Merge pull request #346 from EBI-Metagenomics/develop

v2.4.40

emgapianns/management/commands/import_genomes.py

@@ -41,6 +41,9 @@ def add_arguments(self, parser):
                                  "E.g. root:Host-Associated:Human:Digestive\\ System:Large\\ intestine")
         parser.add_argument('pipeline_version', action='store', type=str,
                             help='Pipeline version tag that catalogue was produced by. E.g. "1.2.1"')
+        parser.add_argument('--update-metadata-only', dest='update_metadata_only', action='store_true', default=False,
+                            help="Only update the metadata of genomes in an existing catalogue; "
+                                 "i.e. reparse the MGYG*.json files.")
         parser.add_argument('--database', type=str,
                             default='default')
 
@@ -105,6 +108,12 @@ def handle_v2(self, *args, **options):
         self.catalogue_dir = os.path.join(self.results_directory, catalogue_dir)
 
         self.database = options['database']
+
+        if options['update_metadata_only']:
+            assert emg_models.GenomeCatalogue.objects.filter(
+                catalogue_id=self.make_slug(catalogue_name, version)
+            ).exists()
+
         self.catalogue_obj = self.get_catalogue(
             catalogue_name,
             version, gold_biome,
@@ -123,12 +132,15 @@ def handle_v2(self, *args, **options):
         sanity_check_catalogue_dir(self.catalogue_dir)
 
         for d in genome_dirs:
-            self.upload_dir(d)
+            self.upload_dir(d, update_metadata_only=options['update_metadata_only'])
 
         self.upload_catalogue_files()
         self.catalogue_obj.calculate_genome_count()
         self.catalogue_obj.save()
 
+    def make_slug(self, catalogue_name, catalogue_version):
+        return slugify('{0}-v{1}'.format(catalogue_name, catalogue_version).replace('.', '-'))
+
     def get_catalogue(self, catalogue_name, catalogue_version, gold_biome, catalogue_dir, pipeline_version_tag):
         logging.warning('GOLD')
         logging.warning(gold_biome)
@@ -137,7 +149,7 @@ def get_catalogue(self, catalogue_name, catalogue_version, gold_biome, catalogue
         catalogue, _ = emg_models.GenomeCatalogue.objects \
             .using(self.database) \
             .get_or_create(
-                catalogue_id=slugify('{0}-v{1}'.format(catalogue_name, catalogue_version).replace('.', '-')),
+                catalogue_id=self.make_slug(catalogue_name, catalogue_version),
                 defaults={
                     'version': catalogue_version,
                     'name': '{0} v{1}'.format(catalogue_name, catalogue_version),
@@ -148,9 +160,11 @@ def get_catalogue(self, catalogue_name, catalogue_version, gold_biome, catalogue
                 })
         return catalogue
 
-    def upload_dir(self, directory):
+    def upload_dir(self, directory, update_metadata_only=False):
         logger.info('Uploading dir: {}'.format(directory))
         genome, has_pangenome = self.create_genome(directory)
+        if update_metadata_only:
+            return
         self.upload_cog_results(genome, directory)
         self.upload_kegg_class_results(genome, directory)
         self.upload_kegg_module_results(genome, directory)
@@ -208,6 +222,10 @@ def create_genome(self, genome_dir):
             defaults=data)
         g.save(using=self.database)
 
+        # in case we are updating and the geo range metadata has changed:
+        if g.pangenome_geographic_range.exists():
+            g.pangenome_geographic_range.clear()
+
         if geo_locations:
             [self.attach_geo_location(g, l) for l in geo_locations]
 

emgcli/__init__.py

@@ -1 +1 @@
-__version__: str = "2.4.39"
+__version__: str = "2.4.40"

pyproject.toml

@@ -117,7 +117,7 @@ max-line-length = 119
 """
 
 [tool.bumpversion]
-current_version = "2.4.39"
+current_version = "2.4.40"
 
 [[tool.bumpversion.files]]
 filename = "emgcli/__init__.py"

tests/webuploader/test_data/genomes/uhgg/2.0.1/MGYG000000001/MGYG000000001.json

@@ -0,0 +1,35 @@
+{
+    "accession": "MGYG000000001",
+    "completeness": 90.59,
+    "contamination": 0.7,
+    "eggnog_coverage": 93.78,
+    "ena_sample_accession": "ERS370061",
+    "ena_study_accession": "ERP105624",
+    "gc_content": 28.26,
+    "genome_accession": "GUT_GENOME000001",
+    "geographic_origin": "Europe",
+    "gold_biome": "root:Host-Associated:Human:Digestive System:Large intestine",
+    "ipr_coverage": 86.42,
+    "length": 3219617,
+    "n_50": 47258,
+    "nc_rnas": 63,
+    "num_contigs": 137,
+    "num_proteins": 3182,
+    "pangenome": {
+        "geographic_range": [
+            "North America",
+            "South America"
+        ],
+        "num_genomes_non_redundant": 4,
+        "num_genomes_total": 4,
+        "pangenome_accessory_size": 1804,
+        "pangenome_core_size": 1350,
+        "pangenome_size": 3154
+    },
+    "rna_16s": 99.74,
+    "rna_23s": 99.83,
+    "rna_5s": 88.24,
+    "taxon_lineage": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495;s__GCA-900066495 sp902362365",
+    "trnas": 20,
+    "type": "Isolate"
+}