Merge pull request #26 from ICR-RSE-Group/fix_issue_25

Fix_issue_25

Author: msarkis-icr

pages/run_pipeline.py

@@ -35,12 +35,13 @@ def reset_button_state():
 button_clicked = ss_values["button_clicked"]
 custom_sample_list = ss_values["custom_sample_list"]  # only availanle if custom sample is selected
 BED_FILE = ss_values["BED_FILE"]
-samples = ["demo", "customised"]  # , "test"]
+samples = ["demo", "customised"]
 
 # Create the selectbox and update session state
 pipeline_options = ["select"] + list(map_pipeline_project.keys())
 index = pipeline_options.index(PIPELINE)
-PIPELINE = st.selectbox("Select a pipeline", options=pipeline_options, index=index)  # , key="PIPELINE")
+PIPELINE = st.selectbox("Select a pipeline", options=pipeline_options, index=index)
+adapt_samples = False
 # adding "select" as the first and default choice
 if PIPELINE != "select":
     project_options = list(map_pipeline_project[PIPELINE].keys())
@@ -74,7 +75,6 @@ def reset_button_state():
             st.write("Your custom samples:", custom_sample_list)
             ss_set("custom_sample_list", custom_sample_list)
 
-    adapt_samples = False
     if(map_pipeline_project[PIPELINE][PROJECT]["adapt_samples"]):
         adapt_samples = st.checkbox("Adapt samples prior to running nextflow", 
                             value=False,

shared/command_helper.py

@@ -1,5 +1,5 @@
 import os
-from typing import Tuple, Optional
+import streamlit as st
 
 def get_path_to_script(
     selected_pipeline: str,
@@ -27,7 +27,7 @@ def pipe_cmd(
     selected_pipeline="",
     selected_project="",
     cmd_num=0,
-    selected_samples="all",
+    selected_samples="",
     work_dir="work",
     output_dir="output",
     custom_sample_list=[],
@@ -38,15 +38,13 @@ def pipe_cmd(
     def get_pipeline_command():
         """Generate the pipeline execution command based on the sample selection."""
         path_to_script = get_path_to_script(selected_pipeline, selected_project, selected_samples)
-
-        # not sure if this is the best thing-using job id for filenamne
-        log_out = f"{work_dir}/logs/%j.out"
-        log_err = f"{work_dir}/logs/%j.err"
 
         args = []
         base_cmd = f"bash {path_to_script}" #default
 
         if selected_samples == "demo":
+            log_out = f"{work_dir}/logs/log_demo.out"
+            log_err = f"{work_dir}/logs/log_demo.err"
             base_cmd = f"sbatch -o {log_out} -e {log_err}"
             args += [path_to_script, work_dir, output_dir]
 
@@ -64,7 +62,8 @@ def get_pipeline_command():
                 args += ["--adapt-samples"]
             if bed_file:
                 args += ["--bed", bed_file]
-
+        
+        # note: I use logs/log_{samplename} for sample logs
         preamble = f"""
         mkdir -p {work_dir}/logs
         cd {work_dir}
@@ -75,16 +74,16 @@ def get_pipeline_command():
 
     # Command mappings
     command_map = {
-        0: get_pipeline_command(),
-        1: f"squeue -u {username}",
-        2: (
+        0: get_pipeline_command,
+        1: lambda: f"squeue -u {username}",
+        2: lambda: (
             f"sacct --user {username} "
             "--format UID,User,JobID,JobName,Submit,Elapsed,Partition,"
             "NNodes,NCPUS,TotalCPU,CPUTime,ReqMem,MaxRSS,WorkDir,State,"
             "Account,AllocTres -P"
         ),
-        3: "echo hello from nextflow-on-Alma app",
+        3: lambda: "echo hello from nextflow-on-Alma app",
     }
 
     # Return the corresponding command
-    return command_map.get(cmd_num, "echo 'Invalid command number'")
+    return command_map.get(cmd_num, lambda: "echo 'Invalid command number'")()

tabs/tab_command.py

@@ -11,7 +11,7 @@ def tab(
     MY_SSH,
     selected_pipeline,
     selected_project,
-    selected_samples="all",
+    selected_samples="",
     work_dir="work",
     output_dir="output",
     custom_sample_list=[],
@@ -21,7 +21,7 @@ def tab(
 ):
     # --- Initialize session state ---
     st.session_state.setdefault("username", username)
-    st.session_state.setdefault("JOB_ID", "17379785")
+    st.session_state.setdefault("JOB_ID", "")
     st.session_state.setdefault("run_pipeline_clicked", False)
 
     # --- Display username input ---
@@ -77,17 +77,21 @@ def run_nextflow():
         if st.session_state["JOB_ID"]:
             st.success(f"Running Job ID: {st.session_state['JOB_ID']}")
 
+    get_sample_list = lambda selected_samples, custom_sample_list: [selected_samples] if selected_samples == 'demo' else custom_sample_list
+    parsed_sample_list = get_sample_list(selected_samples, custom_sample_list)
     # --- Logs tab ---
     with tabL:
+        # when checking logs, ask user to select one (drop-down list) of his samples at a time : demo or customised sample
         if st.button("Get Logs"):
-            # st.write("📦 session_state:", dict(st.session_state))
-            job_id = st.session_state.get("JOB_ID")
-            st.write("📌 Accessed JOB_ID:", job_id)  # DEBUG
-            if not job_id:
+            _sample_to_log = st.selectbox("Choose an option", parsed_sample_list)
+            st.write("You selected:", _sample_to_log)
+            #job_id = st.session_state.get("JOB_ID")
+            #st.write("📌 Accessed JOB_ID:", job_id)  # DEBUG
+            if not _sample_to_log:
                 st.error("No job was launched yet")
             else:
-                log_out = f"{work_dir}/logs/{job_id}.out"
-                log_err = f"{work_dir}/logs/{job_id}.err"
+                log_out = f"{work_dir}/logs/log_{_sample_to_log}.out"
+                log_err = f"{work_dir}/logs/log_{_sample_to_log}.err"
                 tO, tE = st.tabs(["Output", "Error"])
                 outputO, outputE = tO.empty(), tE.empty()
                 with st.spinner("Fetching logs..."):
@@ -98,6 +102,7 @@ def run_nextflow():
     with tabQ:
         if st.button("Check slurm queues"):
             output = st.empty()
+            st.write(cmd_hlp.pipe_cmd(st.session_state["username"], cmd_num=1))
             with st.spinner("Checking queue..."):
                 with hlp.st_capture(output.code):
                     cmd_pipeline = cmd_hlp.pipe_cmd(st.session_state["username"], cmd_num=1)