MAAP-Project · bsatoriu · Oct 30, 2023 · Aug 21, 2023 · Sep 7, 2023 · Sep 15, 2023
diff --git a/base_images/isce2/docker/Dockerfile b/base_images/isce2/docker/Dockerfile
@@ -5,7 +5,7 @@ ARG DEBIAN_FRONTEND=noninteractive
 
 # install maap-py library
 ENV MAAP_CONF='/maap-py/'
-RUN git clone --single-branch --branch v3.0.1 https://github.com/MAAP-Project/maap-py.git \
+RUN git clone --single-branch --branch v3.1.3 https://github.com/MAAP-Project/maap-py.git \
     && cd maap-py \
     && pip install -e .
 
@@ -30,13 +30,14 @@ RUN mkdir /projects
 WORKDIR /projects
 RUN sed -i -e 's/\/root/\/projects/g' /etc/passwd
 
-RUN conda install -y -c conda-forge mamba=1.3.1
-RUN pip install pyOpenSSL==23.2.0
+RUN conda install -y -c conda-forge pyOpenSSL=23.2.0 && \
+    conda install -y -n base conda-libmamba-solver=23.7.0 && \
+    conda config --set solver libmamba
 
 # need to uninstall jupyter_server_terminals as it conflicts with Jupyterlab 3.4.x. Doesn't seem to break anything
 # but can get rid of if/when we upgrade jlab
-RUN mamba install -y -c conda-forge -c plant plant=0.1.89dev isce2=2.6.2 matplotlib=3.5.1 Cython=0.29.28 \
-    numba=0.55.1 pygeos=0.14.0 pyproj=3.4.1 rasterio=1.3.6 && \
+RUN conda install -y --solver=libmamba -c conda-forge -c plant plant=0.1.89dev isce2=2.6.2 matplotlib=3.6.2 Cython=0.29.33 \
+    numba=0.56.4 pygeos=0.14 pyproj=3.4.1 rasterio=1.3.4 && \
     pip uninstall -y jupyter_server_terminals && \
     find /opt/conda/ -follow -type f -name '*.a' -delete && \
     find /opt/conda/ -follow -type f -name '*.js.map' -delete && \

diff --git a/base_images/isce3/docker/Dockerfile b/base_images/isce3/docker/Dockerfile
@@ -5,7 +5,7 @@ ARG DEBIAN_FRONTEND=noninteractive
 
 # install maap-py library
 ENV MAAP_CONF='/maap-py/'
-RUN git clone --single-branch --branch v3.0.1 https://github.com/MAAP-Project/maap-py.git \
+RUN git clone --single-branch --branch v3.1.3 https://github.com/MAAP-Project/maap-py.git \
     && cd maap-py \
     && pip install -e .
 
@@ -16,10 +16,11 @@ RUN mkdir /projects
 WORKDIR /projects
 RUN sed -i -e 's/\/root/\/projects/g' /etc/passwd
 
-RUN conda install -y -c conda-forge mamba=1.4.2
-RUN pip install pyOpenSSL==23.2.0
+RUN conda install -y -c conda-forge pyOpenSSL=23.2.0 && \
+    conda install -y -n base conda-libmamba-solver=23.7.0 && \
+    conda config --set solver libmamba
 
-RUN mamba install -y -c conda-forge isce3=0.12.0 xarray=2023.4.2 \
+RUN conda install -y --solver=libmamba -c conda-forge isce3=0.12.0 xarray=2023.4.2 \
     hvplot=0.8.3 fsspec=2023.5.0 scikit-learn=1.2.2 && \
     find /opt/conda/ -follow -type f -name '*.a' -delete && \
     find /opt/conda/ -follow -type f -name '*.js.map' -delete && \

diff --git a/base_images/pangeo/docker/Dockerfile b/base_images/pangeo/docker/Dockerfile
@@ -5,16 +5,19 @@ ARG DEBIAN_FRONTEND=noninteractive
 
 # install maap-py library
 ENV MAAP_CONF='/maap-py/'
-RUN git clone --single-branch --branch v3.0.1 https://github.com/MAAP-Project/maap-py.git \
+RUN git clone --single-branch --branch v3.1.3 https://github.com/MAAP-Project/maap-py.git \
     && cd maap-py \
     && pip install -e .
 
 RUN mkdir /projects
 WORKDIR /projects
 RUN sed -i -e 's/\/root/\/projects/g' /etc/passwd
 
-RUN conda install -c conda-forge mamba && \
-    mamba install -c conda-forge -y gdal=3.6.2 matplotlib=3.6.2 Cython=0.29.33 h5py=3.7.0 numba=0.56.4 \
+RUN conda install -y -c conda-forge pyOpenSSL=23.2.0 && \
+    conda install -y -n base conda-libmamba-solver=23.7.0 && \
+    conda config --set solver libmamba
+
+RUN conda install -y --solver=libmamba -c conda-forge gdal=3.6.2 matplotlib=3.6.2 Cython=0.29.33 h5py=3.7.0 numba=0.56.4 \
     pygeos=0.14 pyproj=3.4.1 rasterio=1.3.4 scipy=1.10.0 \
     && find /opt/conda/ -follow -type f -name '*.a' -delete \
     && find /opt/conda/ -follow -type f -name '*.js.map' -delete \

diff --git a/base_images/r/docker/Dockerfile b/base_images/r/docker/Dockerfile
@@ -5,7 +5,7 @@ ARG DEBIAN_FRONTEND=noninteractive
 
 # install maap-py library
 ENV MAAP_CONF='/maap-py/'
-RUN git clone --single-branch --branch v3.0.1 https://github.com/MAAP-Project/maap-py.git \
+RUN git clone --single-branch --branch v3.1.3 https://github.com/MAAP-Project/maap-py.git \
     && cd maap-py \
     && pip install -e .
 
@@ -16,10 +16,11 @@ RUN mkdir /projects
 WORKDIR /projects
 RUN sed -i -e 's/\/root/\/projects/g' /etc/passwd
 
-RUN conda install -y -c conda-forge mamba=1.3.1
-RUN pip install pyOpenSSL==23.2.0
+RUN conda install -y -c conda-forge pyOpenSSL=23.2.0 && \
+    conda install -y -n base conda-libmamba-solver=23.7.0 && \
+    conda config --set solver libmamba
 
-RUN mamba install -y -c conda-forge r==4.2 r-rgdal==1.5_32 r-sf==1.0_7 r-irkernel==1.3.2 r-gridExtra==2.3 \
+RUN conda install -y --solver=libmamba -c conda-forge r==4.2 r-rgdal==1.5_32 r-sf==1.0_7 r-irkernel==1.3.2 r-gridExtra==2.3 \
     r-tidyverse==2.0.0 r-randomForest==4.7_1.1 r-raster==3.6_20 r-data.table==1.14.8 r-rlist==0.4.6.2 \
     r-gdalutils==2.0.3.2 r-stringr==1.5.0 && \
     find /opt/conda/ -follow -type f -name '*.a' -delete && \

diff --git a/base_images/rgedi/docker/Dockerfile b/base_images/rgedi/docker/Dockerfile
@@ -2,7 +2,7 @@ FROM continuumio/miniconda3:4.12.0
 
 # install maap-py library
 ENV MAAP_CONF='/maap-py/'
-RUN git clone --single-branch --branch v3.0.1 https://github.com/MAAP-Project/maap-py.git \
+RUN git clone --single-branch --branch v3.1.3 https://github.com/MAAP-Project/maap-py.git \
     && cd maap-py \
     && pip install -e .
 
@@ -11,9 +11,13 @@ WORKDIR /projects
 RUN sed -i -e 's/\/root/\/projects/g' /etc/passwd && echo "source activate r-with-gdal" > ~/.bashrc
 RUN apt-get update && apt-get install -y libxt-dev && apt-get clean
 
-RUN conda install -y -c conda-forge mamba && \
-    mamba install -y -c conda-forge nb_conda_kernels
-RUN mamba create --name r-with-gdal -c conda-forge -c r -c csdms-stack gdal r-rgdal r-sf r-irkernel r-gridExtra r-tidyverse \
+RUN conda install -y -c conda-forge pyOpenSSL=23.2.0 && \
+    conda install -y -n base conda-libmamba-solver=23.7.0 && \
+    conda config --set solver libmamba
+
+RUN conda install -y --solver=libmamba -c conda-forge nb_conda_kernels
+
+RUN conda create --name r-with-gdal --solver=libmamba -c conda-forge -c r -c csdms-stack gdal r-rgdal r-sf r-irkernel r-gridExtra r-tidyverse \
     r-randomForest r-raster r-data.table r-rlist r-gdalutils r-stringr r-devtools sysroot_linux-64=2.17 gcc r-lwgeom szip --yes && \
     /opt/conda/bin/conda clean -afy
 RUN mkdir -p ~/.R/ && echo "LDFLAGS=-lproj" >> ~/.R/Makevars && \

diff --git a/base_images/vanilla/docker/Dockerfile b/base_images/vanilla/docker/Dockerfile
@@ -1,21 +1,27 @@
 FROM continuumio/miniconda3:22.11.1
+ENV LANG en_US.UTF-8
+ENV TZ US/Pacific
+ARG DEBIAN_FRONTEND=noninteractive
 
 # install maap-py library
 ENV MAAP_CONF='/maap-py/'
-RUN git clone --single-branch --branch v3.0.1 https://github.com/MAAP-Project/maap-py.git \
+RUN git clone --single-branch --branch v3.1.3 https://github.com/MAAP-Project/maap-py.git \
     && cd maap-py \
     && pip install -e .
 
 RUN mkdir /projects
 WORKDIR /projects
 RUN sed -i -e 's/\/root/\/projects/g' /etc/passwd
 
-RUN conda install -c conda-forge mamba && \
-    mamba install -c conda-forge -y gdal=3.4.1 matplotlib=3.5.1 Cython=0.29.28 h5py=3.6.0 numba=0.55.1 \
-    pygeos=0.12.0 pyproj=3.3.0 rasterio=1.2.10 scipy=1.8.0 && \
-    find /opt/conda/ -follow -type f -name '*.a' -delete && \
-    find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
-    /opt/conda/bin/conda clean -afy
+RUN conda install -y -c conda-forge pyOpenSSL=23.2.0 && \
+    conda install -y -n base conda-libmamba-solver=23.7.0 && \
+    conda config --set solver libmamba
+
+RUN conda install -y --solver=libmamba -c conda-forge gdal=3.6.2 matplotlib=3.6.2 Cython=0.29.33 h5py=3.7.0 numba=0.56.4 \
+    pygeos=0.14 pyproj=3.4.1 rasterio=1.3.4 scipy=1.10.0 \
+    && find /opt/conda/ -follow -type f -name '*.a' -delete \
+    && find /opt/conda/ -follow -type f -name '*.js.map' -delete \
+    && /opt/conda/bin/conda clean -afy
 
 ARG IMAGE_REF
 ENV DOCKERIMAGE_PATH=${IMAGE_REF}
diff --git a/jupyterlab3/docker/Dockerfile b/jupyterlab3/docker/Dockerfile
@@ -23,14 +23,15 @@ RUN apt-get clean && apt-get update && \
 RUN echo "Checking if environment.yml exists for ${BASE_IMAGE_TYPE}" \
     ; if [ -f "/${BASE_IMAGE_TYPE}/environment.yml" ]; then \
         echo "Installing packages from '/${BASE_IMAGE_TYPE}/environment.yml'" \
-        ; mamba env update --name base --file "/${BASE_IMAGE_TYPE}/environment.yml" \
+        ; conda env update --name base --file "/${BASE_IMAGE_TYPE}/environment.yml" --solver libmamba \
     ; else \
         echo "Installing packages from '/shared/environment.yml'" \
-        ; mamba env update --name base --file "/shared/environment.yml" \
+        ; conda env update --name base --file "/shared/environment.yml" --solver libmamba \
     ; fi
 
 RUN npm install typescript -g
 RUN pip install jupyter-server==2.5.0
+RUN pip install jupyter-resource-usage==0.7.2
 
 # Adjust permissions on home directory so writable by group root.
 RUN chgrp -Rf root /home/$NB_USER && chmod -Rf g+w /home/$NB_USER
@@ -50,18 +51,18 @@ RUN jupyter labextension disable @jupyterlab/apputils-extension:announcements
 ###############################
 # Custom Jupyter Extensions
 ###############################
-RUN jupyter labextension install @maap-jupyterlab/dps-jupyter-extension@0.4.6 --no-build
+RUN jupyter labextension install @maap-jupyterlab/dps-jupyter-extension@0.5.1 --no-build
 
 # PyPi package prepended with 'maap' so it more easily discoverable
-RUN pip install maap-jupyter-server-extension==1.1.1
+RUN pip install maap-jupyter-server-extension==1.2.2
 RUN jupyter server extension enable jupyter_server_extension
 
-RUN jupyter labextension install @maap-jupyterlab/algorithms_jupyter_extension@0.1.1 --no-build
+RUN jupyter labextension install @maap-jupyterlab/algorithms_jupyter_extension@0.2.0 --no-build
 RUN jupyter labextension install @maap-jupyterlab/[email protected] --no-build
 RUN jupyter labextension install @maap-jupyterlab/[email protected] --no-build
 RUN jupyter labextension install @maap-jupyterlab/[email protected] --no-build
-RUN jupyter labextension install @maap-jupyterlab/[email protected].3 --no-build
-RUN jupyter labextension install @maap-jupyterlab/maap-help-jupyter-extension@0.0.46 --no-build
+RUN jupyter labextension install @maap-jupyterlab/[email protected].5 --no-build
+RUN jupyter labextension install @maap-jupyterlab/maap-help-jupyter-extension@1.0.0 --no-build
 RUN jupyter labextension install @maap-jupyterlab/[email protected] --no-build
 
 RUN jupyter lab build && \

diff --git a/jupyterlab3/entrypoint.sh b/jupyterlab3/entrypoint.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # A more robust method of constructing the workspace url prefix
-get_workspace_url_prefix() {
+get_request_data() {
 	python3 - <<END
 import os
 import json
@@ -13,11 +13,10 @@ namespace = "$1"
 # Replicate Che's namespace converter policy
 # by substituting any non-alphanumeric characters with hyphens.
 namespace = re.sub("[^0-9a-zA-Z-]+", "-", namespace)
+api_endpoint = "$2"
 
 svc_host = os.environ.get('KUBERNETES_SERVICE_HOST')
 svc_host_https_port = os.environ.get('KUBERNETES_SERVICE_PORT_HTTPS')
-che_workspace_id = os.environ.get('CHE_WORKSPACE_ID')
-che_machine_name = os.environ.get('CHE_MACHINE_NAME').lower().replace('/', '-')
 
 with open ("/var/run/secrets/kubernetes.io/serviceaccount/token", "r") as t:
     token=t.read()
@@ -26,33 +25,50 @@ headers = {
     'Authorization': 'Bearer ' + token,
 }
 
-request_string = 'https://' + svc_host + ':' + svc_host_https_port + '/api/v1/namespaces/' + namespace +  '/endpoints/'
+request_string = 'https://' + svc_host + ':' + svc_host_https_port + '/api/v1/namespaces/' + namespace +  '/' + api_endpoint + '/'
 httprequest = Request(request_string, headers=headers)
 context = ssl._create_unverified_context()
 with urlopen(httprequest, context=context) as raw_response:
     response = raw_response.read().decode()
 data = json.loads(response)
+print(data)
+
+END
+}
+
+# A more robust method of constructing the workspace url prefix
+get_workspace_url_prefix() {
+	python3 - <<END
+data=$(get_request_data "$1" "endpoints")
+
+import os
+che_workspace_id = os.environ.get('CHE_WORKSPACE_ID')
+che_machine_name = os.environ.get('CHE_MACHINE_NAME').lower().replace('/', '-')
 
 endpoints = data['items']
 for endpoint in endpoints:
     if che_machine_name in endpoint['metadata']['name']:
         if che_workspace_id == endpoint['metadata']['labels']['che.workspace_id']:
             print("/%s/%s" % (endpoint['metadata']['name'], endpoint['subsets'][0]['ports'][0]['name']))
             break
+
 END
 }
 
 for i in {1..300}
 do
     echo "Attempt $i to construct PREVIEW_URL"
     PREVIEW_URL=$(get_workspace_url_prefix "$CHE_WORKSPACE_NAMESPACE-che") # Che 7 OPS configuration where the (actual) namespace is "<username>-che"
+    NAMESPACE="$CHE_WORKSPACE_NAMESPACE-che"
     if test -z "$PREVIEW_URL"
     then
         PREVIEW_URL=$(get_workspace_url_prefix "$CHE_WORKSPACE_NAMESPACE-$CHE_WORKSPACE_ID") # Che 7 UAT configuration fallback where the default namespace is "<username>-<workspaceid>", this will be deprecated
+        NAMESPACE="$CHE_WORKSPACE_NAMESPACE-$CHE_WORKSPACE_ID"
     fi
     if test -z "$PREVIEW_URL"
     then
         PREVIEW_URL=$(get_workspace_url_prefix "$CHE_WORKSPACE_ID") # Che 6 configuration fallback where the default namespace is the workspace id, this will be deprecated
+        NAMESPACE="$CHE_WORKSPACE_ID"
     fi
     if ! test -z "$PREVIEW_URL" # exit loop when it has a preview_url
     then
@@ -115,13 +131,37 @@ mkdir -p /projects/.ssh/
 chmod 700 /projects/.ssh/
 service ssh restart
 
+# Get maximum memory allocation for this workspace to display at bottom of notebook
+get_max_memory() {
+	python3 - <<END
+data_pods=$(get_request_data "$1" "pods")
+
+import os
+import sys
+che_workspace_id = os.environ.get('CHE_WORKSPACE_ID')
+
+for item in data_pods['items']: 
+    if che_workspace_id == item['metadata']['labels'].get('che.workspace_id'):
+        for container in item['spec']['containers']:
+            if container['name']=="jupyter":
+                print(container['resources']['limits']['memory'])
+                sys.exit()
+
+print(8489271296) #default memory
+END
+}
+
+MEMORY=$(get_max_memory "$NAMESPACE")
+
 # TBD maap-py install
 
+source /opt/conda/bin/activate base
+export SHELL=/bin/bash
 VERSION=$(jupyter lab --version)
 if [[ $VERSION > '2' ]] && [[ $VERSION < '3' ]]; then
-    SHELL=/bin/bash jupyter lab --ip=0.0.0.0 --port=3100 --allow-root --NotebookApp.token='' --NotebookApp.base_url=$PREVIEW_URL --no-browser --debug
+    jupyter lab --ip=0.0.0.0 --port=3100 --allow-root --NotebookApp.token='' --NotebookApp.base_url=$PREVIEW_URL --no-browser --debug
 elif [[ $VERSION > '3' ]] && [[ $VERSION < '4' ]]; then
-    SHELL=/bin/bash jupyter lab --ip=0.0.0.0 --port=3100 --allow-root --ContentsManager.allow_hidden=True --ServerApp.token='' --ServerApp.base_url=$PREVIEW_URL --no-browser --debug --ServerApp.disable_check_xsrf=True
+    jupyter lab --ip=0.0.0.0 --port=3100 --allow-root --ContentsManager.allow_hidden=True --ServerApp.token='' --ServerApp.base_url=$PREVIEW_URL --no-browser --debug --ServerApp.disable_check_xsrf=True --ResourceUseDisplay.mem_limit=$MEMORY --ResourceUseDisplay.mem_warning_threshold=0.2
 else
     echo "Error! Jupyterlab version not supported."
-fi
+fi
diff --git a/jupyterlab3/environments.json b/jupyterlab3/environments.json
@@ -37,7 +37,7 @@
         "auth_server": "auth.maap-project.org",
         "mas_server": "mas.maap-project.org",
         "edsc_server": "ade.maap-project.org:30052",
-        "workspace_bucket": "maap-ops-dataset",
+        "workspace_bucket": "maap-ops-workspace",
         "default_host": false
     }
 ]
diff --git a/jupyterlab3/pangeo/environment.yml b/jupyterlab3/pangeo/environment.yml
@@ -18,7 +18,14 @@ dependencies:
   - shapely=2.0.1
   - xmltodict=0.13.0
   - xarray=2023.5.0
+  - pip
   - pip:
     - rio_tiler==4.1.11
     - pystac_client==0.6.1
-    - git+https://github.com/MAAP-Project/[email protected]#egg-info=stac_ipyleaflet
+    - git+https://github.com/MAAP-Project/[email protected]#egg-info=stac_ipyleaflet
+variables:
+  TITILER_STAC_ENDPOINT: 'https://titiler-stac.maap-project.org/'
+  TITILER_ENDPOINT: 'https://titiler.maap-project.org/'
+  STAC_CATALOG_NAME: 'MAAP STAC'
+  STAC_CATALOG_URL: 'https://stac.maap-project.org/'
+  STAC_BROWSER_URL: 'https://stac-browser.maap-project.org/'