Add views to add, delete, and display groups.

docs/CHANGELOG.md

@@ -25,6 +25,7 @@ to [Common Changelog](https://common-changelog.org)
 
 ### Added
 
+- Add views to add, delete, and display groups. ([#86](https://github.com/metagenlab/zDB/pull/86)) (Niklaus Johner)
 - Allow defining groups of genomes in input file. ([#82](https://github.com/metagenlab/zDB/pull/82)) (Niklaus Johner)
 - Add view to produce custom plots (phylogenetic trees and table). ([#78](https://github.com/metagenlab/zDB/pull/78)) (Niklaus Johner)
 - Add AMRs and VFs to search index. ([#73](https://github.com/metagenlab/zDB/pull/73)) (Niklaus Johner)

testing/webapp/test_groups.py

@@ -0,0 +1,53 @@
+from django.conf import settings
+from django.test import SimpleTestCase
+from lib.db_utils import DB
+
+
+class TestGroupsViews(SimpleTestCase):
+
+    def test_groups_overview(self):
+        resp = self.client.get("/groups/")
+        self.assertEqual(200, resp.status_code)
+        self.assertTemplateUsed(resp, 'chlamdb/groups_overview.html')
+
+        groups = [
+            '<a href=/groups/positive>positive</a>',
+            '<a href=/groups/negative>negative</a>',
+            '<a href=/groups/all>all</a>']
+        self.assertEqual(groups, resp.context["groups"])
+        for group in groups:
+            self.assertContains(resp, group)
+
+        self.assertContains(resp, 'Add new group')
+
+    def test_add_and_delete_group_view(self):
+        resp = self.client.get("/groups/add/")
+        self.assertEqual(200, resp.status_code)
+        self.assertTemplateUsed(resp, 'chlamdb/group_add.html')
+        self.assertEqual(list(resp.context.get("form").fields.keys()),
+                         ['group_name', 'genomes'])
+
+        db = DB.load_db_from_name(settings.BIODB_DB_PATH)
+        data = {"group_name": "test_group", "genomes": ["group:negative", "1"]}
+        resp = self.client.post("/groups/add/", data=data)
+        self.assertEqual(302, resp.status_code)
+        self.assertEqual('/groups/test_group', resp.url)
+        self.assertTrue(db.get_group("test_group"))
+
+        resp = self.client.post("/groups/test_group/delete/")
+        self.assertEqual(302, resp.status_code)
+        self.assertEqual('/groups/', resp.url)
+        self.assertFalse(db.get_group("test_group"))
+
+    def test_group_details_view(self):
+        resp = self.client.get("/groups/positive")
+        self.assertEqual(200, resp.status_code)
+        self.assertTemplateUsed(resp, 'chlamdb/group_details.html')
+        genomes = [
+            '<a href="/extract_contigs/1">Klebsiella pneumoniae R6724_16313</a>',
+            '<a href="/extract_contigs/2">Klebsiella pneumoniae R6726_16314</a>']
+        self.assertEqual(
+            [row.accession for i, row in resp.context["genome_table"]["table_data"].iterrows()],
+            genomes)
+        for genome in genomes:
+            self.assertContains(resp, genome, html=True)

testing/webapp/test_views.py

@@ -13,6 +13,7 @@
 
 untested_patterns = {
     '^favicon\\.ico$',
+    r'^groups/([a-zA-Z0-9_\.\(\)\-\'\s]+)/delete/$',
     '^module_cat_info/([a-zA-Z0-9_\\.]+)/([a-zA-Z0-9_\\.\\+-]+)$',
     '^plot_region/$',
     '^robots.txt$',
@@ -55,6 +56,9 @@
     '/FAQ',
     '/genomes',
     '/get_cog/3/L?h=1&h=2&h=3',
+    '/groups/',
+    '/groups/add/',
+    '/groups/positive',
     '/gwas_amr/',
     '/gwas_cog/',
     '/gwas_ko/',

webapp/assets/css/style_FILE_zDB.css

@@ -1781,3 +1781,5 @@ form.example input[type=text] {
 .bootstrap-select.form-control.input-group-btn {
     z-index: auto;
 }
+
+a.button_link { text-decoration: none; color: rgb(255, 255, 255);}

webapp/chlamdb/forms.py

@@ -712,3 +712,51 @@ def clean_entries(self):
                                       code="invalid")
             entries.append(self.Entry(entry_id, label, object_type))
         return entries
+
+
+def make_group_add_form(db):
+
+    accession_choices = AccessionFieldHandler().get_choices(
+        with_plasmids=False)
+
+    class GroupAddForm(forms.Form):
+        group_name = forms.CharField(max_length=50,
+                                     required=True)
+        genomes = forms.MultipleChoiceField(
+            choices=accession_choices,
+            widget=Select2Multiple(
+                url="autocomplete_taxid",
+                forward=(forward.Field("genomes", "exclude_taxids_in_groups"),),
+                attrs={"data-close-on-select": "false",
+                       "data-placeholder": "Nothing selected"}),
+            required=True)
+
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, **kwargs)
+            self.db = db
+            self.helper = FormHelper()
+            self.helper.form_method = "post"
+
+            self.helper.layout = Layout(
+                Fieldset(
+                    " ",
+                    Row('group_name'),
+                    Row('genomes', style="margin-top:1em"),
+                    Submit('submit', 'Submit',
+                           style="padding-left:15px; margin-top:15px; margin-bottom:15px "),
+                    css_class="col-lg-5 col-md-6 col-sm-6")
+            )
+
+        def clean_group_name(self):
+            group_name = self.cleaned_data["group_name"]
+            if self.db.get_group(group_name):
+                raise ValidationError(f'Group "{group_name}" already exists.')
+            return group_name
+
+        def get_taxids(self):
+            indices = self.cleaned_data["genomes"]
+            taxids, plasmids = AccessionFieldHandler().extract_choices(
+                indices, False)
+            return taxids
+
+    return GroupAddForm

webapp/chlamdb/urls.py

@@ -2,7 +2,7 @@
 from django.urls import re_path
 from django.views.generic import TemplateView
 from django.views.generic.base import RedirectView
-from views import (autocomplete, custom_plots, entry_lists, fam, gwas,
+from views import (autocomplete, custom_plots, entry_lists, fam, groups, gwas,
                    hits_extraction, locus, tabular_comparison, venn, views)
 
 favicon_view = RedirectView.as_view(url='/assets/favicon.ico', permanent=True)
@@ -52,8 +52,12 @@
     re_path(r'^gwas_ko/', gwas.KoGwasView.as_view(), name="gwas_ko"),
     re_path(r'^gwas_cog/', gwas.CogGwasView.as_view(), name="gwas_cog"),
     re_path(r'^gwas_amr/', gwas.AmrGwasView.as_view(), name="gwas_amr"),
+    re_path(r'^groups/add/$', groups.GroupAdd.as_view(), name=groups.GroupAdd.view_name),  # noqa
+    re_path(r'^groups/([a-zA-Z0-9_\.\(\)\-\'\s]+)/delete/$', groups.GroupDelete.as_view(), name=groups.GroupDelete.view_name),  # noqa
+    re_path(r'^groups/([a-zA-Z0-9_\.\(\)\-\'\s]+)', groups.GroupDetails.as_view(), name=groups.GroupDetails.view_name),  # noqa
+    re_path(r'^groups/$', groups.GroupsOverview.as_view(), name=groups.GroupsOverview.view_name),   # noqa
     re_path(r'^get_cog/([a-zA-Z0-9_\.]+)/([a-zA-Z0-9_\.\%]+)$', views.get_cog, name="get_cog"),  # noqa
-    re_path(r'^genomes', views.genomes, name='genomes'),
+    re_path(r'^genomes', views.Genomes.as_view(), name=views.Genomes.view_name),
     re_path(r'^favicon\.ico$', favicon_view),
     re_path(r'^FAQ', views.faq, name='FAQ'),
     re_path(r'^fam_vf/(VFG[0-9]+)$', fam.FamVfView.as_view(), name="fam_vf"),

webapp/lib/db_utils.py

@@ -1270,13 +1270,17 @@ def get_term_id(self, term, create_if_absent=False, ontology="Annotation Tags"):
             gc_term_id = result[0][0]
         return gc_term_id
 
-    def get_genomes_description(self):
+    def get_genomes_description(self, taxids=None):
         """
         Returns the description of the genome as it has been read from the
         genbank files, indexed by taxon_id. The output also contains a flag
         has_plasmid indicating whether the genome contains a plasmid or not.
         """
-
+        if taxids:
+            plchd = self.gen_placeholder_string(taxids)
+            where_clause = f"WHERE entry.taxon_id IN ({plchd})"
+        else:
+            where_clause = ""
         has_plasmid_query = (
             "SELECT * "
             "FROM bioentry_qualifier_value AS has_plasmid "
@@ -1293,13 +1297,13 @@ def get_genomes_description(self):
             "INNER JOIN taxon_name as txn_name ON entry.taxon_id=txn_name.taxon_id "
             "INNER JOIN term AS orga_term ON orga.term_id=orga_term.term_id "
             " AND orga_term.name=\"organism\" "
-            "GROUP BY entry.taxon_id;"
+            f"{where_clause} GROUP BY entry.taxon_id;"
         )
-        descr = self.server.adaptor.execute_and_fetchall(query)
+        descr = self.server.adaptor.execute_and_fetchall(query, taxids)
         columns = ["taxon_id", "description", "has_plasmid"]
         return DB.to_pandas_frame(descr, columns).set_index(["taxon_id"])
 
-    def get_genomes_infos(self):
+    def get_genomes_infos(self, taxids=None):
         """
         Note: for efficiency sake, it would be possible to order the different
          tables by taxon_id, walk through the table using zip in an iteator
@@ -1308,30 +1312,35 @@ def get_genomes_infos(self):
          However, given the small size of the dataset, it's probably not worth
          the implementation effort.
         """
+        if taxids:
+            plchd = self.gen_placeholder_string(taxids)
+            where_clause = f"WHERE taxon_id IN ({plchd})"
+        else:
+            where_clause = ""
 
         query = (
             "SELECT entry.taxon_id, entry.taxon_id, COUNT(*) "
             " FROM seqfeature AS seq "
             " INNER JOIN term AS cds ON cds.term_id = seq.type_term_id AND cds.name=\"CDS\" "
             " INNER JOIN bioentry AS entry ON entry.bioentry_id = seq.bioentry_id "
-            " GROUP BY entry.taxon_id;"
+            f"{where_clause} GROUP BY entry.taxon_id;"
         )
-        n_prot_results = self.server.adaptor.execute_and_fetchall(query)
+        n_prot_results = self.server.adaptor.execute_and_fetchall(query, taxids)
 
         query = (
             "SELECT entry.taxon_id, COUNT(*) "
             "FROM bioentry AS entry "
-            "GROUP BY entry.taxon_id;"
+            f"{where_clause} GROUP BY entry.taxon_id;"
         )
-        n_contigs = self.server.adaptor.execute_and_fetchall(query)
+        n_contigs = self.server.adaptor.execute_and_fetchall(query, taxids)
 
         cols = ["taxon_id", "completeness", "contamination",
                 "gc", "length", "coding_density"]
         query = (
             "SELECT taxon_id, completeness, contamination, gc, length, "
-            "coding_density from genome_summary;"
+            f"coding_density from genome_summary {where_clause};"
         )
-        all_other_results = self.server.adaptor.execute_and_fetchall(query)
+        all_other_results = self.server.adaptor.execute_and_fetchall(query, taxids)
 
         df_n_prot = DB.to_pandas_frame(
             n_prot_results, ["taxon_id", "id", "n_prot"]).set_index("taxon_id")
@@ -1476,6 +1485,18 @@ def load_groups(self, groups, group_taxons):
         self.load_data_into_table("groups", groups)
         self.load_data_into_table("taxon_in_group", group_taxons)
 
+    def delete_group(self, group_name):
+        sql = f"DELETE FROM taxon_in_group WHERE group_name='{group_name}';"
+        self.server.adaptor.execute(sql)
+        sql = f"DELETE FROM groups WHERE group_name='{group_name}';"
+        self.server.adaptor.execute(sql)
+        self.commit()
+        return
+
+    def get_group(self, group_name):
+        query = f"SELECT * FROM groups WHERE group_name='{group_name}' LIMIT 1;"
+        return self.server.adaptor.execute_and_fetchall(query)
+
     def get_groups(self):
         query = "SELECT * FROM groups;"
         return self.server.adaptor.execute_and_fetchall(query)

webapp/templates/chlamdb/genomes.html

@@ -1,91 +1,46 @@
-
 <!DOCTYPE html>
 
-
 <html>
 
 <head>
 
-   <link rel= "stylesheet" href="style_home.css">
-    {% load static %}
-    {% load custom_tags %}
-    {% include "chlamdb/header.html" %}
-    {% include "chlamdb/style_menu.html" %}
+  <link rel= "stylesheet" href="style_home.css">
+  {% load static %}
+  {% load custom_tags %}
+  {% include "chlamdb/header.html" %}
+  {% include "chlamdb/style_menu.html" %}
 
 </head>
 
 <body>
-    <div class="container-fluid" id="main_container">
-      <div class="row">
-        <div id="wrapper">
-            <div id="page-content-wrapper">
-              <div class="row">
-                <div class="col-lg-12">
-                   {% include "chlamdb/menu.html" %}
-
-                    <hr class="lines-home">
-                    <div class="tab-pane" id="genomes" style="margin-right: 1em; overflow-x:auto;">
-
-                          <table class="display" id="genomes_table">
-                            <thead>
-
-
-                                <tr>
-                            {% for header in data_table_header %}
-                            <th>{{header}}</th>
-                            {% endfor %}
-
-                                </tr>
-                            </thead>
-                            <tbody>
-                              {% for entry in data_table %}
-                                <tr>
-                                  <td><a href="{% url 'extract_contigs' entry.0  %}">{{entry.1}}</a></td>
-                                  <td>{{entry.2}}</td>
-                                  <td>{{entry.3}}</td>
-                                  <td>{{entry.4}}</td>
-                                  <td>{{entry.5}}</td>
-                                  <td>{{entry.6}}</td>
-                                  <td>{{entry.7}}</td>
-                                  <td><a href="{{ entry.8 }}"> .faa </a></td>
-                                  <td><a href="{{ entry.9 }}"> .fna </a></td>
-                                  <td><a href="{{ entry.10 }}"> .ffn </a></td>
-                                  <td><a href="{{ entry.11 }}"> .gbk </a></td>
-                                </tr>
-                              {% endfor %}
-                              </tbody>
-                        </table>     
-
-                        <div class="panel panel-success" style="  width:100%; margin-top: 2em;">
-                          <div class="panel-heading" style="width:100%;">
-                              <h3 class="panel-title">Help</h3>
-                          </div>
-
-                          <p style="padding:1em 3em 1em 1em; line-height: 160% ; width:100%" >This table contains the list of genomes included in the database and a summary of their content. <br> Clicking on the genome name (first column) a second table with the protein content is displayed. It shows to which contig each protein belongs and provides the link to the locus tags.
-                          <br> Fasta and gbk files can be downloaded.
-                          </p>
-                      </div>
-           </div>
-
-<script>
-
-$(document).ready(function() {
-  $("#genomes_table").DataTable({
-    columns: [
-      { data: "genome", className: "editable" },
-      { data: "GC" },
-      { data: "n_prot"},
-      { data: "n_contigs"},
-      { data: "size" },
-      { data: "perc_coding"},
-      { data: "has_plasmid"},
-      { data: "faa_seq"},
-      { data: "fna_seq"},
-      { data: "ffn_seq"},
-      { data: "gbk_file"}
-    ]
-  });}
-);
-
-</script>
+  <div class="container-fluid" id="main_container">
+    <div class="row">
+      <div id="wrapper">
+        <div id="page-content-wrapper">
+          <div class="row">
+            <div class="col-lg-12">
+              {% include "chlamdb/menu.html" %}
+
+              <hr class="lines-home">
+              <div class="tab-pane" id="genomes" style="margin-right: 1em; overflow-x:auto;">
+
+                {% include "chlamdb/result_table.html" with results=results %}
+
+                <div class="panel panel-success" style="  width:100%; margin-top: 2em;">
+                  <div class="panel-heading" style="width:100%;">
+                    <h3 class="panel-title">Help</h3>
+                  </div>
+
+                  <p style="padding:1em 3em 1em 1em; line-height: 160% ; width:100%" >
+                    {{results.table_help|safe}}
+                  </p>
+                </div>
+              </div>
+            </div>
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+</body>
 </html>