update workspace

.gitignore

@@ -1,4 +1,4 @@
-workspaces-streamlit-template
+workspaces-flashtaggerviewer
 build
 dist
 myenv

README.md

@@ -55,7 +55,7 @@ save_params()
 
 - in `src/common.py` update the name of your app and the repository name
 - in `clean-up-workspaces.py` update the name of the workspaces directory to `/workspaces-<your-repository-name>`
-    - e.g. for the streamlit template it's "/workspaces-streamlit-template"
+    - e.g. for the streamlit template it's "/workspaces-flashtaggerviewer"
 - chose one of the Dockerfiles depending on your use case:
     - `Dockerfile` build OpenMS including TOPP tools
     - `Dockerfile_simple` uses pyOpenMS only

clean-up-workspaces.py

@@ -6,7 +6,7 @@
 from datetime import datetime
 
 # Define the workspaces directory
-workspaces_directory = Path("/workspaces-streamlit-template")
+workspaces_directory = Path("/workspaces-flashtaggerviewer")
 
 # Get the current time in seconds
 current_time = time.time()

pages/6_📖_TOPP-Workflow_Docs.py

@@ -170,19 +170,19 @@
     """
 # Get all file paths as strings from self.param entry.
 mzML_files = self.file_manager.get_files(self.params["mzML-files])
-# mzML_files = ['../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Control.mzML', '../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Treatment.mzML']
+# mzML_files = ['../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Control.mzML', '../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Treatment.mzML']
 
 # Creating output files for a TOPP tool, setting a new file type and result subdirectory name.
 feature_detection_out = self.file_manager.get_files(mzML_files, set_file_type="featureXML", set_results_dir="feature-detection")
-# feature_detection_out = ['../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Control.featureXML', '../workspaces-streamlit-template/default/topp-workflow/results/feature-detection/Treatment.featureXML']
+# feature_detection_out = ['../workspaces-flashtaggerviewer/default/topp-workflow/results/feature-detection/Control.featureXML', '../workspaces-flashtaggerviewer/default/topp-workflow/results/feature-detection/Treatment.featureXML']
 
 # Setting a name for the output directory automatically (useful if you never plan to access these files in the results section).
 feature_detection_out = self.file_manager.get_files(mzML_files, set_file_type="featureXML", set_results_dir="auto")
-# feature_detection_out = ['../workspaces-streamlit-template/default/topp-workflow/results/6DUd/Control.featureXML', '../workspaces-streamlit-template/default/topp-workflow/results/6DUd/Treatment.featureXML']
+# feature_detection_out = ['../workspaces-flashtaggerviewer/default/topp-workflow/results/6DUd/Control.featureXML', '../workspaces-flashtaggerviewer/default/topp-workflow/results/6DUd/Treatment.featureXML']
 
 # Combining all mzML files to be passed to a TOPP tool in a single run. Using "collected" files as argument for self.file_manager.get_files will "un-collect" them.
 mzML_files = self.file_manager.get_files(mzML_files, collect=True)
-# mzML_files = [['../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Control.mzML', '../workspaces-streamlit-template/default/topp-workflow/input-files/mzML-files/Treatment.mzML']]
+# mzML_files = [['../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Control.mzML', '../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Treatment.mzML']]
     """
 )
 
@@ -277,15 +277,15 @@
 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
+FeatureFinderMetabo -in ../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Treatment.mzML -out ../workspaces-flashtaggerviewer/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
+FeatureFinderMetabo -in ../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Control.mzML -out ../workspaces-flashtaggerviewer/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
+FeatureFinderMetabo -in ../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Treatment.mzML -out ../workspaces-flashtaggerviewer/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':
@@ -315,7 +315,7 @@
 
 
 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
+FeatureFinderMetabo -in ../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Control.mzML -out ../workspaces-flashtaggerviewer/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':
@@ -347,19 +347,19 @@
 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
+python src/python-tools/example.py ../workspaces-flashtaggerviewer/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
+python src/python-tools/example.py ../workspaces-flashtaggerviewer/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"
+        "../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Control.mzML",
+        "../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Treatment.mzML"
     ],
     "out": [],
     "number-slider": 6,
@@ -370,11 +370,11 @@
 
 
 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
+SiriusExport -in ../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Control.mzML ../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Treatment.mzML -in_featureinfo ../workspaces-flashtaggerviewer/default/topp-workflow/results/feature-detection/Control.featureXML ../workspaces-flashtaggerviewer/default/topp-workflow/results/feature-detection/Treatment.featureXML -out ../workspaces-flashtaggerviewer/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
+SiriusExport -in ../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Control.mzML ../workspaces-flashtaggerviewer/default/topp-workflow/input-files/mzML-files/Treatment.mzML -in_featureinfo ../workspaces-flashtaggerviewer/default/topp-workflow/results/feature-detection/Control.featureXML ../workspaces-flashtaggerviewer/default/topp-workflow/results/feature-detection/Treatment.featureXML -out ../workspaces-flashtaggerviewer/default/topp-workflow/results/sirius-export/sirius.ms
 Total time to run command: 0.65 seconds
 
 Number of features to be processed: 0

src/Workflow.py

@@ -146,7 +146,7 @@ def pp(self) -> None:
             st.error('Please select at least one mzML file.')
             return
 
-        base_path = join('..', 'workspaces-streamlit-template', 'default')
+        base_path = join('..', 'workspaces-flashtaggerviewer', 'default')
 
         uploaded_files = []
         for in_mzML in in_mzMLs:

src/common.py

@@ -11,7 +11,7 @@
 
 # set these variables according to your project
 APP_NAME = "OpenMS Streamlit App"
-REPOSITORY_NAME = "streamlit-template"
+REPOSITORY_NAME = "flashtaggerviewer"
 
 
 def load_params(default: bool = False) -> dict[str, Any]:
@@ -111,7 +111,7 @@ def page_setup(page: str = "") -> dict[str, Any]:
             st.session_state.location = "online"
         # if we run the packaged windows version, we start within the Python directory -> need to change working directory to ..\streamlit-template
         if "windows" in sys.argv:
-            os.chdir("../streamlit-template")
+            os.chdir("../flashtaggerviewer")
         # Define the directory where all workspaces will be stored
         workspaces_dir = Path("..", "workspaces-" + REPOSITORY_NAME)
         if st.session_state.location == "online":