Merge pull request #40 from neuroscout/output

Separate output dir, add LICENSE

Author: adelavega

Dockerfile

@@ -4,6 +4,7 @@ FROM poldracklab/fitlins
 # Set user back to root
 USER root
 RUN chown -R root /src /work
+RUN mkdir /data
 
 # Install neurodebian/datalad
 ARG DEBIAN_FRONTEND=noninteractive
@@ -15,10 +16,10 @@ RUN git config --global  user.email "[email protected]"
 
 # Install additional neuroscout + dependencies
 RUN /bin/bash -c "source activate neuro \
-      && pip install -q --no-cache-dir -e /src/fitlins[all]" \
+      && pip install -q --no-cache-dir -e git+https://github.com/poldracklab/fitlins.git@cceba1a46#egg=fitlins" \
     && sync
 
-# Copy the current directory contents into the container at /app (using COPY instead of ADD to keep it lighter)
+# Copy the current directory contents into the container
 COPY [".", "/src/neuroscout"]
 
 RUN /bin/bash -c "source activate neuro \
@@ -29,8 +30,7 @@ RUN /bin/bash -c "source activate neuro \
       && pip install -q --no-cache-dir --upgrade -r /src/neuroscout/requirements.txt" \
     && sync
 
-
-WORKDIR /work
+WORKDIR /data
 
 # Change entrypoint to neuroscout
 ENTRYPOINT ["/neurodocker/startup.sh", "neuroscout"]

LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2018, neuroscout
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -13,15 +13,14 @@ The easiest way to get Neuroscout running is using Docker. Just pull it from Doc
 Neuroscout is easy to use. Assuming you've already created an analysis on neuroscout.org, and have its analysis id (e.g.: `5xH937f`) you can run it in one line:
 
     docker run -it neuroscout/neuroscout-cli run 5xH937f
-    
+
 Neuroscout will download the necessary images, analysis bundle, and fit your model.
 
-It's probably best to mount a local volume to the work dir, to access the outputs, and cache any downloaded MRI images:
+To cache the downloaded data, and output the results to a separate folder, mount the appropriate volumes:
 
-    docker run -it -v /local/dir:/work neuroscout/neuroscout-cli run 5xH937f
-    
+    docker run -it -v /local/datadir:/data -v /local/outdir:/out neuroscout/neuroscout-cli run 5xH937f -o /out
 
-See the output of `neuroscout --help` for more informations:
+See the output of `neuroscout --help` for more information:
 
 ```
 Usage:

neuroscout_cli/commands/install.py

@@ -62,23 +62,21 @@ def download_data(self):
         remote_files = self.resources['func_paths'] + self.resources['mask_paths']
         remote_path = self.resources['preproc_address']
 
-        deriv_dir = Path(self.dataset_dir) / 'derivatives'
+        preproc_dir = Path(self.dataset_dir) / 'derivatives' / 'fmriprep'
 
         try:
-            if not (deriv_dir / 'fmriprep').exists():
+            if not preproc_dir.exists():
                 # Use datalad to install the raw BIDS dataset
                 install(source=remote_path,
-                        path=(deriv_dir / 'fmriprep').as_posix())
-
-            preproc_dir = deriv_dir / 'fmriprep' / 'fmriprep'
-            get([(preproc_dir / f).as_posix() for f in remote_files])
+                        path=str(preproc_dir))
+            if (preproc_dir / 'fmriprep').exists():
+                get([str(preproc_dir / 'fmriprep' / f) for f in remote_files])
         except Exception as e:
             message = e.failed[0]['message']
-            if 'Failed to clone data from any candidate source URL' not in message[0]:
+            if 'Failed to clone data from any candidate' not in message[0]:
                 raise ValueError("Datalad failed. Reason: {}".format(message))
 
             logging.info("Attempting HTTP download...")
-            preproc_dir = deriv_dir / 'fmriprep'
             for i, resource in enumerate(remote_files):
                 filename = preproc_dir / resource
                 logging.info("{}/{}: {}".format(i+1, len(remote_files), resource))

neuroscout_cli/commands/run.py

@@ -18,6 +18,8 @@ def run(self):
         out_dir = self.options.pop('-o')
         if out_dir == "bundle_dir":
             out_dir = (install_command.bundle_dir).absolute()
+        else:
+            out_dir = Path(out_dir)
 
         tmp_out = mkdtemp()