diff --git a/custom_files/pipeline_project_map.json b/custom_files/pipeline_project_map.json new file mode 100644 index 0000000..6102957 --- /dev/null +++ b/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"] +} diff --git a/custom_files/user_whitelist.tsv b/custom_files/user_whitelist.tsv new file mode 100644 index 0000000..117c283 --- /dev/null +++ b/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 diff --git a/index.py b/index.py index 9fe4685..c2b0241 100644 --- a/index.py +++ b/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 diff --git a/pages/login.py b/pages/login.py deleted file mode 100644 index b9c6609..0000000 --- a/pages/login.py +++ /dev/null @@ -1,45 +0,0 @@ -import streamlit as st - -import shared.sessionstate as ss -import tabs.tab_logon as tl - -header = """ - - icr -🍃 RUN-NEXTFLOW🍃- - """ -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) - - -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: - display() diff --git a/pipeline_project_map.py b/pipeline_project_map.py new file mode 100644 index 0000000..a18c037 --- /dev/null +++ b/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) diff --git a/tabs/tab_command.py b/tabs/tab_command.py index 2a9e0fd..9697976 100644 --- a/tabs/tab_command.py +++ b/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) diff --git a/views/login.py b/views/login.py new file mode 100644 index 0000000..92e1c4b --- /dev/null +++ b/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 = """ + + icr -🍃 RUN-NEXTFLOW🍃- + """ +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"⚠ī¸ Access Restricted ⚠ī¸\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:** [schelpdesk@icr.ac.uk](mailto:schelpdesk@icr.ac.uk)\n\n" + "Thank you for your understanding." + ) + + st.info( + "ℹī¸ **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() diff --git a/pages/run_pipeline.py b/views/run_pipeline.py similarity index 69% rename from pages/run_pipeline.py rename to views/run_pipeline.py index 1584ed4..1b770ac 100644 --- a/pages/run_pipeline.py +++ b/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 = """ @@ -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: