Added initial news section in dashboard and database model

covigator/__init__.py

@@ -1,4 +1,4 @@
-VERSION = "v2.2.2"
+VERSION = "v2.2.3"
 ANALYSIS_PIPELINE_VERSION = "v0.15.0"
 
 MISSENSE_VARIANT = "missense_variant"

covigator/dashboard/tabs/overview.py

@@ -1,6 +1,8 @@
 import dash_bootstrap_components as dbc
 from dash import html
-
+from sqlalchemy.orm import Session
+from covigator.database.queries import Queries
+from dash.dependencies import Output, Input, State
 
 def get_tab_overview():
 
@@ -110,8 +112,38 @@ def get_tab_overview():
                                             ],
                                             outline=False,
                                             style={"width": "40rem", "height": "15rem", "margin-left": "40px"},
-                                        )]
-                                    ),
+                                        ),
+                                        html.Br(),
+                                        dbc.Card(
+                                            [
+                                                dbc.CardBody(
+                                                    dbc.Row([
+                                                        dbc.Col([
+                                                            html.Div(
+                                                                children=[
+                                                                    html.H2("Covigator News Section"),
+                                                                    html.P(
+                                                                        """
+                                                                        Here you can find information about new data 
+                                                                        releases, updates to Coivgator NGS pipeline or 
+                                                                        Covigator python package
+                                                                        """),
+                                                                    html.Br(),
+                                                                    html.Div(
+                                                                        id="news_section",
+                                                                        children=get_news(Session)
+                                                                    )
+                                                                ]
+                                                            )
+                                                        ])
+                                                    ])
+                                                )
+
+                                            ],
+                                            outline=False,
+                                            style={"width": "40rem", "height": "15rem", "margin-left": "40px"},
+                                        )
+                                    ]),
                                 ])),
                             html.Br(),
                             html.Br(),
@@ -132,4 +164,16 @@ def get_header():
                     [html.Div([html.H1("Welcome to CoVigator Dashboard")], style={"text-align": "left"})],
                     id="title")], width=4),
                 dbc.Col([None], width=2)
-        ], id="header", className="row flex-display",)
+        ], id="header", className="row flex-display",)
+
+
+def get_news(session: Session):
+    queries = Queries(session=session)
+    newest_news = queries.get_top_news(n=3)
+    children = []
+    #for this_news in newest_news.iterrows():
+    #    news_item = []
+    #    news_item.append(html.H3(this_news.message))
+    #    news_item.append(html.P(this_news.publishing_date))
+    #    children.extend(news_item)
+    return children

covigator/database/model.py

@@ -52,6 +52,8 @@ def get_table_versioned_name(basename, config: Configuration):
 CONSTELLATION_SITES_TABLE_NAME = get_table_versioned_name('lineage_defining_variant', config=config)
 LINEAGE_SITES_JUNCTION_TABLE_NAME = get_table_versioned_name('lineage_variant', config=config)
 VARIANT_LEVEL_CONSTRAINT_NAME = get_table_versioned_name('variant_level', config=config)
+NEWS_SECTION_TABLE_NAME = get_table_versioned_name('news_section', config=config)
+NEWS_TYPE_CONSTRAINT_NAME = get_table_versioned_name('news_type', config=config)
 SEPARATOR = ";"
 
 Base = declarative_base()
@@ -1208,3 +1210,21 @@ class LineageVariant(Base):
     pango_lineage_id = Column(ForeignKey(Lineages.pango_lineage_id), primary_key=True)
     variant_id = Column(ForeignKey(LineageDefiningVariants.variant_id), primary_key=True)
 
+
+class NewsType(enum.Enum):
+    __constraint_name__ = NEWS_TYPE_CONSTRAINT_NAME
+
+    RELEASE = 1
+    WARNINGS = 2
+    BUGS = 3
+
+class NewsSection(Base):
+    """
+    Table to hold information for news section
+    """
+    __tablename__ = NEWS_SECTION_TABLE_NAME
+
+    message_text = Column(String, primary_key=True)
+    publishing_date = Column(DateTime(timezone=True), nullable=False, default=datetime.now())
+    message_type = Column(Enum(NewsType, name=NewsType.__constraint_name__))
+

covigator/database/queries.py

@@ -15,7 +15,7 @@
     VariantType, PrecomputedAnnotation, PrecomputedOccurrence, PrecomputedTableCounts, \
     PrecomputedVariantAbundanceHistogram, PrecomputedSynonymousNonSynonymousCounts, RegionType, Domain, \
     LastUpdate, SampleCovid19Portal, VariantObservationCovid19Portal, VariantCovid19Portal, Lineages, LineageVariant, \
-    LineageDefiningVariants
+    LineageDefiningVariants, NewsSection
 from covigator.exceptions import CovigatorQueryException, CovigatorDashboardMissingPrecomputedData
 
 
@@ -160,8 +160,8 @@ def get_lineage_defining_variants(self) -> pd.DataFrame:
         # Rename columns to match columns used in recurrent/intrahost mutations tab
         lineage_variants["dna_mutation"] = lineage_variants.apply(lambda x: x.variant_id if pd.isnull(x.hgvs)
                                                                   else None, axis=1)
-        lineage_variants = lineage_variants.rename(columns={"hgvs":"hgvs_p"})
-        aa_level_mutations = lineage_variants[~pd.isnull(lineage_variants.hgvs_p)].loc[:, ['pangolin_lineage','hgvs_p']]
+        lineage_variants = lineage_variants.rename(columns={"hgvs": "hgvs_p"})
+        aa_level_mutations = lineage_variants[~pd.isnull(lineage_variants.hgvs_p)].loc[:, ['pangolin_lineage', 'hgvs_p']]
         aa_level_mutations = aa_level_mutations.sort_values(['hgvs_p', 'pangolin_lineage']).groupby('hgvs_p')['pangolin_lineage'].agg(','.join)
         aa_level_mutations = aa_level_mutations.reset_index()
 
@@ -844,3 +844,8 @@ def windowed_query(self, query, column, windowsize):
         for whereclause in self.column_windows(query.session, column, windowsize):
             for row in query.filter(whereclause).order_by(column):
                 yield row
+
+    def get_top_news(self, n=5):
+        query = self.session.query(NewsSection.message_text).order_by(NewsSection.publishing_date, desc)
+        news = pd.read_sql(query.statement, self.session.bind).head(n)
+        return news