Update GUI to allow user to select workdir, inputs, etc

custom_files/pipeline_project_map.json

@@ -0,0 +1,5 @@
+{
+    "epi2me-human-variation": ["nf-long-reads"],
+    "epi2me-somatic-variation": ["mopopgen-support"],
+    "nfcore-rnaseq": ["nf-tp53"]
+}

custom_files/user_whitelist.tsv

@@ -0,0 +1,7 @@
+username	group	account-code
+admin	admin	None
+msarkis	SCIENCOM	None
+ralcraft	SCIENCOM	None
+sstephens	OGENETIC	None
+jhouseham	UNKNOWN	None
+ahyde1	MOPOPGEN	None

index.py

@@ -9,8 +9,8 @@
 
 
 def main():
-    p1 = st.Page("pages/login.py")
-    p2 = st.Page("pages/run_pipeline.py")
+    p1 = st.Page("views/login.py")
+    p2 = st.Page("views/run_pipeline.py")
     nav_pages = [p1, p2]
     pages = {"p1": p1, "p2": p2}
     st.session_state["pages"] = pages

pipeline_project_map.py

@@ -0,0 +1,11 @@
+import json
+
+
+def load_json_to_dict(file_path):
+    with open(file_path, "r") as file:
+        data = json.load(file)
+    return data
+
+
+file_path = "custom_files/pipeline_project_map.json"
+map_pipeline_project = load_json_to_dict(file_path)

tabs/tab_command.py

@@ -5,7 +5,9 @@
 import pandas as pd
 import streamlit as st
 
-# from ping3 import ping
+# Initialize session state variables
+if "run_pipeline_clicked" not in st.session_state:
+    st.session_state.run_pipeline_clicked = False
 
 
 @contextmanager
@@ -67,6 +69,9 @@ def tab(username, MY_SSH, selected_pipeline, selected_project, selected_samples=
         )
 
     def run_nextflow():  # username, MY_SSH, selected_pipeline, selected_project):
+        st.success("Button clicked!")
+        print("run_nextflow was called")
+        return True  # temporary
         cmd_pipeline = pipe_cmd(
             username, selected_pipeline, selected_project, cmd_num=0, selected_samples="all"
         )  # develop this
@@ -90,5 +95,14 @@ def check_queue():  # username):
             st.error(err_str)
 
     left_column, right_column = st.columns(2)
-    left_column.button(f"Run the selected nextflow pipeline for {username}", on_click=run_nextflow)
+    # disable button once the user click a first time. by default it gets disabled after calling the callback
+    v = left_column.button(
+        f"Run the selected nextflow pipeline for {username}", disabled=st.session_state.run_pipeline_clicked
+    )  # on_click=run_nextflow,
+    if v:
+        st.session_state.run_pipeline_clicked = True
+        run_nextflow()
+        print("session value:", st.session_state.run_pipeline_clicked)
+    #   st.session_state.run_pipeline_clicked = True
+
     right_column.button(f"Check queue for {username}", key="checkqueue", on_click=check_queue)

views/login.py

@@ -0,0 +1,85 @@
+import pandas as pd
+import streamlit as st
+
+import shared.sessionstate as ss
+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=
+        "color:darkred;font-size:40px;"> -🍃 </span><span style=
+        "color:green;font-size:40px;">RUN-NEXTFLOW</span><span style=
+        "color:darkred;font-size:40px;">🍃- </span>
+        """
+st.markdown(header, unsafe_allow_html=True)
+
+st.write("---  ")
+
+st.write("## Login")
+st.write("Login to your alma account before running a nextflow pipeline.")
+
+OK, MY_SSH, username = tl.tab()
+
+ss.ss_set("LOGIN_OK", OK)
+ss.ss_set("MY_SSH", MY_SSH)
+ss.ss_set("user_name", username)
+
+
+# I want to move between tabs automatically
+# move between tabs
+def display():
+    st.session_state["run_pipeline"] = True
+    if st.session_state.get("run_pipeline", False) and "login" in st.session_state:
+        if "pages" in st.session_state:
+            page = st.session_state["pages"].get("p2", None)
+            if page:
+                st.switch_page(page)
+
+
+def display_restricted_access(username):
+    st.error(
+        f"⚠️ Access Restricted ⚠️\n\n"
+        f"Dear {username},\n\n"
+        "We apologize, but access to the nextflow-app is currently restricted. "
+        "For any requests or further information, please contact our support team.\n\n"
+        "**Contact Information:**\n"
+        "- **Name:** Mira Sarkis\n"
+        "- **Department:** Scientific Computing Helpdesk (SCHelpdesk)\n"
+        "- **Email:** [[email protected]](mailto:[email protected])\n\n"
+        "Thank you for your understanding."
+    )
+
+    st.info(
+        "ℹ️ **Note:** Please include your username and the reason for your request "
+        "when contacting the support team. This will help us process your request more efficiently."
+    )
+
+
+def update_session_info(group, cost_account):
+    ss.ss_set("user_group", group)
+    ss.ss_set("user_cost_account", cost_account)
+
+
+def check_whiteList(username):
+    whitelist = "custom_files/user_whitelist.tsv"
+    df = pd.read_csv(whitelist, delimiter="\t")
+    row = df.loc[df["username"] == username]
+    if row.empty:  # user not on the white liste
+        return False
+
+    # update session info
+    update_session_info(row["group"], row["account-code"])
+    return True
+
+
+if "login" not in st.session_state:
+    st.session_state["login"] = {}
+if "run_pipeline" not in st.session_state:
+    st.session_state["run_pipeline"] = False
+
+if OK:
+    if not check_whiteList(username):
+        display_restricted_access(username)
+    else:
+        display()

pages/run_pipeline.py → views/run_pipeline.py

@@ -2,6 +2,18 @@
 
 import shared.sessionstate as ss
 import tabs.tab_command as tt
+from pipeline_project_map import map_pipeline_project
+
+# Initialize session state variables
+if "select1_value" not in st.session_state:
+    st.session_state.select1_value = None
+if "select2_value" not in st.session_state:
+    st.session_state.select2_value = None
+
+
+def reset_button_state():
+    st.session_state.button_clicked = False
+
 
 header = """
         <span style="color:black;">
@@ -22,23 +34,21 @@
 MY_SSH = ss.ss_get("MY_SSH")
 username = ss.ss_get("user_name")
 
-pipelines = ["epi2me-human-variation", "epi2me-somatic-variation", "nfcore-rnaseq"]
-projects = ["nf-long-reads", "nf-tp53", "mopopgen-support"]
 samples = ["all", "demo"]  # , "customised"]
-
-map_pipeline_project = {
-    "epi2me-human-variation": ["nf-long-reads"],
-    "epi2me-somatic-variation": ["nf-tp53"],
-    "nfcore-rnaseq": ["mopopgen-support"],
-}
 selected_project = None
 selected_samples = None
+
 # adding "select" as the first and default choice
 selected_pipeline = st.selectbox("Select a pipeline", options=["select"] + list(map_pipeline_project.keys()))
 # display selectbox 2 if selected_pipeline is not "select"
 if selected_pipeline != "select":
-    selected_project = st.selectbox("Select your project", options=map_pipeline_project[selected_pipeline])
-    selected_samples = st.selectbox("Select your samples", samples)
+    selected_project = st.selectbox(
+        "Select your project",
+        options=map_pipeline_project[selected_pipeline],
+        on_change=reset_button_state,
+        key="select_pipeline",
+    )
+    selected_samples = st.selectbox("Select your samples", samples, on_change=reset_button_state, key="selecct_samples")
 
 # passing inputs between tabs
 if LOGIN_OK: