WIP: working on demos for bips server

bips/service/base.py

@@ -10,7 +10,10 @@
 from cherrypy import expose
 import numpy as np
 
+import lg_authority
+
 from ..workflows import get_workflows, get_workflow
+from .demos.dicomconvert import unzip_and_extract
 
 MEDIA_DIR = os.path.join(os.path.dirname(__file__), 'scripts')
 FILE_DIR = os.path.join(os.getcwd(), 'files')
@@ -43,7 +46,10 @@ def default(self, o):
         except TypeError:
             return ""
 
+@lg_authority.groups('auth')
 class BIPS(object):
+    auth = lg_authority.AuthRoot()
+
     def __init__(self, *args, **kwargs):
         tags = []
         mapper = {}
@@ -101,17 +107,6 @@ def tags(self, query):
         cherrypy.response.headers['Content-Type'] = 'application/json'
         return json.dumps(tags)
 
-    """
-        msg = ["<h2>Welcome to BIPS</h2>"]
-        msg.append('<ul>')
-        for wf, value in get_workflows():
-            msg += [('<li><a href="info?uuid=%s">%s</a> <a href="configure'
-                     '?uuid=%s">Configure</a> %s</li>') % (wf, wf, wf,
-                                        value['object'].help.split('\n')[1])]
-        msg.append('</li>')
-        return '\n'.join(msg)
-    """
-
     @expose
     def info(self, uuid):
         wf = get_workflow(uuid)
@@ -122,24 +117,7 @@ def info(self, uuid):
         cherrypy.response.headers['Content-Type'] = 'application/json'
         return json.dumps({'jsonconfig': json_str, 'workflowconfig': config_str},
                           cls=MyEncoder)
-    '''
-            msg = """
-
-    var str = JSON.stringify(%s, null, 2);
-    $(this).append('<h3>Workflow info</h3>');
-    console.log($(this));
-    /*
-    document.write('<pre>' + syntaxHighlight(str) +'</pre>');
-    var str2 = JSON.stringify(%s, null, 2);
-    document.write('<h3>Workflow config</h3>')
-    document.write('<pre>' + syntaxHighlight(str2) +'</pre>');
-    document.write('<h3>Workflow graph</h3>')
-    document.write('<img src="%s" />')
-    */
-    </script>
-    """ % (json_str, config_str, img_file)
-            return msg
-    '''
+
     @expose
     def configure(self, uuid):
         wf = get_workflow(uuid)
@@ -151,6 +129,12 @@ def demo(self):
             msg = fp.readlines()
         return msg
 
+    @expose
+    def demo_convert(self):
+        with open(os.path.join(MEDIA_DIR, 'demo_convert.html')) as fp:
+            msg = fp.readlines()
+        return msg
+
     @expose
     def uploadhandler(self, **kwargs):
         if 'files[]' not in kwargs:
@@ -185,15 +169,53 @@ def uploadhandler(self, **kwargs):
         else:
             out = {}
         cherrypy.response.headers['Content-Type'] = 'application/json'
-        return json.dumps([out])
+        return json.dumps([[out]])
+
+    @expose
+    def dicomuploadhandler(self, **kwargs):
+        cherrypy.log('dcmhandler: %s' % str(kwargs))
+        if 'files[]' not in kwargs:
+            return
+        myFile = kwargs['files[]']
+        outfile = os.path.join(FILE_DIR, myFile.filename)
+        with open(outfile, 'wb') as fp:
+            shutil.copyfileobj(myFile.file, fp)
+        cherrypy.log('Saved file: %s' % outfile)
+        if os.path.isfile(outfile):
+            print "getting info: %s" % outfile
+            info = unzip_and_extract(outfile, FILE_DIR)
+            os.unlink(outfile)
+            print info
+            out = []
+            for key, value in sorted(info.items()):
+                info = value
+                out.append({"index": info['idx'],
+                            "name": info['name'],
+                            "metaname": info['metapath'],
+                            'error': info['err_status'] == 'err',
+                            "size": ' x '.join([str(val) for val in info['size']]),
+                            "url": "%sfiles\/%s" % (url_prefix, info['filepath']),
+                            "metaurl": "%sfiles\/%s" % (url_prefix, info['metapath']),
+                            "delete_url": "%sdeletehandler?file=%s" % (url_prefix, info['filepath']),
+                            "delete_type": "DELETE"
+                })
+            out = [out]
+        else:
+            out = {}
+        print 'out', out
+        cherrypy.response.headers['Content-Type'] = 'application/json'
+        return json.dumps(out)
 
     @expose
     def deletehandler(self, file):
         outfile = os.path.join(FILE_DIR, file)
         if os.path.isfile(outfile):
             cherrypy.log('Deleting file: %s' % outfile)
             os.unlink(outfile)
-            os.unlink(outfile+'.png')
+            if os.path.exists(outfile + '.png'):
+                os.unlink(outfile+'.png')
+            if os.path.exists(outfile + '.json'):
+                os.unlink(outfile+'.json')
 
 def open_page():
     #pass
@@ -204,7 +226,12 @@ def start_service():
     if not os.path.exists(FILE_DIR):
         os.mkdir(FILE_DIR)
     config = {'/': {'tools.staticdir.on': True,
-                    'tools.staticdir.dir': os.getcwd()},
+                    'tools.staticdir.dir': os.getcwd(),
+                    'tools.lg_authority.on': False,
+                    'tools.lg_authority.site_storage': 'sqlite3',
+                    'tools.lg_authority.site_storage_conf':
+                            { 'file': os.path.abspath('test.db') }
+                    },
               '/css': {'tools.staticdir.on': True,
                        'tools.staticdir.dir': os.path.join(MEDIA_DIR, 'css')},
               '/js': {'tools.staticdir.on': True,
@@ -218,7 +245,7 @@ def start_service():
               '/files': {'tools.staticdir.on': True,
                          'tools.staticdir.dir': FILE_DIR},
               }
-    #start webservice
+    #    #start webservice
     certfile = os.path.join(os.environ['HOME'], 'certinfo')
     if os.path.exists(certfile):
         cherrypy.log('Loading cert info: %s' % certfile)

bips/service/demos/__init__.py

@@ -0,0 +1 @@
+

bips/service/demos/dicomconvert.py

@@ -0,0 +1,80 @@
+from glob import glob
+import os
+import string
+
+from tempfile import mkdtemp
+from dcmstack import parse_and_stack, NiftiWrapper
+
+def sanitize_path_comp(path_comp):
+    result = []
+    for char in path_comp:
+        if not char in string.letters + string.digits + '-_.':
+            result.append('_')
+        else:
+            result.append(char)
+    return ''.join(result)
+
+def get_dicom_info(dicom_dir, dest):
+    """Return a freesurfer style dicom info generator
+    """
+    fl = sorted(glob(os.path.join(dicom_dir, '*.dcm')))
+    stack = parse_and_stack(fl, force=True, warn_on_except=True)
+    info = {}
+    for key in sorted(stack):
+        key_fields = key.split('-')
+        idx = int(key_fields[0])
+        name = key_fields[1]
+        stack_object = stack[key]
+        if not stack_object.error:
+            size = list(stack_object.get_shape())
+            if len(size) == 3:
+                size.append(1)
+            err_status = 'ok'
+            out_fn = sanitize_path_comp(key) + '.nii.gz'
+            out_path = os.path.join(dest, out_fn)
+            nii = stack_object.to_nifti(embed_meta=True)
+            nii_wrp = NiftiWrapper(nii)
+            meta_fn = out_fn + '.json'
+            meta_path = os.path.join(dest, meta_fn)
+            with open(meta_path, 'w') as fp:
+                fp.write(nii_wrp.meta_ext.to_json())
+            nii.to_filename(out_path)
+        else:
+            size = [0, 0, 0, 0]
+            err_status = 'err'
+            out_fn = None
+            meta_fn = None
+        filepath = out_fn
+        filename = stack_object._files_info[0][2]
+        info[idx] = dict(idx=idx, name=name, err_status=err_status,
+                         size=size, filename=filename,
+                         filepath=filepath,
+                         metapath=meta_fn)
+        size = [str(val) for val in size]
+        print '\t'.join([str(idx), name, err_status] + size + [filename])
+    return info
+
+def unzip_and_extract(filename, dest):
+    outdir = mkdtemp()
+    if '.tgz' in filename or '.tar.gz' in filename:
+        import tarfile
+        bundle =  tarfile.open(filename, 'r')
+    elif '.zip' in filename:
+        import zipfile
+        bundle =  zipfile.ZipFile(filename, 'r')
+    else:
+        raise ValueError('Unknown compression format. Only zip and tar+gzip supported')
+    bundle.extractall(outdir)
+    dcmdir = None
+    print outdir
+    for r,d,f in os.walk(outdir):
+        print r
+        for files in f:
+            print files
+            if files.endswith(".dcm"):
+                dcmdir = r
+                break
+    print dcmdir
+    info = get_dicom_info(dcmdir, dest)
+    return info
+

bips/service/scripts/cors/postmessage.html

@@ -15,7 +15,7 @@
 <head>
 <meta charset="utf-8">
 <title>jQuery File Upload Plugin postMessage API</title>
-<script src="//ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script>
+<script src="//ajax.googleapis.com/ajax/libs/jquery/1.8.1/jquery.min.js"></script>
 </head>
 <body>
 <script>

bips/service/scripts/cors/result.html

@@ -1,7 +1,7 @@
 <!DOCTYPE HTML>
 <!--
 /*
- * jQuery Iframe Transport Plugin Redirect Page 2.0
+ * jQuery Iframe Transport Plugin Redirect Page 2.0.1
  * https://github.com/blueimp/jQuery-File-Upload
  *
  * Copyright 2010, Sebastian Tschan
@@ -16,5 +16,9 @@
 <meta charset="utf-8">
 <title>jQuery Iframe Transport Plugin Redirect Page</title>
 </head>
-<body><script>document.body.innerHTML=decodeURIComponent(window.location.search.slice(1));</script></body>
-</html>
+<body>
+<script>
+document.body.innerText=document.body.textContent=decodeURIComponent(window.location.search.slice(1));
+</script>
+</body>
+</html>