Minor release 1.0.4

docker/emhub_otf/Dockerfile

@@ -0,0 +1,119 @@
+FROM nvcr.io/hpc/relion:5.0.0
+
+LABEL maintainer="walid"
+
+# Point to existing CUDA
+ENV CUDA_HOME=/usr/local/cuda
+ENV CUDAHOME=/usr/local/cuda
+ENV PATH=/usr/local/cuda/bin:$PATH
+ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
+ENV CPATH=/usr/local/cuda/include:$CPATH
+
+ENV PATH=/usr/local/relion/bin:$PATH
+ENV LD_LIBRARY_PATH=/usr/local/relion/lib:$LD_LIBRARY_PATH
+
+# Add NVIDIA CUDA repo for Ubuntu 22.04 (CUDA 12.3)
+#RUN apt-get update && apt-get install -y wget gnupg ca-certificates && \
+#    wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.1-1_all.deb && \
+#    dpkg -i cuda-keyring_1.1-1_all.deb && \
+#    apt-get update
+
+# Install system + EMHub dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    cuda-toolkit-12-3 \
+    libcufft-dev-12-3 \
+    libcurand-dev-12-3 \
+    software-properties-common \
+    git \
+    curl \
+    wget \
+    unzip \
+    libxml2-dev \
+    libxslt1-dev \
+    libfftw3-dev \
+    libpng-dev \
+    libjpeg-dev \
+    libtiff5-dev \
+    redis \
+    redis-server \
+    libopenblas-dev \
+    liblapack-dev \
+    libatlas-base-dev \
+    gfortran \
+    build-essential \
+    #python3-pip \
+    #python3-redis \
+    #python3-hiredis \
+    && rm -rf /var/lib/apt/lists/*
+
+# crYOLO Dependencies
+RUN add-apt-repository ppa:deadsnakes/ppa \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends \
+    python3.8 \
+    python3.8-dev \
+    python3.8-distutils \
+    libgtk-3-dev \
+    libglib2.0-dev \
+    pkg-config \
+    && rm -rf /var/lib/apt/lists/*
+
+# Switch to a clean working dir
+WORKDIR /opt
+
+# Install PIP 3.8
+RUN curl -O https://bootstrap.pypa.io/pip/3.8/get-pip.py \
+    && python3.8 get-pip.py \
+    && rm get-pip.py
+
+# Install crYOLO
+RUN pip3 install --upgrade pip setuptools wheel \
+    && pip3 install --use-pep517 "cryolo[cu11]"
+
+# Install MotionCor3
+RUN wget https://github.com/czimaginginstitute/MotionCor3/releases/download/v1.0.1/MotionCor3_1.0.1_10-26-2023.zip \
+    && unzip /opt/MotionCor3_1.0.1_10-26-2023.zip \
+    && cp /opt/MotionCor3_1.0.1_Cuda122_10-26-2023 /usr/bin/MotionCor3 \
+    && rm /opt/MotionCor3*
+
+# Install ctffind5
+RUN curl -L -o ctffind-5.0.2.tar.gz "https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-5.0.2.tar.gz&file=1" \
+    && tar -xzf ctffind-5.0.2.tar.gz \
+    && cp /opt/cisTEM/bin/* /usr/local/bin \
+    && rm -r /opt/cisTEM ctffind-5.0.2.tar.gz
+
+# Install Redis & friends
+RUN apt -y remove python3-blinker
+RUN pip3 install "redis[hiredis]" \
+    && pip3 install "setuptools<65" \
+    && pip3 install blinker
+
+# Install EMTools
+RUN git clone https://github.com/3dem/emtools.git /opt/emtools \
+    && pip3 install /opt/emtools/ \
+    && rm -r /opt/emtools
+
+# Clone the EMHub repository
+RUN git clone https://github.com/3dem/emhub.git /opt/emhub \
+    && pip3 install /opt/emhub/ \
+    && rm -r /opt/emhub
+
+# Clone the EMWrap respository
+RUN git clone https://github.com/3dem/emwrap.git /opt/emwrap \
+    && pip3 install /opt/emwrap/ \
+    && rm -r /opt/emwrap
+
+# Copy the Relion binaries and fake libtiff.so.6 for relion
+RUN cp /lib/x86_64-linux-gnu/libtiff.so.5 /lib/x86_64-linux-gnu/libtiff.so.6 \
+    && cp /usr/local/relion/sm80/bin/* /usr/local/bin \
+    && cp /usr/local/relion/sm80/lib/* /usr/local/lib
+
+RUN ln -s /usr/bin/python3.8 /usr/bin/python
+
+WORKDIR /root
+
+# Set entrypoint (interactive shell)
+ENTRYPOINT ["/bin/bash"]
+#
+## CMD to provide a default action
+#CMD ["--help"]

emhub/__init__.py

@@ -31,7 +31,7 @@
 from glob import glob
 
 
-__version__ = '1.0.3'
+__version__ = '1.0.4rc2'
 
 
 def create_app(test_config=None):
@@ -47,7 +47,7 @@ def create_app(test_config=None):
                         send_json_data, send_error, shortname, pairname)
     from .utils.mail import MailManager
 
-    from emtools.utils import Pretty
+    from emtools.utils import Pretty, Path
 
     # create and configure the app
     emhub_instance_path = os.environ.get('EMHUB_INSTANCE', None)
@@ -135,6 +135,7 @@ def load_module(module_name):
     app.jinja_loader = jinja2.FileSystemLoader(template_folders)
 
     def register_basic_params(kwargs):
+        kwargs['current_app'] = app
         kwargs['is_devel'] = app.is_devel
         kwargs['version'] = __version__
         kwargs['emhub_title'] = app.config.get('EMHUB_TITLE', '')
@@ -215,32 +216,29 @@ def login():
         next_content = flask.request.args.get('next_content', 'dashboard')
         return _redirect('main', content_id=next_content)
 
-    @app.route('/do_login', methods=['POST'])
-    def do_login():
-        """ This view will be called as POST from the user login page. """
-        username = flask.request.form['username']
-        password = flask.request.form['password']
-        next_content = flask.request.form.get('next_content', 'index')
-        authenticated = None
+    def _default_login_user(username, password):
         user = None
 
         if not app.config.get('CASE_SENSITIVE_USERNAMES', True):
             username = username.lower()
 
-        user = app.dm.get_user_by(username=username)
-
-        if user:  # First check that the user in the db, then try to authenticate
+        if user := app.dm.get_user_by(username=username):  # First check that the user in the db, then try to authenticate
+            # Local authentication
+            if not user.check_password(password):
+                user = None
 
-            auth_local = user.auth_local or not app.use_ldap
+        return user
 
-            if auth_local:
-                if not user.check_password(password):
-                    user = None
-            else:
-                response = ldap_manager.authenticate(username, password)
-                # Specifics are configurable.  That information is not presently used.
-                if response.status != flask_ldap3_login.AuthenticationResponseStatus.success:
-                    user = None  # Failed authentication
+    @app.route('/do_login', methods=['POST'])
+    def do_login():
+        """ This view will be called as POST from the user login page. """
+        username = flask.request.form['username']
+        password = flask.request.form['password']
+        next_content = flask.request.form.get('next_content', 'index')
+        authenticated = None
+
+        login_user_func = getattr(app, 'login_user', _default_login_user)
+        user = login_user_func(username, password)
 
         if not user:
             flask.flash('Invalid username or password')
@@ -258,7 +256,7 @@ def do_switch_login():
         """ This view will be called as POST from a currently logged admin user.
          It will allow admins to login as another users for troubleshooting.
         """
-        if not app.user.is_admin:
+        if not app.user.is_manager:
             return send_error("Current user is not admin!")
 
         username = flask.request.json['username']
@@ -294,6 +292,10 @@ def reset_password_request():
             msg = "ERROR: email can not be empty."
         elif user is None:
             msg = "ERROR: this email does not seen registered with any user."
+        elif app.mm is None:
+            msg = ("ERROR: You need to configure a Mail server within EMhub"
+                   "to send reset password instructions. Please contact an "
+                   "admin to do it or set you a temporary password.")
         else:
             msg = ("Instructions about how to reset your password has been "
                    "sent to your email.")
@@ -375,7 +377,7 @@ def get_content():
 
     @app.template_filter('basename')
     def basename(filename):
-        return os.path.basename(filename) if filename else ''
+        return os.path.basename(Path.rmslash(filename)) if filename else ''
 
     @app.template_filter('id_from_label')
     def id_from_label(label):
@@ -413,6 +415,43 @@ def pretty_elapsed(ts):
     def url_for_content(contentId, **kwargs):
         return flask.url_for('main', _external=True, content_id=contentId, **kwargs)
 
+    def booking_cost(b):
+        """ Calculate the cost of a booking.
+        By default, it will be calculated based on the number of days
+        and the cost per day of the resource.
+        This function could be re-defined to change how to calculate
+        the booking costs. For example, one could compute the
+        booking cost per hours.
+        """
+        return b.total_cost
+
+    def get_ldap_username(email):
+        ldap_username = None
+
+        if not app.config.get('CASE_SENSITIVE_USERNAMES', True):
+            email = email.lower()
+
+        user = app.dm.get_user_by(username=email)
+
+        if user:  # First check that the user in the db, then try to authenticate
+
+            auth_local = user.auth_local or not app.use_ldap
+
+            if auth_local:
+                raise Exception("LDAP authentication is not configured.")
+            else:
+                with app.ldap_manager.connection as conn:
+                    search_filter = f'(mail={email})'
+                    # attributes=['sAMAccountName'] retrieves the short username
+                    conn.search(
+                        search_base=app.config['LDAP_BASE_DN'],
+                        search_filter=search_filter,
+                        attributes=['sAMAccountName']
+                    )
+                    ldap_username = conn.entries[0].sAMAccountName.value if conn.entries else None
+
+        return ldap_username
+
     app.jinja_env.globals.update(url_for_content=url_for_content)
     app.jinja_env.add_extension('jinja2.ext.do')
     app.jinja_env.filters['basename'] = basename
@@ -450,7 +489,7 @@ def url_for_content(contentId, **kwargs):
 
     if app.use_ldap:
         import flask_ldap3_login
-        ldap_manager = flask_ldap3_login.LDAP3LoginManager(app)
+        app.ldap_manager = flask_ldap3_login.LDAP3LoginManager(app)
 
     if app.config.get('MAIL_SERVER', None):
         app.mm = MailManager(app)
@@ -475,6 +514,10 @@ def url_for_content(contentId, **kwargs):
 
     app.jinja_env.filters['pretty_datetime'] = app.dm.local_datetime
 
+    app.booking_cost = booking_cost
+    app.get_ldap_username = get_ldap_username
+
+
     extra_setup = load_module('app_setup')
     if extra_setup and 'setup_app' in dir(extra_setup):
         print(f"Extending app setup from: {extra_setup.__file__}")