Merge pull request #61 from t0mdavid-m/fix_scan_no

Small Bugfixes
t0mdavid-m · Oct 1, 2024 · cef5868 · cef5868
2 parents 5160c12 + f74c0c9
commit cef5868
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Showing 7 changed files with 11 additions and 10 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -65,11 +65,11 @@ RUN (type -p wget >/dev/null || (apt-get update && apt-get install wget -y)) \
 	&& apt-get install gh -y
 
 # Download and install mamba.
-ENV PATH="/root/mambaforge/bin:${PATH}"
+ENV PATH="/root/miniforge3/bin:${PATH}"
 RUN wget -q \
-    https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
-    && bash Mambaforge-Linux-x86_64.sh -b \
-    && rm -f Mambaforge-Linux-x86_64.sh
+    https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
+    && bash Miniforge3-Linux-x86_64.sh -b \
+    && rm -f Miniforge3-Linux-x86_64.sh
 RUN mamba --version
 
 # Setup mamba environment.
@@ -153,7 +153,7 @@ COPY pages/ /app/pages
 COPY clean-up-workspaces.py /app/clean-up-workspaces.py
 
 # add cron job to the crontab
-RUN echo "0 3 * * * /root/mambaforge/envs/streamlit-env/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -
+RUN echo "0 3 * * * /root/miniforge3/envs/streamlit-env/bin/python /app/clean-up-workspaces.py >> /app/clean-up-workspaces.log 2>&1" | crontab -
 
 # create entrypoint script to start cron service and launch streamlit app
 RUN echo "#!/bin/bash" > /app/entrypoint.sh

diff --git a/js-component/dist/assets/index-dbcc4222.js → js-component/dist/assets/index-5c11f032.js b/js-component/dist/assets/index-dbcc4222.js → js-component/dist/assets/index-5c11f032.js
diff --git a/js-component/dist/index.html b/js-component/dist/index.html
@@ -5,7 +5,7 @@
     <link rel="icon" href="./favicon.ico" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>openms-streamlit-vue-component</title>
-    <script type="module" crossorigin src="./assets/index-dbcc4222.js"></script>
+    <script type="module" crossorigin src="./assets/index-5c11f032.js"></script>
     <link rel="stylesheet" href="./assets/index-944dcd57.css">
   </head>
   <body>

diff --git a/openms-streamlit-vue-component b/openms-streamlit-vue-component
diff --git a/pages/FLASHTaggerViewer.py b/pages/FLASHTaggerViewer.py
@@ -74,7 +74,6 @@ def sendDataToJS(selected_data, layout_info_per_exp, grid_key='flash_viewer_grid
     tag_df = pd.read_csv(tsv_buffer, sep='\t')
 
     # Complete df
-    tag_df['Scan'] = 0
     tag_df['StartPosition'] = tag_df['StartPosition'] - 1
     tag_df['EndPos'] = tag_df['StartPosition'] + tag_df['Length'] - 1
     tag_df = tag_df.rename(

diff --git a/src/components.py b/src/components.py
@@ -4,7 +4,7 @@
 
 # Create a _RELEASE constant. We'll set this to False while we're developing
 # the component, and True when we're ready to package and distribute it.
-_RELEASE = True
+_RELEASE = False
 
 
 def flash_viewer_grid_component(components, data, component_key='flash_viewer_grid'):

diff --git a/src/workflow/CommandExecutor.py b/src/workflow/CommandExecutor.py
@@ -183,6 +183,8 @@ def run_topp(self, tool: str, input_output: dict, write_log: bool = True, params
                         command += [str(v_v) for v_v in v]
                     elif str(v) == 'true':
                         command += [f"-{k}"]
+                    elif str(v) == 'false':
+                        continue
                     else:
                         command += [f"-{k}", str(v)]
             commands.append(command)