Merge pull request #49 from CBICA/ag-dev

Ag dev to ge-dev

.dockerignore

@@ -1,5 +1,8 @@
 .github
+.git
 test
+test_data
+output_folder
 **/*.nii.gz
 build
 **/build

Dockerfile

@@ -42,10 +42,11 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 ARG CUDA_VERSION
 
 COPY --chown=$MAMBA_USER:$MAMBA_USER requirements.txt /tmp/requirements.txt
+RUN grep -v -E '^(torch)' /tmp/requirements.txt > /tmp/requirements2.txt
 USER root
 RUN apt-get update && apt-get install -y python3-tk git
 USER $MAMBA_USER
-RUN pip install --verbose -r /tmp/requirements.txt && pip uninstall -y torch && pip install --verbose torch==2.3.1 --index-url https://download.pytorch.org/whl/cu${CUDA_VERSION}
+RUN pip install --verbose -r /tmp/requirements2.txt && pip uninstall -y torch && pip install --verbose torch==2.3.1 --index-url https://download.pytorch.org/whl/cu${CUDA_VERSION}
 RUN mkdir ~/dummyinput && mkdir ~/dummyoutput
 RUN git clone https://github.com/CBICA/PredCRD.git && cd PredCRD && pip install -e .
 RUN git clone https://github.com/CBICA/DLWMLS.git && cd DLWMLS && pip install -e . && DLWMLS -i ~/dummyinput -o ~/dummyoutput

requirements.txt

@@ -3,7 +3,7 @@ spare-scores
 NiChartHarmonize
 DLICV
 DLMUSE
-NiChart_DLMUSE
+NiChart_DLMUSE>=1.0.9
 DLWMLS @ git+https://github.com/CBICA/DLWMLS
 
 # general python dependencies

src/viewer/utils/utils_menu.py

@@ -16,6 +16,7 @@ def menu() -> Any:
         email = st.session_state.cloud_session_token['email']
         logout_url = "https://cbica-nichart.auth.us-east-1.amazoncognito.com/logout?client_id=4shr6mm2h0p0i4o9uleqpu33fj&response_type=code&scope=email+openid+phone&redirect_uri=https://cbica-nichart-alb-272274500.us-east-1.elb.amazonaws.com/oauth2/idpresponse"
         st.sidebar.info(f"Logged in as {email}.")
+        st.sidebar.info(f"User ID: {st.session_state.cloud_user_id}")
         ## TODO: Make this button also delete user data automatically
         st.sidebar.button("Log out", on_click=redirect, args=(logout_url,))
     if st.session_state.pipeline == "Home":

src/viewer/utils/utils_session.py

@@ -26,19 +26,19 @@ def config_page() -> None:
 
 ## Function to parse AWS login (if available)
 def process_session_token():
-    '''
-    WARNING: We use unsupported features of Streamlit
-             However, this is quite fast and works well with
-             the latest version of Streamlit (1.27)
-             Also, this does not verify the session token's
-             authenticity. It only decodes the token.
-    '''
-    headers = _get_websocket_headers()
+    #headers = _get_websocket_headers()
+    headers = st.context.headers
     if not headers or "X-Amzn-Oidc-Data" not in headers:
         return {}
     return jwt.decode(
         headers["X-Amzn-Oidc-Data"], algorithms=["ES256"], options={"verify_signature": False}
     )
+
+def process_session_user_id():
+    headers = st.context.headers
+    if not headers or "X-Amzn-Oidc-Identity" not in headers:
+        return "NO_USER_FOUND"
+    return headers["X-Amzn-Oidc-Identity"]
 
 
 def init_session_state() -> None:
@@ -64,10 +64,12 @@ def init_session_state() -> None:
             st.session_state.cloud_session_token = process_session_token()
             if st.session_state.cloud_session_token:
                 st.session_state.has_cloud_session = True
+                st.session_state.cloud_user_id = process_session_user_id()
             else:
                 st.session_state.has_cloud_session = False
         else:
             st.session_state.has_cloud_session = False
+
 
         ###################################
 
@@ -195,9 +197,17 @@ def init_session_state() -> None:
         # Set initial values for paths
         st.session_state.paths["root"] = os.path.dirname(os.path.dirname(os.getcwd()))
         st.session_state.paths["init"] = st.session_state.paths["root"]
-        st.session_state.paths["dir_out"] = os.path.join(
-            st.session_state.paths["root"], "output_folder"
-        )
+        if st.session_state.has_cloud_session:
+            user_id = st.session_state.cloud_user_id
+            st.session_state.paths["dir_out"] = os.path.join(
+                st.session_state.paths["root"], "output_folder", user_id
+            )
+        else:
+            st.session_state.paths["dir_out"] = os.path.join(
+                st.session_state.paths["root"], "output_folder"
+            )
+
+
         if not os.path.exists(st.session_state.paths["dir_out"]):
             os.makedirs(st.session_state.paths["dir_out"])
 

src/viewer/utils/utils_st.py

@@ -217,7 +217,7 @@ def help_working_dir():
 
             - On the desktop app, you can initiate a NiChart pipeline by selecting the **working directory** from a previously completed task.
 
-            - On the cloud app, the results are deleted in regular intervals, so they may not be available.
+            - On the cloud app, the results are deleted in regular intervals, so they may not be available if you come back later.
             """
         )
     col1, col2 = st.columns([0.5, 0.1])