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README.rst

@@ -28,7 +28,7 @@ Creating a conda environment and installing the library (tested with OSX)
 =========================================================================
 
 macOS
------  
+-----
 .. code-block:: bash
 
 	$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
@@ -75,10 +75,10 @@ This program will convert a BIDS MRI dataset to a NIDM-Experiment RDF document.
 
    This program will represent a BIDS MRI dataset as a NIDM RDF document and provide user with opportunity to annotate
    the dataset (i.e. create sidecar files) and associate selected variables with broader concepts to make datasets more
-   FAIR. 
+   FAIR.
 
    Note, you must obtain an API key to Interlex by signing up for an account at scicrunch.org then going to My Account
-   and API Keys.  Then set the environment variable INTERLEX_API_KEY with your key. 
+   and API Keys.  Then set the environment variable INTERLEX_API_KEY with your key.
 
    optional arguments:
      -h, --help            show this help message and exit
@@ -183,7 +183,7 @@ If you want to merge NIDM files on subject ID see pynidm merge
     -o, --out_file TEXT         File to write concatenated NIDM files
                               [required]
     --help                      Show this message and exit.
-  
+
 visualize
 ---------
 This command will produce a visualization(pdf) of the supplied NIDM files
@@ -197,7 +197,7 @@ named the same as the input files and stored in the same directories.
     -nl, --nidm_file_list TEXT  A comma separated list of NIDM files with full
                               path  [required]
     --help                      Show this message and exit.
-  
+
 merge
 -----
 This function will merge NIDM files.  See command line parameters for
@@ -268,25 +268,25 @@ Options:
   -nl, --nidm_file_list TEXT      A comma-separated list of NIDM files with
                                   full path  [required]
   -r, --regularization TEXT       Parameter, if set, will return the results of
-  				  the linear regression with L1 or L2 regularization 
-				  depending on the type specified, and the weight 
+  				  the linear regression with L1 or L2 regularization
+				  depending on the type specified, and the weight
 				  with the maximum likelihood solution. This will
 				  prevent overfitting. (Ex: -r L1)
   -model, --ml TEXT 		  An equation representing the linear
   				  regression. The dependent variable comes
 				  first, followed by "=" or "~", followed by
 				  the independent variables separated by "+"
-				  (Ex: -model "fs_003343 = age*sex + sex + 
+				  (Ex: -model "fs_003343 = age*sex + sex +
 				  age + group + age*group + bmi") [required]
   -contstant, --ctr TEXT       	  Parameter, if set, will return differences in
   				  variable relationships by group. One or
-				  multiple parameters can be used (multiple 
+				  multiple parameters can be used (multiple
 				  parameters should be separated by a comma-
 				  separated list) (Ex: -contrast group,age)
   -o, --output_file TEXT          Optional output file (TXT) to store results
                                   of query
   --help                          Show this message and exit.
-  
+
 To use the linear regression algorithm successfully, structure, syntax, and querying is important. Here is how to maximize the usefulness of the tool:
 
 
@@ -304,7 +304,7 @@ Now that we have selected the variables, we can perform a linear regression. In
 The command to use for this particular data is:
 pynidm linear-regression -nl /simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/CMU_a/nidm.ttl,/simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/CMU_b/nidm.ttl -model "fs_000008 = DX_GROUP + PIQ_tca9ck + http://uri.interlex.org/ilx_0100400" -contrast "DX_GROUP" -r L1
 
--nl specifies the file(s) to pull data from, while -model is the model to perform a linear regression model on. In this case, the variables are fs_000008 (the dependent variable, supratentorial brain volume), DX_GROUP (diagnostic group), PIQ_tca9ck (PIQ), and http://uri.interlex.org/ilx_0100400 (age at scan). The -contrast parameter says to contrast the data using DX_GROUP, and then do a L1 regularization to prevent overfitting. 
+-nl specifies the file(s) to pull data from, while -model is the model to perform a linear regression model on. In this case, the variables are fs_000008 (the dependent variable, supratentorial brain volume), DX_GROUP (diagnostic group), PIQ_tca9ck (PIQ), and http://uri.interlex.org/ilx_0100400 (age at scan). The -contrast parameter says to contrast the data using DX_GROUP, and then do a L1 regularization to prevent overfitting.
 
 Details on the REST API URI format and usage can be found below.
 
@@ -645,4 +645,3 @@ Additional NIDM-related Tools
 * Freesurfer stats -> NIDM <https://github.com/repronim/segstats_jsonld>
 * FSL structural segmentation -> NIDM <https://github.com/ReproNim/fsl_seg_to_nidm>
 * ANTS structural segmentation -> NIDM <https://github.com/ReproNim/ants_seg_to_nidm>
-

docker/Dockerfile

@@ -35,4 +35,3 @@ RUN git config --global user.name "docker user" && git config --global user.emai
 ENV TMPDIR=/opt/project/cache
 
 COPY . .
-

docker/Dockerfile-datalad

@@ -11,4 +11,3 @@ RUN wget -O- http://neuro.debian.net/lists/bionic.us-nh.full | tee /etc/apt/sour
 RUN apt-get install -y git-annex-standalone
 
 RUN datalad install ///abide2/RawData/NYU_1
-

docker/README.md

@@ -1,7 +1,7 @@
 # Docker and REST API
 
 This dockerfile can be used to create a development docker container suitable for both
-interactive use and also as a proof of concept REST API server. 
+interactive use and also as a proof of concept REST API server.
 
 #Build the container
 
@@ -11,7 +11,7 @@ To build the container, start in this directory and use the command:
 ```
 ./build.sh
 ```
- 
+
 ## Interactive
 
 You can then run the container interactively with:
@@ -25,13 +25,13 @@ in the directory /opt/PyNIDM in the container.
 ## REST Server
 
 This section assumes you have the PyNIDM source code in ~/PyNIDM. You should
-also put any NIDM ttl files you want the REST s     erver to process somewhere under the 
+also put any NIDM ttl files you want the REST s     erver to process somewhere under the
 ~/PyNIDM/ttl directory.  Once you have done those things, use the command:
 ```
 ./runrest.sh
 ```
 
-This should start a HTTP server that is listening on port 5000 of your 
+This should start a HTTP server that is listening on port 5000 of your
 local system.  You should be able to connect to the following routes:
 ```
 http://localhost:5000/projects
@@ -41,5 +41,5 @@ http://localhost:5000/projects/[Project-UUID]/subjects/[Subject-UUID]
 ```
 
 After the server is started you can continue to modify the files in your
-~/PyNIDM/ttl directory and those changes will immediately be reflected in the 
+~/PyNIDM/ttl directory and those changes will immediately be reflected in the
 REST API results.

docker/build.sh

@@ -2,4 +2,4 @@
 
 mkdir -p ../cache
 sudo docker build -f Dockerfile -t pynidm .
-sudo docker build -f Dockerfile-rest -t pynidm-rest .
+sudo docker build -f Dockerfile-rest -t pynidm-rest .

docker/rest-blaze.py

@@ -1,51 +1,62 @@
 #!/usr/bin/python
 
-from flask import Flask, request
-from flask_restful import Resource, Api
 import glob
-from nidm.experiment.tools.rest import RestParser
+import os
+from flask import Flask, request
 from flask_cors import CORS
+from flask_restful import Api, Resource
+from nidm.experiment.tools.rest import RestParser
 import simplejson
-import os
+
 
 def getTTLFiles():
     files = []
-    for filename in glob.glob('/opt/project/ttl/**/*.ttl', recursive=True):
+    for filename in glob.glob("/opt/project/ttl/**/*.ttl", recursive=True):
         files.append(filename)
     return files
 
+
 class NIDMRest(Resource):
     def get(self, all):
-
         query_bits = []
         for a in request.args.keys():
             query_bits.append("{}={}".format(a, request.args.get(a)))
         query = "&".join(query_bits)
 
         files = getTTLFiles()
         if len(files) == 0:
-            return ({'error' : 'No NIDM files found. You may need to add NIDM ttl files to ~/PyNIDM/ttl'})
-        restParser = RestParser(output_format=RestParser.OBJECT_FORMAT, verbosity_level=5)
-
-        json_str = simplejson.dumps(restParser.run(files, "{}?{}".format(all, query)), indent=2)
-        response = app.response_class(response=json_str, status=200, mimetype='application/json')
+            return {
+                "error": "No NIDM files found. You may need to add NIDM ttl files to ~/PyNIDM/ttl"
+            }
+        restParser = RestParser(
+            output_format=RestParser.OBJECT_FORMAT, verbosity_level=5
+        )
+
+        json_str = simplejson.dumps(
+            restParser.run(files, "{}?{}".format(all, query)), indent=2
+        )
+        response = app.response_class(
+            response=json_str, status=200, mimetype="application/json"
+        )
 
         return response
 
+
 class Instructions(Resource):
     def get(self):
-
-        return ({'message' : 'You probably want to start at {}projects  See instructions at PyNIDM/docker/README.md for details on the API and loading data.'.format(request.url_root)})
-
+        return {
+            "message": "You probably want to start at {}projects  See instructions at PyNIDM/docker/README.md for details on the API and loading data.".format(
+                request.url_root
+            )
+        }
 
 
 app = Flask(__name__)
 CORS(app)
 api = Api(app)
-api.add_resource(Instructions, '/')
-api.add_resource(NIDMRest, '/<path:all>')
-
-if __name__ == '__main__':
+api.add_resource(Instructions, "/")
+api.add_resource(NIDMRest, "/<path:all>")
 
-    os.system('java -server -Xmx512mb -jar /opt/blazegraph.jar')
-    app.run(debug=True, host='0.0.0.0')
+if __name__ == "__main__":
+    os.system("java -server -Xmx512mb -jar /opt/blazegraph.jar")
+    app.run(debug=True, host="0.0.0.0")

docs/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)