use pyalma package instead of ssh.py

.github/workflows/python-package-ci.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        if [ -f requirements.txt ]; then pip install --no-cache-dir -r requirements.txt; fi
     - name: Verify Streamlit app
       run: |
         timeout 10s streamlit run index.py || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

.gitignore

@@ -0,0 +1 @@
+.nf-env

requirements.txt

@@ -1,4 +1,5 @@
 pandas==2.2.3
-paramiko==3.5.0
+paramiko>3.5.0
 streamlit==1.39.0
 pre-commit==4.0.1
+pyalma @ git+https://github.com/ICR-RSE-Group/pyalma.git@main

tabs/tab_command.py

@@ -1,13 +1,13 @@
-import datetime
 from contextlib import contextmanager, redirect_stdout
 from io import StringIO
 
-import pandas as pd
 import streamlit as st
 
 # Initialize session state variables
 if "run_pipeline_clicked" not in st.session_state:
     st.session_state.run_pipeline_clicked = False
+if "check_queue" not in st.session_state:
+    st.session_state.check_queue = False
 
 
 @contextmanager
@@ -77,22 +77,24 @@ def run_nextflow():  # username, MY_SSH, selected_pipeline, selected_project):
         )  # develop this
         st.write("Command used:")
         st.code(cmd_pipeline)
-        out_str, err_str = MY_SSH.run_cmd(cmd_pipeline, string=True)
+        _dict = MY_SSH.run_cmd(cmd_pipeline)
 
     def check_queue():  # username):
+        st.session_state.check_queue = True
+
+    if st.session_state.check_queue:
         cmd_pipeline = pipe_cmd(username, None, None, cmd_num=1)
         st.write("Command used:")
         st.code(cmd_pipeline)
-        out_str, err_str = MY_SSH.run_cmd(cmd_pipeline, string=True)
-        if err_str == "":
+        _dict = MY_SSH.run_cmd(cmd_pipeline)
+        if _dict["err"] == None:
             st.write("Output:")
-            st.code(out_str)
+            st.code(_dict["output"])
             st.write(
                 "If you see '***' job on compute node, that suggests that the job has been sent to the cluster (in the queue (PD) or running (R))"
             )
-
         else:
-            st.error(err_str)
+            st.error(_dict["err"])
 
     left_column, right_column = st.columns(2)
     # disable button once the user click a first time. by default it gets disabled after calling the callback

tabs/tab_logon.py

@@ -2,8 +2,7 @@
 from io import StringIO
 
 import streamlit as st
-
-import shared.ssh as ssh
+from pyalma import LocalFileReader, SshClient
 
 
 @contextmanager
@@ -41,21 +40,17 @@ def tab():
             OK = True
         else:
             with st.spinner("Validating login"):
-                MY_SSH = ssh.SshConnection("remote", username, password, server=server)
-
+                MY_SSH = SshClient(server, username, password)
                 print("Validating login...")
-                cmd = "cd ~ && ls -l1"
-                results_str, error_str = MY_SSH.run_cmd(cmd)
-
-                if error_str:
-                    print("Errors", error_str)
-                else:
-                    print("Session validated successfully")
 
-                OK = error_str == ""
+                _dict = MY_SSH.run_cmd("cd ~ &ls -l")
+                OK = _dict["err"] is None
                 if OK:
+                    print("Session validated successfully")
                     st.success("Session validated successfully")
                 else:
-                    st.error("Correct login details and try again")
+                    print("Errors", _dict["err"])
+                    err_msg = "Connection failed: " + _dict["err"]
+                    st.error(err_msg)
 
     return OK, MY_SSH, username

views/login.py

@@ -5,11 +5,9 @@
 import tabs.tab_logon as tl
 
 header = """
-        <span style="color:black;">
-        <img src="https://www.icr.ac.uk/assets/img/logo.png"
-        alt="icr" width="200px"></span><span style=
+        <span style=
         "color:darkred;font-size:40px;"> -🍃 </span><span style=
-        "color:green;font-size:40px;">RUN-NEXTFLOW</span><span style=
+        "color:green;font-size:40px;">RUN NEXTFLOW on ALMA</span><span style=
         "color:darkred;font-size:40px;">🍃- </span>
         """
 st.markdown(header, unsafe_allow_html=True)

views/run_pipeline.py

@@ -16,11 +16,9 @@ def reset_button_state():
 
 
 header = """
-        <span style="color:black;">
-        <img src="https://www.icr.ac.uk/assets/img/logo.png"
-        alt="icr" width="200px"></span><span style=
+        <span style=
         "color:darkred;font-size:40px;"> -🍃 </span><span style=
-        "color:green;font-size:40px;">RUN-NEXTFLOW</span><span style=
+        "color:green;font-size:40px;">RUN NEXTFLOW on ALMA</span><span style=
         "color:darkred;font-size:40px;">🍃- </span>
         """
 st.markdown(header, unsafe_allow_html=True)