create README.rst, fix file saving

README.rst

@@ -0,0 +1,26 @@
+NeuroVault Collection Downloader
+================================
+
+CLI tool for bulk downloads of NeuroVault data.
+
+* Free software: Apache Software License 2.0
+
+
+Installation
+------------
+
+`pip install git+https://github.com/NeuroVault/neurovault_collection_downloader.git`
+
+Usage
+-----
+
+1. Create a text file with one collection ID (a number or string of capital letters in case of private collection) per line.
+2. `neurovault_collection_downloader collections.txt /output_directory`
+
+Credits
+-------
+
+This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

neurovault_collection_downloader/cli.py

@@ -15,7 +15,11 @@ def mkdir_p(path):
             pass
         else: raise
 
-def fetch_collection(col_id, destination_folder):
+def fetch_collection(col_id, destination_folder, 
+                     alt_label=None, exclude_tag=None):
+    if exclude_tag is not None:
+        if not isinstance(exclude_tag, list):
+            exclude_tag = [exclude_tag]
     images_url_template = "http://neurovault.org/api/collections/%s/images/"
     next_url = images_url_template%col_id
     images = []
@@ -26,13 +30,30 @@ def fetch_collection(col_id, destination_folder):
         images += data['results']
         next_url = data['next']
 
-    col_folder = os.path.join(destination_folder, "%s"%col_id)
+    if alt_label is not None:
+        col_folder = os.path.join(destination_folder, alt_label)
+    else:
+        col_folder = os.path.join(destination_folder, "%s"%col_id)
+
     mkdir_p(col_folder)
-    json.dump(images, open(os.path.join(col_folder, "images.json"), "w"), 
+    json.dump(images, 
+              open(os.path.join(col_folder, "images.json"), "w"), 
               indent=4, sort_keys=True)
     for image in images:
         click.echo("fetching %s"%image['file'])
-        urllib.request.urlretrieve(image['file'], os.path.join(col_folder, str(image['id']) + ".nii.gz"))
+        fname = os.path.basename(image['file'])
+        exclude_img = False
+        if exclude_tag is not None:
+            for et in exclude_tag:
+                if fname.find(et)>-1:
+                    exclude_img = True
+        if not exclude_img:
+            print("saving",
+                  image['file'],"to",
+                  os.path.join(col_folder, fname))
+            urllib.request.urlretrieve(
+                image['file'], 
+                os.path.join(col_folder, fname))
 
 
 @click.command()

requirements_dev.txt

@@ -1,11 +1,11 @@
-pip==18.1
+pip==19.1.1
 bumpversion==0.5.3
-wheel==0.32.1
+wheel==0.33.4
 watchdog==0.9.0
-flake8==3.5.0
-tox==3.5.2
-coverage==4.5.1
-Sphinx==1.8.1
-twine==1.12.1
+flake8==3.7.8
+tox==3.13.2
+coverage==4.5.3
+Sphinx==2.1.2
+twine==1.13.1