Fix Workflow pages and Layout Managers crashing on a fresh install

content/FLASHDeconv/FLASHDeconvLayoutManager.py

@@ -34,6 +34,10 @@
     # "sequence view" and "internal fragment map" added when "input_sequence" is submitted
 ]
 
+# page_setup() first: it initialises st.session_state['workspace'], which the
+# cache access below needs when this page is opened by direct link.
+params = page_setup()
+
 # Setup cache access
 file_manager = FileManager(
     st.session_state["workspace"],
@@ -226,8 +230,6 @@ def setSequenceView():
         COMPONENT_NAMES = COMPONENT_NAMES + ['sequence_view', 'internal_fragment_map']
 
 
-# page initialization
-params = page_setup()
 
 # when sequence is submitted, add "Sequence View" as a component option
 setSequenceView()

content/FLASHTnT/FLASHTnTLayoutManager.py

@@ -28,6 +28,10 @@
     'ms1_deconv_heat_map'
 ]
 
+# page_setup() first: it initialises st.session_state['workspace'], which the
+# cache access below needs when this page is opened by direct link.
+params = page_setup()
+
 # Setup cache access
 file_manager = FileManager(
     st.session_state["workspace"],
@@ -201,8 +205,6 @@ def handleSettingButtons():
                                                for exp in uploaded_layout]
             st.session_state.num_of_experiment_to_show = len(uploaded_layout)
 
-# page initialization
-params = page_setup()
 
 # handles "onclick" of buttons
 if st.session_state.get("edit_mode") is None:

src/Workflow.py

@@ -12,10 +12,11 @@
 from src.parse.deconv import parseDeconv
 from src.workflow.WorkflowManager import WorkflowManager
 
+# Example inputs shipped with the default demo workspace.
 EXAMPLE_DATA = [
-    'example-data/deconv/example_lc_ms.mzML',
-    'example-data/tnt/example_native_aqpz.mzML',
-    'example-data/tnt/example_native_antibody.mzML',
+    'example-data/workspaces/default/flashdeconv/input-files/mzML-files/example_fd.mzML',
+    'example-data/workspaces/default/flashtnt/input-files/mzML-files/example_spectrum_aqpz.mzML',
+    'example-data/workspaces/default/flashtnt/input-files/mzML-files/example_spectrum_antibody.mzML',
 ]
 
 class TagWorkflow(WorkflowManager):
@@ -33,7 +34,7 @@ def upload(self)-> None:
             self.ui.upload_widget(key="mzML-files", name="MS data", file_types="mzML", fallback=EXAMPLE_DATA)
         with t[1]:
             self.ui.upload_widget(key="fasta-file", name="Database", file_types="fasta",
-                                  fallback='example-data/tnt/example_database.fasta')
+                                  fallback='example-data/workspaces/default/flashtnt/input-files/fasta-file/example_database.fasta')
 
 
     @st.fragment

src/render/compression.py

@@ -60,7 +60,7 @@ def downsample_heatmap(data, max_datapoints=20000, rt_bins=400, mz_bins=50, logg
         return data
 
     # Count peaks
-    total_count = sorted_data.select(pl.count()).item()
+    total_count = sorted_data.select(pl.len()).item()
 
     # Extract arrays for scipy
     mass_array = sorted_data['mass'].to_numpy()

src/workflow/StreamlitUI.py

@@ -1672,7 +1672,8 @@ def export_parameters_markdown(self):
         if len(tool_text) > 1:
             tool_text = ", ".join(tool_text[:-1]) + " and " + tool_text[-1]
         else:
-            tool_text = tool_text[0]
+            # No .ini files yet when the TOPP tools are not installed.
+            tool_text = tool_text[0] if tool_text else ""
 
         result = subprocess.run(
             "FileFilter --help", shell=True, text=True, capture_output=True