updated naming entries for resources object to fix bug with only one …

…paf object. #28
legumeinfo · Aug 22, 2023 · 1e0bb15 · 1e0bb15
1 parent 5ef4b38
commit 1e0bb15
Showing 1 changed file with 21 additions and 17 deletions.
diff --git a/scripts/process_collections.py b/scripts/process_collections.py
@@ -526,26 +526,30 @@ def add_collections(self, collection_type, genus, species):
                                                 {"assembly": parent1},
                                                 {"assembly": parent2},
                                             ],
-                                            "tracks": [],
+                                            "tracks": [paf_lookup.replace(".gz", "")],
                                         }
                                     ]
                                 }
-                dotplot_url = f"{self.jbrowse_url}/?config=config.json&session=spec-{dotplot_view}"  # build the URL for the resource
-                dotplot_data = {
-                    "name": f"JBrowse2 {lookup}",
-                    "URL": str(dotplot_url).replace(
-                        "'", "%22"
-                    ),  # url encode for .yml file and Jekyll linking
-                    "description": "JBrowse2 Dotplot View",
-                }  # the object that will be written into the .yml file
-                if strain_lookup not in self.infraspecies_resources:
-                    self.infraspecies_resources[
-                        strain_lookup
-                    ] = []  # initialize infraspecies list within species
-                if self.jbrowse_url:  # dont add data if no jbrowse url set
-                    self.infraspecies_resources[strain_lookup].append(
-                        dotplot_data
-                    )  # add data for later writing in resources
+                                dotplot_url = f"{self.jbrowse_url}/?config=config.json&session=spec-{dotplot_view}"  # build the URL for the resource
+                                dotplot_data = {
+                                    "name": f"JBrowse2 {paf_lookup}",
+                                    "URL": str(dotplot_url).replace(
+                                        "'", "%22"
+                                    ),  # url encode for .yml file and Jekyll linking
+                                    "description": "JBrowse2 Dotplot View",
+                                }  # the object that will be written into the .yml file
+                                if strain_lookup not in self.infraspecies_resources:
+                                    self.infraspecies_resources[
+                                        strain_lookup
+                                    ] = (
+                                        []
+                                    )  # initialize infraspecies list within species
+                                if (
+                                    self.jbrowse_url
+                                ):  # dont add data if no jbrowse url set
+                                    self.infraspecies_resources[strain_lookup].append(
+                                        dotplot_data
+                                    )  # add data for later writing in resources
             readme_url = f"{self.datastore_url}/{collection_dir}README.{name}.yml"  # species collection readme
             readme_response = None
             if from_github: