feat: functional project views, moving to dev

src/aind_qc_portal/docdb/database.py

@@ -131,10 +131,21 @@ def get_all():
 @pn.cache(ttl=TIMEOUT_1H)
 def get_project(project: str):
     filter = {"data_description.project_name": project}
-    limit = 10
-    paginate_batch_size = 100
+    limit = 0
+    paginate_batch_size = 500
     response = client.retrieve_docdb_records(
         filter_query=filter,
+        projection={
+            "_id": 1,
+            "name": 1,
+            "location": 1,
+            "subject.subject_id": 1,
+            "subject.genotype": 1,
+            "session.session_type": 1,
+            "session.session_start_time": 1,
+            "data_description.data_level": 1,
+            "data_description.project_name": 1,
+        },
         limit=limit,
         paginate_batch_size=paginate_batch_size,
     )

src/aind_qc_portal/qc_project_app.py

@@ -0,0 +1,128 @@
+"""QC Project App
+
+Generates a view of a single project's asset records and a dataframe with links out to the QC pages
+
+Intended to be the main entry point for a project's data
+"""
+import panel as pn
+import altair as alt
+import param
+import pandas as pd
+from aind_qc_portal.docdb.database import get_project, _raw_name_from_derived
+from aind_qc_portal.utils import OUTER_STYLE, set_background, format_link, AIND_COLORS, df_timestamp_range
+
+set_background()
+
+
+class Settings(param.Parameterized):
+    project_name = param.String(default="Learning mFISH-V1omFISH")
+
+
+settings = Settings()
+pn.state.location.sync(settings, {"project_name": "project_name"})
+
+
+class ProjectView():
+
+    def __init__(self):
+        self._get_assets()
+
+    def _get_assets(self):
+        """Get all assets with this project name"""
+        print(settings.project_name)
+        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)
+
+            record_data = {
+                '_id': record['_id'],
+                'raw': record['data_description']['data_level'] == 'raw',
+                'project_name': record['data_description']['project_name'],
+                'location': record['location'],
+                'name': record['name'],
+                'session_start_time': record['session']['session_start_time'],
+                'session_type': record['session']['session_type'],
+                'subject_id': record['subject']['subject_id'],
+                'genotype': record['subject']['genotype'],
+                'group': groups[raw_name],
+            }
+            data.append(record_data)
+
+            # Parse the asset history
+
+        self.data = pd.DataFrame(data)
+        self.data["timestamp"] = pd.to_datetime(self.data["session_start_time"])
+        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)
+        }
+
+        # 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)
+
+    def get_data(self):
+        return self.data[["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"""
+
+        # Calculate the time range to show on the x axis
+        (min_range, max_range, range_unit, format) = df_timestamp_range(
+            self.data
+        )
+
+        chart = (
+            alt.Chart(self.data)
+            .mark_bar()
+            .encode(
+                x=alt.X(
+                    "Date:T",
+                    title="Time",
+                    scale=alt.Scale(domain=[min_range, max_range]),
+                    axis=alt.Axis(format=format, tickCount=range_unit),
+                ),
+                y=alt.Y("group:N", title="Raw asset"),
+                tooltip=[
+                    "name",
+                    "session_type",
+                    "subject_id",
+                    "genotype",
+                    "Date",
+                ],
+                color=alt.Color("subject_id:N"),
+            )
+        )
+
+        return pn.pane.Vega(chart, sizing_mode="stretch_width", styles=OUTER_STYLE)
+
+md = f"""
+<h1 style="color:{AIND_COLORS["dark_blue"]};">
+    QC Portal - Project View
+</h1>
+Main entrypoint for projects. Shows all assets flagged for each project and links to the QC pages.
+"""
+
+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)
+row = pn.Row(pn.HSpacer(), col, pn.HSpacer())
+
+row.servable(title="AIND QC - Project")

src/aind_qc_portal/utils.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 import panel as pn
-from aind_data_schema.core.quality_control import QualityControl, Status
+from aind_data_schema.core.quality_control import Status
 
 ASSET_LINK_PREFIX = "/qc_asset_app?id="
 QC_LINK_PREFIX = "/qc_app?id="