Merge pull request #49 from axelwalter/update-topp-framework

update TOPP framework
OpenMS · May 6, 2024 · 79d7aaa · 79d7aaa
2 parents e2f082d + 5c75afb
commit 79d7aaa
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Showing 9 changed files with 211 additions and 282 deletions.
diff --git a/pages/3_📖_TOPP_Workflow_Framework.py b/pages/3_📖_TOPP_Workflow_Framework.py
@@ -23,24 +23,9 @@
 - workflow output updates automatically in short intervalls
 - user can leave the app and return to the running workflow at any time
 - quickly build a workflow with multiple steps channelling files between steps
-#
 """
 )
 
-with st.expander("**Example User Interface**", True):
-    t =  st.tabs(["📁 **File Upload**", "⚙️ **Configure**", "🚀 **Run**", "📊 **Results**"])
-    with t[0]:
-        wf.show_file_upload_section()
-
-    with t[1]:
-        wf.show_parameter_section()
-
-    with t[2]:
-        wf.show_execution_section()
-
-    with t[3]:
-        wf.show_results_section()
-
 st.markdown(
 """
 ## Quickstart
@@ -117,26 +102,26 @@
 **3. Choose `self.ui.input_python` to automatically generate complete input sections for a custom Python tool:**
 
 Takes the obligatory **script_file** argument. The default location for the Python script files is in `src/python-tools` (in this case the `.py` file extension is optional in the **script_file** argument), however, any other path can be specified as well. Parameters need to be specified in the Python script in the **DEFAULTS** variable with the mandatory **key** and **value** parameters.
-
-Here are the options to use as dictionary keys for parameter definitions (see `src/python-tools/example.py` for an example):
-
-Mandatory keys for each parameter
-- **key:** a unique identifier
-- **value:** the default value
-
-Optional keys for each parameter
-- **name:** the name of the parameter
-- **hide:** don't show the parameter in the parameter section (e.g. for **input/output files**)
-- **options:** a list of valid options for the parameter
-- **min:** the minimum value for the parameter (int and float)
-- **max:** the maximum value for the parameter (int and float)
-- **step_size:** the step size for the parameter (int and float)
-- **help:** a description of the parameter
-- **widget_type:** the type of widget to use for the parameter (default: auto)
-- **advanced:** whether or not the parameter is advanced (default: False)
-
 """)
 
+with st.expander("Options to use as dictionary keys for parameter definitions (see `src/python-tools/example.py` for an example)"):
+    st.markdown("""
+**Mandatory** keys for each parameter
+- *key:* a unique identifier
+- *value:* the default value
+
+**Optional** keys for each parameter
+- *name:* the name of the parameter
+- *hide:* don't show the parameter in the parameter section (e.g. for **input/output files**)
+- *options:* a list of valid options for the parameter
+- *min:* the minimum value for the parameter (int and float)
+- *max:* the maximum value for the parameter (int and float)
+- *step_size:* the step size for the parameter (int and float)
+- *help:* a description of the parameter
+- *widget_type:* the type of widget to use for the parameter (default: auto)
+- *advanced:* whether or not the parameter is advanced (default: False)
+""")
+
 st.code(
 getsource(Workflow.configure)
 )
@@ -201,7 +186,7 @@
 """)
 
 st.code("""
-self.executor.run_command(["command", "arg1", "arg2", ...], write_log=True)
+self.executor.run_command(["command", "arg1", "arg2", ...])
 """)
 
 st.markdown(
@@ -266,134 +251,4 @@
     st.help(CommandExecutor.run_command)
     st.help(CommandExecutor.run_multiple_commands)
     st.help(CommandExecutor.run_topp)
-    st.help(CommandExecutor.run_python)
-
-with st.expander("**Example output of the complete example workflow**"):
-    st.code("""
-STARTING WORKFLOW
-
-Number of input mzML files: 2
-
-Running 2 commands in parallel...
-
-Running command:
-FeatureFinderMetabo -in ../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Treatment.mzML -out ../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Treatment.featureXML -algorithm:common:chrom_peak_snr 4.0 -algorithm:common:noise_threshold_int 1000.0
-Waiting for command to finish...
-
-Running command:
-FeatureFinderMetabo -in ../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Control.mzML -out ../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Control.featureXML -algorithm:common:chrom_peak_snr 4.0 -algorithm:common:noise_threshold_int 1000.0
-Waiting for command to finish...
-
-Process finished:
-FeatureFinderMetabo -in ../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Treatment.mzML -out ../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Treatment.featureXML -algorithm:common:chrom_peak_snr 4.0 -algorithm:common:noise_threshold_int 1000.0
-Total time to run command: 0.55 seconds
-
-Progress of 'loading mzML':
-  Progress of 'loading spectra list':
-
-    89.06 %               
-  -- done [took 0.17 s (CPU), 0.17 s (Wall)] -- 
-  Progress of 'loading chromatogram list':
-
-  -- done [took 0.00 s (CPU), 0.00 s (Wall)] -- 
-
--- done [took 0.18 s (CPU), 0.18 s (Wall) @ 40.66 MiB/s] -- 
-Progress of 'mass trace detection':
-
--- done [took 0.01 s (CPU), 0.01 s (Wall)] -- 
-Progress of 'elution peak detection':
-
--- done [took 0.07 s (CPU), 0.07 s (Wall)] -- 
-Progress of 'assembling mass traces to features':
-Loading metabolite isotope model with 5% RMS error
-
--- done [took 0.04 s (CPU), 0.04 s (Wall)] -- 
--- FF-Metabo stats --
-Input traces:    1382
-Output features: 1095 (total trace count: 1382)
-FeatureFinderMetabo took 0.47 s (wall), 0.90 s (CPU), 0.43 s (system), 0.47 s (user); Peak Memory Usage: 88 MB.
-
-
-Process finished:
-FeatureFinderMetabo -in ../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Control.mzML -out ../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Control.featureXML -algorithm:common:chrom_peak_snr 4.0 -algorithm:common:noise_threshold_int 1000.0
-Total time to run command: 0.60 seconds
-
-Progress of 'loading mzML':
-  Progress of 'loading spectra list':
-
-    77.09 %               
-  -- done [took 0.16 s (CPU), 0.16 s (Wall)] -- 
-  Progress of 'loading chromatogram list':
-
-  -- done [took 0.00 s (CPU), 0.00 s (Wall)] -- 
-
--- done [took 0.17 s (CPU), 0.17 s (Wall) @ 43.38 MiB/s] -- 
-Progress of 'mass trace detection':
-
--- done [took 0.02 s (CPU), 0.02 s (Wall)] -- 
-Progress of 'elution peak detection':
-
--- done [took 0.07 s (CPU), 0.07 s (Wall)] -- 
-Progress of 'assembling mass traces to features':
-Loading metabolite isotope model with 5% RMS error
-
--- done [took 0.05 s (CPU), 0.05 s (Wall)] -- 
--- FF-Metabo stats --
-Input traces:    1521
-Output features: 1203 (total trace count: 1521)
-FeatureFinderMetabo took 0.51 s (wall), 0.90 s (CPU), 0.45 s (system), 0.45 s (user); Peak Memory Usage: 88 MB.
-
-
-Total time to run 2 commands: 0.60 seconds
-
-Running command:
-python src/python-tools/example.py ../workspaces-streamlit-template/default/topp-workflow/example.json
-Waiting for command to finish...
-
-Process finished:
-python src/python-tools/example.py ../workspaces-streamlit-template/default/topp-workflow/example.json
-Total time to run command: 0.04 seconds
-
-Writing stdout which will get logged...
-Parameters for this example Python tool:
-{
-    "in": [
-        "../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Control.mzML",
-        "../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Treatment.mzML"
-    ],
-    "out": [],
-    "number-slider": 6,
-    "selectbox-example": "c",
-    "adavanced-input": 5,
-    "checkbox": true
-}
-
-
-Running command:
-SiriusExport -in ../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Control.mzML ../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Treatment.mzML -in_featureinfo ../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Control.featureXML ../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Treatment.featureXML -out ../workspaces-streamlit-template/default/topp-workflow/results/sirius-export/sirius.ms
-Waiting for command to finish...
-
-Process finished:
-SiriusExport -in ../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Control.mzML ../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Treatment.mzML -in_featureinfo ../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Control.featureXML ../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Treatment.featureXML -out ../workspaces-streamlit-template/default/topp-workflow/results/sirius-export/sirius.ms
-Total time to run command: 0.65 seconds
-
-Number of features to be processed: 0
-Number of additional MS2 spectra to be processed: 0
-No MS1 spectrum for this precursor. Occurred 0 times.
-0 spectra were skipped due to precursor charge below -1 and above +1.
-Mono charge assumed and set to charge 1 with respect to current polarity 0 times.
-0 features were skipped due to feature charge below -1 and above +1.
-No MS1 spectrum for this precursor. Occurred 0 times.
-0 spectra were skipped due to precursor charge below -1 and above +1.
-Mono charge assumed and set to charge 1 with respect to current polarity 0 times.
-0 features were skipped due to feature charge below -1 and above +1.
-<Number of features to be processed: 0> occurred 2 times
-SiriusExport took 0.61 s (wall), 1.71 s (CPU), 1.06 s (system), 0.65 s (user); Peak Memory Usage: 88 MB.
-<Number of additional MS2 spectra to be processed: 0> occurred 2 times
-
-
-WORKFLOW FINISHED
-    """, language="neon")
-
-
-
+    st.help(CommandExecutor.run_python)
diff --git a/src/Workflow.py b/src/Workflow.py
@@ -27,7 +27,7 @@ def configure(self) -> None:
         )
         with t[0]:
             # Parameters for FeatureFinderMetabo TOPP tool.
-            self.ui.input_TOPP("FeatureFinderMetabo")
+            self.ui.input_TOPP("FeatureFinderMetabo", custom_defaults={"algorithm:common:noise_threshold_int": 1000.0})
         with t[1]:
             # A single checkbox widget for workflow logic.
             self.ui.input_widget("run-adduct-detection", False, "Adduct Detection")
@@ -42,8 +42,12 @@ def configure(self) -> None:
             self.ui.input_python("example")
 
     def execution(self) -> None:
-        # Get mzML input files from self.params.
-        # Can be done without file manager, however, it ensures everything is correct.
+        # Any parameter checks, here simply checking if mzML files are selected
+        if not self.params["mzML-files"]:
+            self.logger.log("ERROR: No mzML files selected.")
+            return
+
+        # Get mzML files with FileManager
         in_mzML = self.file_manager.get_files(self.params["mzML-files"])
 
         # Log any messages.
@@ -63,7 +67,7 @@ def execution(self) -> None:
             # Run MetaboliteAdductDecharger for adduct detection, with disabled logs.
             # Without a new file list for output, the input files will be overwritten in this case.
             self.executor.run_topp(
-                "MetaboliteAdductDecharger", {"in": out_ffm, "out_fm": out_ffm}, write_log=False
+                "MetaboliteAdductDecharger", {"in": out_ffm, "out_fm": out_ffm}
             )
 
         # Example for a custom Python tool, which is located in src/python-tools.

diff --git a/src/python-tools/example.py b/src/python-tools/example.py
@@ -35,18 +35,20 @@
     },
     {
         "key": "selectbox-example",
+        "name": "select something",
         "value": "a",
         "options": ["a", "b", "c"],
     },
     {
         "key": "adavanced-input",
+        "name": "advanced parameter",
         "value": 5,
         "step_size": 5,
         "help": "An advanced example parameter.",
         "advanced": True,
     },
     {
-        "key": "checkbox", "value": True
+        "key": "checkbox", "value": True, "name": "boolean"
     }
 ]