Merge pull request CenterForOpenScience#265 from TomBaxter/feature/svcs-86

[SVCS-86] Add Papaya Renderer for Dicom and NifTi Files

Author: cslzchen

mfr/core/utils.py

@@ -1,3 +1,6 @@
+from time import time
+from os.path import getctime
+
 from stevedore import driver
 
 from mfr.core import exceptions
@@ -106,3 +109,8 @@ def sizeof_fmt(num, suffix='B'):
             return '%3.1f%s%s' % (num, unit, suffix)
         num /= 1000.0
     return '%.1f%s%s' % (num, 'Y', suffix)
+
+def file_expired(path: str, ttl: int) -> bool:
+    if (time() - getctime(path)) >= ttl:
+        return True
+    return False

mfr/extensions/papaya/__init__.py

@@ -0,0 +1 @@
+from .render import PapayaRenderer  # noqa

mfr/extensions/papaya/render.py

@@ -0,0 +1,46 @@
+import os
+import shutil
+
+from mako.lookup import TemplateLookup
+
+from mfr.core import utils
+from mfr.core import extension
+from mfr.extensions import settings as ext_settings
+from mfr.extensions.papaya import settings
+
+
+class PapayaRenderer(extension.BaseRenderer):
+
+    data_dir = settings.DATA_DIR
+    data_ttl = settings.DATA_TTL
+    comp_ext = ext_settings.COMPRESSED_EXT
+
+    TEMPLATE = TemplateLookup(
+        directories=[
+            os.path.join(os.path.dirname(__file__), 'templates')
+        ]).get_template('viewer.mako')
+
+    def render(self):
+        self.remove_old_files()
+        file_name = os.path.basename(self.file_path)
+        if self.metadata.ext in self.comp_ext.keys():
+            second_ext = '.{}'.format(self.metadata.name.split('.')[-1])
+            if second_ext in self.comp_ext[self.metadata.ext]:
+                file_name = file_name + second_ext
+        file_name = file_name + self.metadata.ext
+        shutil.copyfile(self.file_path, self.data_dir + file_name)
+        return self.TEMPLATE.render(base=self.assets_url, file_name=file_name)
+
+    def remove_old_files(self):
+
+        for data_file in os.listdir(self.data_dir):
+            if utils.file_expired(self.data_dir + data_file, self.data_ttl):
+                os.unlink(self.data_dir + data_file)
+
+    @property
+    def file_required(self):
+        return True
+
+    @property
+    def cache_result(self):
+        return True

mfr/extensions/papaya/settings.py

@@ -0,0 +1,8 @@
+from mfr import settings
+
+config = settings.child('PAPAYA_EXTENSION_CONFIG')
+
+# Directory to temporarily store papaya image files
+DATA_DIR = 'mfr/extensions/papaya/static/data/'
+# Files older then this many seconds will be deleted from DATA_DIR at the beggining of each render.
+DATA_TTL = 300

mfr/extensions/papaya/static/README-papaya.txt

@@ -0,0 +1,7 @@
+Currently using a custom built papaya.js with option to remove the ability to open new files from the users desktop.
+
+https://github.com/TomBaxter/Papaya/tree/feature/noNewFiles
+
+I have sent them a PR, hopefully they bite.
+
+https://github.com/rii-mango/Papaya/pull/101

mfr/extensions/papaya/static/data/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore