diff --git a/src/aind_qc_portal/qc_project_app.py b/src/aind_qc_portal/qc_project_app.py
index 9fd1661..1dcc79c 100644
--- a/src/aind_qc_portal/qc_project_app.py
+++ b/src/aind_qc_portal/qc_project_app.py
@@ -22,7 +22,8 @@ class Settings(param.Parameterized):
pn.state.location.sync(settings, {"project_name": "project_name"})
-class ProjectView():
+class ProjectView(param.Parameterized):
+ subject_filter = param.String(default="")
def __init__(self):
self._get_assets()
@@ -33,12 +34,9 @@ def _get_assets(self):
records = get_project(settings.project_name)
data = []
- groups = {}
for record in records:
raw_name = _raw_name_from_derived(record['name'])
-
- if raw_name not in groups:
- groups[raw_name] = len(groups)
+ subject_id = record.get('subject', {}).get('subject_id')
record_data = {
'_id': record.get('_id'),
@@ -48,9 +46,8 @@ def _get_assets(self):
'name': record.get('name'),
'session_start_time': record.get('session', {}).get('session_start_time'),
'session_type': record.get('session', {}).get('session_type'),
- 'subject_id': record.get('subject', {}).get('subject_id'),
+ 'subject_id': subject_id,
'genotype': record.get('subject', {}).get('genotype'),
- 'group': groups.get(raw_name),
}
data.append(record_data)
@@ -59,26 +56,31 @@ def _get_assets(self):
return
self.data = pd.DataFrame(data)
- self.data["timestamp"] = pd.to_datetime(self.data["session_start_time"])
+ self.data["timestamp"] = pd.to_datetime(self.data["session_start_time"], format='mixed', utc=True)
self.data["Date"] = self.data["timestamp"].dt.strftime("%Y-%m-%d %H:%M:%S")
self.data["S3 link"] = self.data["location"].apply(lambda x: format_link(x, text="S3 link"))
self.data["Subject view"] = self.data["_id"].apply(lambda x: format_link(f"/qc_asset_app?id={x}"))
self.data["QC view"] = self.data["_id"].apply(lambda x: format_link(f"/qc_app?id={x}"))
self.data.sort_values(by="timestamp", ascending=True, inplace=True)
- unique_groups = self.data["group"].unique()
- group_mapping = {
- group: new_group for new_group, group in enumerate(unique_groups)
- }
+ self.data.sort_values(by="subject_id", ascending=True, inplace=True)
+
+ def get_subjects(self):
+ if self.data is None:
+ return []
- # Replace the 'group' column with the new group values
- self.data["group"] = self.data["group"].map(group_mapping)
- self.data.sort_values(by="group", ascending=True, inplace=True)
+ return self.data["subject_id"].unique()
def get_data(self):
if self.data is None:
return None
- return self.data[["subject_id", "Date", "S3 link", "Subject view", "QC view", "genotype", "session_type", "raw"]]
+
+ if self.subject_filter:
+ filtered_df = self.data[self.data["subject_id"].str.contains(self.subject_filter, case=False, na=False)]
+ else:
+ filtered_df = self.data
+
+ return filtered_df[["subject_id", "Date", "S3 link", "Subject view", "QC view", "genotype", "session_type", "raw"]]
def history_panel(self):
"""Create a plot showing the history of this asset, showing how assets were derived from each other"""
@@ -102,7 +104,7 @@ def history_panel(self):
scale=alt.Scale(domain=[min_range, max_range]),
axis=alt.Axis(format=format, tickCount=range_unit),
),
- y=alt.Y("group:N", title="Raw asset"),
+ y=alt.Y("subject_id:N", title="Subject ID"),
tooltip=[
"name",
"session_type",
@@ -112,26 +114,39 @@ def history_panel(self):
],
color=alt.Color("subject_id:N"),
)
+ .properties(width=900)
)
return pn.pane.Vega(chart, sizing_mode="stretch_width", styles=OUTER_STYLE)
+project_view = ProjectView()
md = f"""
- QC Portal - Project View
+ {settings.project_name}
-Main entrypoint for projects. Shows all assets flagged for each project and links to the QC pages.
+{len(project_view.data)} data assets are associated with this project.
"""
header = pn.pane.Markdown(md, width=1000, styles=OUTER_STYLE)
-project_view = ProjectView()
chart_pane = project_view.history_panel()
-df_pane = pn.pane.DataFrame(project_view.get_data(), width=1000, escape=False, index=False, styles=OUTER_STYLE)
-col = pn.Column(header, chart_pane, df_pane)
+df_pane = pn.pane.DataFrame(project_view.get_data(), width=950, escape=False, index=False)
+
+
+def update_subject_filter(event):
+ project_view.subject_filter = event.new
+ df_pane.object = project_view.get_data()
+
+
+subject_filter = pn.widgets.Select(name="Subject filter", options=list(project_view.get_subjects()))
+subject_filter.param.watch(update_subject_filter, "value")
+
+df_col = pn.Column(subject_filter, df_pane, styles=OUTER_STYLE)
+
+col = pn.Column(header, chart_pane, df_col)
row = pn.Row(pn.HSpacer(), col, pn.HSpacer())
row.servable(title="AIND QC - Project")
diff --git a/src/aind_qc_portal/utils.py b/src/aind_qc_portal/utils.py
index 68dbb35..65a0c8f 100644
--- a/src/aind_qc_portal/utils.py
+++ b/src/aind_qc_portal/utils.py
@@ -98,6 +98,8 @@ def df_timestamp_range(df, column="timestamp"):
one_month = timedelta(days=30)
three_months = timedelta(days=90)
one_year = timedelta(days=365)
+ two_year = timedelta(days=730)
+ five_year = timedelta(days=1825)
# Determine the minimum range
if time_range < one_week:
@@ -115,11 +117,23 @@ def df_timestamp_range(df, column="timestamp"):
max_range = max_date + (three_months - time_range) / 2
unit = "week"
format = "%b %d"
- else:
+ elif time_range < one_year:
min_range = min_date - (one_year - time_range) / 2
max_range = max_date + (one_year - time_range) / 2
unit = "month"
format = "%b"
+ elif time_range < two_year:
+ min_range = min_date - (two_year - time_range) / 2
+ max_range = max_date + (two_year - time_range) / 2
+ unit = "year"
+ format = "%b"
+ elif time_range < five_year:
+ min_range = min_date - (five_year - time_range) / 2
+ max_range = max_date + (five_year - time_range) / 2
+ unit = "year"
+ format = "%Y"
+ else:
+ raise ValueError("Time range is too large")
return (min_range, max_range, unit, format)