Re-create data folder, change to importlib for static files (#82)

jbrowse_jupyter/__init__.py

@@ -1,5 +1,6 @@
 # flake8: noqa
 from .jbrowse_config import JBrowseConfig, create
-from .util import  launch, create_component
+from .util import launch, create_component
 from .dev_server import serve
-__all__ = ['JBrowseConfig', 'create', 'launch', 'create_component', 'serve']
+
+__all__ = ["JBrowseConfig", "create", "launch", "create_component", "serve"]

jbrowse_jupyter/dev_server.py

@@ -3,24 +3,24 @@
 import re
 from http.server import HTTPServer, SimpleHTTPRequestHandler
 
-'''
+"""
 This server takes inspiration from multiple solutions to provide:
 * CORS enabled HTTPServer
     - https://gist.github.com/acdha/925e9ffc3d74ad59c3ea
 * Allowing Range Request Server
     - https://github.com/danvk/RangeHTTPServer/blob/master/RangeHTTPServer
 * Adding specific directory
     - https://stackoverflow.com/a/46332163
-'''
+"""
 # CREDIT FOR ENABLING RANGE REQUEST HTTP SERVER:
 # lines 20-31, 34,37-52, 59-107
 # https://github.com/danvk/RangeHTTPServer/blob/master/RangeHTTPServer
 
 
-def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16*1024):
-    '''Like shutil.copyfileobj, but only copy a range of the streams.
+def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024):
+    """Like shutil.copyfileobj, but only copy a range of the streams.
     Both start and stop are inclusive.
-    '''
+    """
     if start is not None:
         infile.seek(start)
     while 1:
@@ -31,39 +31,40 @@ def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16*1024):
         outfile.write(buf)
 
 
-BYTE_RANGE_RE = re.compile(r'bytes=(\d+)-(\d+)?$')
+BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$")
 
 
 def parse_byte_range(byte_range):
     """
     Returns the two numbers in 'bytes=123-456' or throws ValueError.
     The last number or both numbers may be None.
     """
-    if byte_range.strip() == '':
+    if byte_range.strip() == "":
         return None, None
 
     m = BYTE_RANGE_RE.match(byte_range)
     if not m:
-        raise ValueError('Invalid byte range %s' % byte_range)
+        raise ValueError("Invalid byte range %s" % byte_range)
 
     first, last = [x and int(x) for x in m.groups()]
     if last and last < first:
-        raise ValueError('Invalid byte range %s' % byte_range)
+        raise ValueError("Invalid byte range %s" % byte_range)
     return first, last
 
 
-class CustomRequestHandler (SimpleHTTPRequestHandler):
+class CustomRequestHandler(SimpleHTTPRequestHandler):
     """
     Creating a small HTTP request server
     """
+
     def send_head(self):
-        if 'Range' not in self.headers:
+        if "Range" not in self.headers:
             self.range = None
             return SimpleHTTPRequestHandler.send_head(self)
         try:
-            self.range = parse_byte_range(self.headers['Range'])
+            self.range = parse_byte_range(self.headers["Range"])
         except ValueError:
-            self.send_error(400, 'Invalid byte range')
+            self.send_error(400, "Invalid byte range")
             return None
         first, last = self.range
 
@@ -72,28 +73,27 @@ def send_head(self):
         f = None
         ctype = self.guess_type(path)
         try:
-            f = open(path, 'rb')
+            f = open(path, "rb")
         except IOError:
-            self.send_error(404, 'File not found')
+            self.send_error(404, "File not found")
             return None
 
         fs = os.fstat(f.fileno())
         file_len = fs[6]
         if first >= file_len:
-            self.send_error(416, 'Requested Range Not Satisfiable')
+            self.send_error(416, "Requested Range Not Satisfiable")
             return None
 
         self.send_response(206)
-        self.send_header('Content-type', ctype)
+        self.send_header("Content-type", ctype)
 
         if last is None or last >= file_len:
             last = file_len - 1
         response_length = last - first + 1
 
-        self.send_header('Content-Range',
-                         'bytes %s-%s/%s' % (first, last, file_len))
-        self.send_header('Content-Length', str(response_length))
-        self.send_header('Last-Modified', self.date_time_string(fs.st_mtime))
+        self.send_header("Content-Range", "bytes %s-%s/%s" % (first, last, file_len))
+        self.send_header("Content-Length", str(response_length))
+        self.send_header("Last-Modified", self.date_time_string(fs.st_mtime))
         self.end_headers()
         return f
 
@@ -107,11 +107,11 @@ def copyfile(self, source, outputfile):
         copy_byte_range(source, outputfile, start, stop)
 
     def end_headers(self):
-        self.send_header('Access-Control-Allow-Origin', '*')
-        self.send_header('Access-Control-Allow-Methods', 'GET, OPTIONS')
-        self.send_header('Access-Control-Expose-Headers', '*')
-        self.send_header('Accept-Ranges', 'bytes')
-        self.send_header('Content-Type', 'application/octet-stream')
+        self.send_header("Access-Control-Allow-Origin", "*")
+        self.send_header("Access-Control-Allow-Methods", "GET, OPTIONS")
+        self.send_header("Access-Control-Expose-Headers", "*")
+        self.send_header("Accept-Ranges", "bytes")
+        self.send_header("Content-Type", "application/octet-stream")
         SimpleHTTPRequestHandler.end_headers(self)
 
     def translate_path(self, path):
@@ -122,8 +122,9 @@ def translate_path(self, path):
 
 
 class DevServer(HTTPServer):
-    def __init__(self, base_path, server_address,
-                 RequestHandlerClass=CustomRequestHandler):
+    def __init__(
+        self, base_path, server_address, RequestHandlerClass=CustomRequestHandler
+    ):
         self.base_path = base_path
         HTTPServer.__init__(self, server_address, RequestHandlerClass)
 
@@ -144,19 +145,21 @@ def serve(data_path, **kwargs):
         the dev server, default to localhost
     """
     print("=============================================")
-    print("Warning: \n"
-          "This is a development environment.\n"
-          "This is not recommended for production.")
-    port = kwargs.get('port', 8080)
-    host = kwargs.get('host', "localhost")
+    print(
+        "Warning: \n"
+        "This is a development environment.\n"
+        "This is not recommended for production."
+    )
+    port = kwargs.get("port", 8080)
+    host = kwargs.get("host", "localhost")
     # data_path = kwargs.get('path', ".")
     # print('data', data_path)
     # dir_path = os.path.join(os.path.dirname(__file__), data_path)
     # print('dir path', dir_path)
     # print('relative ', os.path.relpath(data_path, os.getcwd()))
     # print('join', os.path.join(os.getcwd(), data_path))
     httpd = DevServer(data_path, (host, port))
-    server = f'http://{host}:{port}'
+    server = f"http://{host}:{port}"
     print("=============================================")
     print(f'Server is now running at \n "{server}"')
     httpd.serve_forever()