     e = database_hooks.RequiredYieldQ30('approximate_genome_size')
-    assert e.evaluate({'approximate_genome_size': 1990.6}) == {
+    assert e.evaluate({'approximate_genome_size': 2100.6}) == {
         '1X': 4,
         '2X': 4,
-        '5X': 8,
-        '10X': 16,
-        '20X': 32
+        '4X': 8,
+        '5X': 16,
+        '10X': 32,
+        '20X': None
     }