Import cleanup + code formatting using black.

biosustain · Dec 12, 2024 · 339ab32 · 339ab32
1 parent d52f9d9
commit 339ab32
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Showing 15 changed files with 651 additions and 389 deletions.
diff --git a/about/views.py b/about/views.py
@@ -1,10 +1,7 @@
-from django.shortcuts import render
-
-# Create your views here.
-
 from django.http import HttpResponse
 from django.template import loader
 
+
 def about(request):
-  template = loader.get_template('about/about.html')
-  return HttpResponse(template.render())
+    template = loader.get_template("about/about.html")
+    return HttpResponse(template.render())
diff --git a/ai_assistant/views.py b/ai_assistant/views.py
@@ -1,13 +1,14 @@
-from django.shortcuts import render
-
-# Create your views here.
-
 from django.http import HttpResponse
 from django.template import loader
 import os
 
+
 def ai_assistant(request):
-  template = loader.get_template('ai_assistant/ai_assistant.html')
-  # The url of the separately deployed AI Assistant web application is included into the render context
-  # as a env variable: ----
-  return HttpResponse(template.render(context={'AI_ASSISTANT_APP_URL': os.environ.get('AI_ASSISTANT_APP_URL')}))
+    template = loader.get_template("ai_assistant/ai_assistant.html")
+    # The url of the separately deployed AI Assistant web application is included into the render context
+    # as a env variable: ----
+    return HttpResponse(
+        template.render(
+            context={"AI_ASSISTANT_APP_URL": os.environ.get("AI_ASSISTANT_APP_URL")}
+        )
+    )
diff --git a/common/csv_export.py b/common/csv_export.py
@@ -1,6 +1,7 @@
-from django.http import HttpResponse, StreamingHttpResponse
+from django.http import StreamingHttpResponse
 import csv
 
+
 # Source: https://docs.djangoproject.com/en/5.0/howto/outputting-csv/
 class Echo:
     """An object that implements just the write method of the file-like
@@ -11,21 +12,24 @@ def write(self, value):
         """Write the value by returning it, instead of storing in a buffer."""
         return value
 
+
 def iter_dict_writer_items(items, field_names):
     pseudo_buffer = Echo()
     writer = csv.DictWriter(pseudo_buffer, fieldnames=field_names)
     yield writer.writeheader()
 
     for item in items:
         yield writer.writerow(item)
-
+
+
 def dict_writer_response(file_name, field_names, rows):
     response = StreamingHttpResponse(
         iter_dict_writer_items(rows, field_names), content_type="text/csv"
     )
-    response['Content-Disposition'] = f"attachment; filename={file_name}"
+    response["Content-Disposition"] = f"attachment; filename={file_name}"
     return response
 
+
 def list_writer_response(file_name, rows):
     pseudo_buffer = Echo()
     writer = csv.writer(pseudo_buffer)
@@ -35,5 +39,5 @@ def list_writer_response(file_name, rows):
     response = StreamingHttpResponse(
         (writer.writerow(row) for row in rows), content_type="text/csv"
     )
-    response['Content-Disposition'] = f"attachment; filename={file_name}"
-    return response
+    response["Content-Disposition"] = f"attachment; filename={file_name}"
+    return response
diff --git a/common/database.py b/common/database.py
@@ -14,10 +14,11 @@
     )
 DB = MONOGO_CLIENT[settings.MONGODB["db_name"]]
 
+
 class MongoDBObjects:
     def __init__(self, collection_name):
         self.collection = DB[collection_name]
-    
+
     def aggregate(self, pipeline, **kwargs):
         return self.collection.aggregate(pipeline, **kwargs)
 
@@ -27,5 +28,6 @@ def find(self, filter=None, projection=None, **kwargs):
             if not "_id" in projection:
                 projection["_id"] = 0
         return self.collection.find(filter=filter, projection=projection, **kwargs)
+
     def find_one(self, *args, **kwargs):
         return self.collection.find_one(*args, **kwargs)
diff --git a/common/datatables.py b/common/datatables.py
@@ -1,5 +1,6 @@
 import re
 
+
 def _parse_get_array(req_get, name):
     data = {}
     for k, v in req_get.items():
@@ -22,6 +23,7 @@ def _parse_get_array(req_get, name):
     data = [data[i] for i in range(len(data))]
     return data
 
+
 def create_datatables_api(
     mongo_aggregate, request_get, select_pipeline, out_keys, as_list=True
 ):
@@ -259,4 +261,4 @@ def create_datatables_api_mongodb(
         "columns": columns,
         "order": order,
     }
-    return response
+    return response
diff --git a/django_project/urls.py b/django_project/urls.py
@@ -14,7 +14,6 @@
     2. Add a URL to urlpatterns:  path('blog/', include('blog.urls'))
 """
 
-from django.contrib import admin
 from django.urls import path
 from django.views.generic import TemplateView
 
@@ -26,52 +25,154 @@
 from gene_function import views as gene_function_views
 from search import views as search_views
 from ai_assistant import views as ai_assistant_views
-import json, requests
 
 
 urlpatterns = [
-    path('robots.txt', TemplateView.as_view(template_name='robots.txt', content_type='text/plain')),
-    path('', home_views.home, name='home'),
-    path('about/', about_views.about, name='about'),
-    path('publications/', publications_views.publications, name='publications'),
-    path('organisms/', organisms_views.organisms, name='organisms'),
-    path('pangenome_analyses/overview/', pangenome_analyses_views.overview, name='pangenome_analyses_overview'),
-    path('pangenome_analyses/overview/csv/', organisms_views.download_organisms_table_csv,
-         name='download_organisms_table_csv'),
-    path('heaps_law/', pangenome_analyses_views.heaps_law, name='heaps_law'),
-    path('cumulative_freq/', pangenome_analyses_views.cumulative_freq, name='cumulative_freq'),
-    path('gene_annotation_distribution/', pangenome_analyses_views.gene_annotation_distribution, name='gene_annotation_distribution'),
-    path('gene_freq/', pangenome_analyses_views.gene_freq, name='gene_freq'),
-    path('hotmap/', pangenome_analyses_views.hotmap, name='hotmap'),
-    path('hotmap/data/', pangenome_analyses_views.hotmap_data, name='hotmap_data'),
-    path('hotmap/csv/', pangenome_analyses_views.download_matrix_csv, name='download_matrix_csv'),
-    path('variant_dominant_freq/', pangenome_analyses_views.variant_dominant_freq, name='variant_dominant_freq'),
-    path('ds_dn_ratio/', pangenome_analyses_views.ds_dn_ratio, name='ds_dn_ratio'),
-    path('pangenome_analyses/gene_annotation/', pangenome_analyses_views.gene_annotation, name='pangenome_analyses_gene_annotation'),
-    path('pangenome_analyses/gene_annotation/json/', pangenome_analyses_views.gene_annotation_json, name='pangenome_analyses_gene_annotation_json'),
-    path('pangenome_analyses/gene_annotation/csv/', pangenome_analyses_views.download_gene_annotation_table_csv,
-         name='download_gene_annotation_table_csv'),
-    path('pangenome_analyses/genome/', pangenome_analyses_views.genome, name='pangenome_analyses_genome'),
-    path('pangenome_analyses/genome/csv/', pangenome_analyses_views.download_genome_info_table_csv, name='download_genome_info_table_csv'),
-    path('pangenome_analyses/genome/json/', pangenome_analyses_views.genome_json, name='pangenome_analyses_genome_json'),
-    path('pangenome_analyses/phylogenetic_tree/', pangenome_analyses_views.phylogenetic_tree, name='pangenome_analyses_phylogenetic_tree'),
-    path('phylotree_plot/', pangenome_analyses_views.phylotree_plot, name='phylotree_plot'),
-    path('gene_function/gene_info/', gene_function_views.gene_info, name='gene_info'),
-    path('gene_function/gene_info/csv/', gene_function_views.download_gene_info_table_csv, name='download_gene_info_table_csv'),
-    path('aa_pos_overview/', gene_function_views.aa_pos_overview, name='aa_pos_overview'),
-    path('msa/', gene_function_views.msa, name='msa'),
-    path('gene_function/genome_info/', gene_function_views.genome_info, name='genome_info'),
-    path('gene_function/genome_info/genes/csv/', gene_function_views.download_genome_info_gene_table_csv, name='download_genome_info_gene_table_csv'),
-    path('genome_barplot/', gene_function_views.genome_barplot, name='genome_barplot'),
-    path('gene_function/genome_gene_info/', gene_function_views.genome_gene_info, name='genome_gene_info'),
-    path('gene_function/pathway_info/', gene_function_views.pathway_info, name='pathway_info'),
-    path('gene_function/pathway_info/genes/json/', gene_function_views.pathway_gene_annotation_json, name='pathway_info_genes_json'),
-    path('search/', search_views.search_results, name='search_results'),
-    path('search/genes_json/', search_views.gene_annotation_json, name='search_genes_json'),
-    path('search/family/csv/', search_views.download_search_family_csv, name='download_search_family_csv'),
-    path('search/species/csv/', search_views.download_search_species_csv, name='download_search_species_csv'),
-    path('search/pathway/csv/', search_views.download_search_pathway_csv, name='download_search_pathway_csv'),
-    path('search/genes/csv/', search_views.download_search_genes_csv, name='download_search_genes_csv'),
-    path('ai_assistant/', ai_assistant_views.ai_assistant, name='ai_assistant')
-    #path('admin/', admin.site.urls)   # make the amdin panel inaccessible via its utl (the admin admin is preserved for the potential future needs)
-]
+    path(
+        "robots.txt",
+        TemplateView.as_view(template_name="robots.txt", content_type="text/plain"),
+    ),
+    path("", home_views.home, name="home"),
+    path("about/", about_views.about, name="about"),
+    path("publications/", publications_views.publications, name="publications"),
+    path("organisms/", organisms_views.organisms, name="organisms"),
+    path(
+        "pangenome_analyses/overview/",
+        pangenome_analyses_views.overview,
+        name="pangenome_analyses_overview",
+    ),
+    path(
+        "pangenome_analyses/overview/csv/",
+        organisms_views.download_organisms_table_csv,
+        name="download_organisms_table_csv",
+    ),
+    path("heaps_law/", pangenome_analyses_views.heaps_law, name="heaps_law"),
+    path(
+        "cumulative_freq/",
+        pangenome_analyses_views.cumulative_freq,
+        name="cumulative_freq",
+    ),
+    path(
+        "gene_annotation_distribution/",
+        pangenome_analyses_views.gene_annotation_distribution,
+        name="gene_annotation_distribution",
+    ),
+    path("gene_freq/", pangenome_analyses_views.gene_freq, name="gene_freq"),
+    path("hotmap/", pangenome_analyses_views.hotmap, name="hotmap"),
+    path("hotmap/data/", pangenome_analyses_views.hotmap_data, name="hotmap_data"),
+    path(
+        "hotmap/csv/",
+        pangenome_analyses_views.download_matrix_csv,
+        name="download_matrix_csv",
+    ),
+    path(
+        "variant_dominant_freq/",
+        pangenome_analyses_views.variant_dominant_freq,
+        name="variant_dominant_freq",
+    ),
+    path("ds_dn_ratio/", pangenome_analyses_views.ds_dn_ratio, name="ds_dn_ratio"),
+    path(
+        "pangenome_analyses/gene_annotation/",
+        pangenome_analyses_views.gene_annotation,
+        name="pangenome_analyses_gene_annotation",
+    ),
+    path(
+        "pangenome_analyses/gene_annotation/json/",
+        pangenome_analyses_views.gene_annotation_json,
+        name="pangenome_analyses_gene_annotation_json",
+    ),
+    path(
+        "pangenome_analyses/gene_annotation/csv/",
+        pangenome_analyses_views.download_gene_annotation_table_csv,
+        name="download_gene_annotation_table_csv",
+    ),
+    path(
+        "pangenome_analyses/genome/",
+        pangenome_analyses_views.genome,
+        name="pangenome_analyses_genome",
+    ),
+    path(
+        "pangenome_analyses/genome/csv/",
+        pangenome_analyses_views.download_genome_info_table_csv,
+        name="download_genome_info_table_csv",
+    ),
+    path(
+        "pangenome_analyses/genome/json/",
+        pangenome_analyses_views.genome_json,
+        name="pangenome_analyses_genome_json",
+    ),
+    path(
+        "pangenome_analyses/phylogenetic_tree/",
+        pangenome_analyses_views.phylogenetic_tree,
+        name="pangenome_analyses_phylogenetic_tree",
+    ),
+    path(
+        "phylotree_plot/",
+        pangenome_analyses_views.phylotree_plot,
+        name="phylotree_plot",
+    ),
+    path("gene_function/gene_info/", gene_function_views.gene_info, name="gene_info"),
+    path(
+        "gene_function/gene_info/csv/",
+        gene_function_views.download_gene_info_table_csv,
+        name="download_gene_info_table_csv",
+    ),
+    path(
+        "aa_pos_overview/", gene_function_views.aa_pos_overview, name="aa_pos_overview"
+    ),
+    path("msa/", gene_function_views.msa, name="msa"),
+    path(
+        "gene_function/genome_info/",
+        gene_function_views.genome_info,
+        name="genome_info",
+    ),
+    path(
+        "gene_function/genome_info/genes/csv/",
+        gene_function_views.download_genome_info_gene_table_csv,
+        name="download_genome_info_gene_table_csv",
+    ),
+    path("genome_barplot/", gene_function_views.genome_barplot, name="genome_barplot"),
+    path(
+        "gene_function/genome_gene_info/",
+        gene_function_views.genome_gene_info,
+        name="genome_gene_info",
+    ),
+    path(
+        "gene_function/pathway_info/",
+        gene_function_views.pathway_info,
+        name="pathway_info",
+    ),
+    path(
+        "gene_function/pathway_info/genes/json/",
+        gene_function_views.pathway_gene_annotation_json,
+        name="pathway_info_genes_json",
+    ),
+    path("search/", search_views.search_results, name="search_results"),
+    path(
+        "search/genes_json/",
+        search_views.gene_annotation_json,
+        name="search_genes_json",
+    ),
+    path(
+        "search/family/csv/",
+        search_views.download_search_family_csv,
+        name="download_search_family_csv",
+    ),
+    path(
+        "search/species/csv/",
+        search_views.download_search_species_csv,
+        name="download_search_species_csv",
+    ),
+    path(
+        "search/pathway/csv/",
+        search_views.download_search_pathway_csv,
+        name="download_search_pathway_csv",
+    ),
+    path(
+        "search/genes/csv/",
+        search_views.download_search_genes_csv,
+        name="download_search_genes_csv",
+    ),
+    path("ai_assistant/", ai_assistant_views.ai_assistant, name="ai_assistant"),
+    # path('admin/', admin.site.urls)   # make the amdin panel inaccessible via its utl (the admin admin is preserved for the potential future needs)
+]
diff --git a/gene_function/models.py b/gene_function/models.py
@@ -1,13 +1,14 @@
 from common import database
 
+
 # Model for the Gene Info table content
 class GeneInfo:
-    objects = database.MongoDBObjects('pankb_gene_info')
+    objects = database.MongoDBObjects("pankb_gene_info")
 
 
 # Model for the Genome Info table content
 class GenomeInfo:
-    objects = database.MongoDBObjects('pankb_genome_info')
+    objects = database.MongoDBObjects("pankb_genome_info")
 
     def get_genome_and_isolation_info_pipeline(genome_match):
         return [
@@ -37,10 +38,8 @@ def get_genome_and_isolation_info(genome_match, projection=None):
                 projection["_id"] = 0
         if projection:
             pipeline.append({"$project": projection})
-        return GenomeInfo.objects.aggregate(
-            pipeline
-        )
+        return GenomeInfo.objects.aggregate(pipeline)
 
 
 class PathwayInfo:
-    objects = database.MongoDBObjects('pankb_pathway_info')
+    objects = database.MongoDBObjects("pankb_pathway_info")