diff --git a/config/phytobsdash_config.toml b/config/phytobsdash_config.toml
index 5b6b9f1be4ea5e881d7fcb430e32608c10b0bee8..7189ca01cd7500befce6fb15a8ac0088739de204 100644
--- a/config/phytobsdash_config.toml
+++ b/config/phytobsdash_config.toml
@@ -1,16 +1,16 @@
[analyst]
url='https://data.phytobs.fr/files/latest/all_sites/Analyst.csv'
separator=";"
-file='data/analyst.pickle'
+file='../data/analyst.pickle'
[hydro]
-file='data/hydro.pickle'
+file='../data/hydro.pickle'
[phytobs]
url='https://data.phytobs.fr/files/latest/all_sites/Phytobs.csv'
separator=";"
-file='data/phytobs.pickle'
+file='../data/phytobs.pickle'
[webapp]
diff --git a/src/pages/about.py b/src/pages/about.py
index a7e5f807726f765aa048050979c2c3a835b2bd3d..4e61666ea9ad7ceb6100f5ca22cf8a5401b7d096 100644
--- a/src/pages/about.py
+++ b/src/pages/about.py
@@ -1,7 +1,7 @@
import dash
from dash import html, dcc
-dash.register_page(__name__)
+dash.register_page(__name__, order=2)
layout = html.Div(
dcc.Markdown('''
diff --git a/src/pages/help.py b/src/pages/help.py
index 8dc730e61551e06ecb961625d21c69742b7c410a..064845e9bee0fce87b85593a9fa35f80391d49fb 100644
--- a/src/pages/help.py
+++ b/src/pages/help.py
@@ -1,7 +1,7 @@
import dash
from dash import html, dcc
-dash.register_page(__name__)
+dash.register_page(__name__, order=3)
layout = html.Div(
dcc.Markdown('''
diff --git a/src/pages/phytobsdash.py b/src/pages/phytobsdash.py
index 573357e03858108fa58835f941186e750b7cb4db..28d583a688fddbbe75e2625bbf6fcd2557267e45 100644
--- a/src/pages/phytobsdash.py
+++ b/src/pages/phytobsdash.py
@@ -22,7 +22,7 @@ LOGGER.setLevel(logging.DEBUG)
controls_by_index = {}
taxon_layers_by_index = {}
-dash.register_page(__name__, path="/", name="Home")
+dash.register_page(__name__, path="/", name="Home", order=0)
def _build_taxon_group_dropdown_options(survey_df):
@@ -34,86 +34,6 @@ def _build_taxon_group_dropdown_options(survey_df):
return options
-def analyst_table_info():
- """
- Create and return a data table displaying analyst information.
-
- :return: The Dash Ag-Grid table for analyst information.
- :rtype: dag.AgGrid
- """
- # Calcul des statistiques pour chaque étude
- df_analyst_table_info = pdt.analyst_df.groupby('Survey').agg({'Sampling date': ['nunique', 'min', 'max'],
- 'Accepted taxon name': ['count', 'nunique'],
- 'Latitude': 'first', 'Longitude': 'first'})
- df_analyst_table_info.columns = ['Samples', 'First sample', 'Latest sample', 'Total occurrences',
- 'Distinct Taxa', 'Latitude', 'Longitude']
-
- df_analyst_table_info.reset_index(inplace=True)
-
- # Création du tableau Ag-Grid
- analyst_table = dag.AgGrid(
- id='analyst-data-table',
- columnDefs=[{"field": col, "headerName": col} for col in df_analyst_table_info.columns],
- rowData=df_analyst_table_info.to_dict('records'),
- defaultColDef={"resizable": True, "sortable": True, "filter": True},
- columnSize="sizeToFit",
- csvExportParams={
- "fileName": "analyst_table.csv",
- },
- )
-
- return analyst_table
-
-
-def phytobs_table_info():
- """
- Create and return a data table displaying phytobs information.
-
- :return: The Dash Ag-Grid table for phytobs information.
- :rtype: dag.AgGrid
- """
- df_phytobs_table_info = pdt.phytobs_df.groupby('Survey').agg({'Sampling date': ['nunique', 'min', 'max'],
- 'Taxonomic group': ['count', 'nunique'],
- 'Latitude': 'first', 'Longitude': 'first'})
- df_phytobs_table_info.columns = ['Samples', 'First sample', 'Latest sample', 'Total Grouped Occurrences',
- 'Distinct Groups', 'Latitude', 'Longitude']
-
- df_phytobs_table_info.reset_index(inplace=True)
-
- # Création du tableau Ag-Grid
- phytobs_table = dag.AgGrid(
- id='phytobs-data-table',
- columnDefs=[{"field": col, "headerName": col} for col in df_phytobs_table_info.columns],
- rowData=df_phytobs_table_info.to_dict('records'),
- defaultColDef={"resizable": True, "sortable": True, "filter": True},
- columnSize="sizeToFit",
- csvExportParams={
- "fileName": "phytobs_table.csv",
- },
- )
-
- return phytobs_table
-
-
-@callback(
- Output("analyst-data-table", "exportDataAsCsv"),
- Input("a-csv-button", "n_clicks"),
-)
-def export_analyst_data_as_csv(n_clicks):
- if n_clicks:
- return True
- return False
-
-
-@callback(
- Output("phytobs-data-table", "exportDataAsCsv"),
- Input("p-csv-button", "n_clicks"),
-)
-def export_phytobs_data_as_csv(n_clicks):
- if n_clicks:
- return True
- return False
-
@callback(
Output('survey-info-layer', 'children'),
@@ -2203,37 +2123,6 @@ layout = html.Div([
style={'max-width': '100%', 'height': '400px', 'position': 'center'},
zoom=5,
)]),
- html.Details(
- open=False,
- children=[
- html.Summary("PHYTOBS SNO Summary Tables"),
- dbc.Alert([
- "Data for the SNO Dashboard is provided by the ",
- html.A(
- 'PHYTOBS file download area',
- href='https://data.phytobs.fr/files/latest/',
- target='_blank',
- className="alert-link",
- )],
- color="light"),
- html.Details(
- open=True,
- children=[
- html.Summary(f"Analyst table ({(pdt.analyst_df['Survey'].nunique())} surveys)"),
- analyst_table_info(),
- html.Button("Download CSV", id="a-csv-button", n_clicks=0),
- ]
- ),
- html.Details(
- open=True,
- children=[
- html.Summary(f"PHYTOBS table ({pdt.phytobs_df['Survey'].nunique()} surveys)"),
- phytobs_table_info(),
- html.Button("Download CSV", id="p-csv-button", n_clicks=0),
- ]
- ),
- ],
- ),
html.Hr(className='bd-hr'),
html.Div(id="graph-panels", children=[]),
html.Div(id='marker-popup', style={'display': 'none'}),
diff --git a/src/pages/summary.py b/src/pages/summary.py
new file mode 100644
index 0000000000000000000000000000000000000000..a1a0d7692769b062029da55c00609b0ea2aca297
--- /dev/null
+++ b/src/pages/summary.py
@@ -0,0 +1,153 @@
+import logging
+
+import dash
+import pandas as pd
+from dash import Dash, html, dcc, callback, Output, Input, ALL, MATCH, State, Patch, ctx
+import dash_ag_grid as dag
+import plotly.figure_factory as ff
+
+import phytobs_data_tools as pdt
+
+dash.register_page(__name__,order=1)
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.DEBUG)
+
+
+def analyst_table_info():
+ """
+ Create and return a data table displaying analyst information.
+
+ :return: The Dash Ag-Grid table for analyst information.
+ :rtype: dag.AgGrid
+ """
+ # Calcul des statistiques pour chaque étude
+ df_analyst_table_info = pdt.analyst_df.groupby('Survey').agg({'Sampling date': ['nunique', 'min', 'max'],
+ 'Accepted taxon name': ['count', 'nunique'],
+ 'Latitude': 'first', 'Longitude': 'first'})
+ df_analyst_table_info.columns = ['Samples', 'First sample', 'Latest sample', 'Total occurrences',
+ 'Distinct Taxa', 'Latitude', 'Longitude']
+
+ df_analyst_table_info.reset_index(inplace=True)
+
+ # Création du tableau Ag-Grid
+ analyst_table = dag.AgGrid(
+ id='analyst-data-table',
+ columnDefs=[{"field": col, "headerName": col} for col in df_analyst_table_info.columns],
+ rowData=df_analyst_table_info.to_dict('records'),
+ defaultColDef={"resizable": True, "sortable": True, "filter": True},
+ columnSize="sizeToFit",
+ csvExportParams={
+ "fileName": "analyst_table.csv",
+ },
+ )
+
+ return analyst_table
+
+
+def phytobs_table_info():
+ """
+ Create and return a data table displaying phytobs information.
+
+ :return: The Dash Ag-Grid table for phytobs information.
+ :rtype: dag.AgGrid
+ """
+ df_phytobs_table_info = pdt.phytobs_df.groupby('Survey').agg({'Sampling date': ['nunique', 'min', 'max'],
+ 'Taxonomic group': ['count', 'nunique'],
+ 'Latitude': 'first', 'Longitude': 'first'})
+ df_phytobs_table_info.columns = ['Samples', 'First sample', 'Latest sample', 'Total Grouped Occurrences',
+ 'Distinct Groups', 'Latitude', 'Longitude']
+
+ df_phytobs_table_info.reset_index(inplace=True)
+
+ # Création du tableau Ag-Grid
+ phytobs_table = dag.AgGrid(
+ id='phytobs-data-table',
+ columnDefs=[{"field": col, "headerName": col} for col in df_phytobs_table_info.columns],
+ rowData=df_phytobs_table_info.to_dict('records'),
+ defaultColDef={"resizable": True, "sortable": True, "filter": True},
+ columnSize="sizeToFit",
+ csvExportParams={
+ "fileName": "phytobs_table.csv",
+ },
+ )
+
+ return phytobs_table
+
+
+@callback(
+ Output("analyst-data-table", "exportDataAsCsv"),
+ Input("a-csv-button", "n_clicks"),
+)
+def export_analyst_data_as_csv(n_clicks):
+ if n_clicks:
+ return True
+ return False
+
+
+@callback(
+ Output("phytobs-data-table", "exportDataAsCsv"),
+ Input("p-csv-button", "n_clicks"),
+)
+def export_phytobs_data_as_csv(n_clicks):
+ if n_clicks:
+ return True
+ return False
+
+
+
+def summary_table_info():
+
+ summary_info = pdt.phytobs_df[['Survey','Sampling date']]
+
+ summary_info["Sampling date"] = pd.to_datetime(summary_info["Sampling date"])
+ summary_info["Start"] = summary_info["Sampling date"].apply(lambda x: pd.offsets.MonthBegin().rollback(x))
+ summary_info["Start"] = summary_info["Start"].apply(lambda x: x.replace(hour=0, minute=0, second=0))
+ summary_info["Finish"] =summary_info['Sampling date'].apply(lambda x: pd.offsets.MonthEnd().rollforward(x))
+ summary_info["Finish"] = summary_info["Finish"].apply(lambda x: x.replace(hour=0, minute=0, second=0))
+ summary_info.drop('Sampling date', axis=1, inplace=True)
+ summary_info=summary_info.drop_duplicates(keep='first')
+ summary_info["Task"] = summary_info["Survey"]
+ summary_info["Resource"] = "Samples"
+
+ summary_info.sort_values(['Task'], inplace=True)
+
+ summary_info.rename(columns={'Task': 'Task', "Start" : "Start", "Finish" : 'Finish'}, inplace=True)
+
+ colors = {
+ 'Samples' : 'rgb(47,164,90)',
+ }
+
+ fig = ff.create_gantt(summary_info, colors=colors, index_col="Resource", show_colorbar=False, title="Overview of Sampling Timespan", group_tasks=True)
+
+ return dcc.Graph(figure=fig)
+
+
+
+layout = html.Div(
+html.Div(
+ children=[
+ html.Div(
+ children=[
+ html.H4(f"Overview of Available Samples"),
+ summary_table_info(),
+ ]
+ ),
+ html.Div(
+ children=[
+ html.H4(f"PHYTOBS taxon groups table ({pdt.phytobs_df['Survey'].nunique()} surveys)"),
+ phytobs_table_info(),
+ html.Button("Download CSV", id="p-csv-button", n_clicks=0),
+ ]
+ ),
+ html.Div(
+ children=[
+ html.H4(f"PHYTOBS analyst taxon table ({pdt.analyst_df['Survey'].nunique()} surveys)"),
+ analyst_table_info(),
+ html.Button("Download CSV", id="a-csv-button", n_clicks=0),
+ ]
+ ),
+ ], className="bd-content-full"
+ ),
+)