xnat_search.py splitted in:

queries.py - contains methods for downloading and searching
datatypereader.py - contains methods for readen datatype and their fields from json files
xsa_skript.py -  skript for starting xsa without a gui

xnat_search_gui.py

@@ -33,11 +33,12 @@ class XnatSearchApp(gtk.Window):
         vbox_root.pack_start(hpaned, True, True, 5)
 
         def on_search_query(_, host, credentials, root_type, query, labels):
-            import xnat_search
+            import xsalogic.datatypereader as type_reader
+            import xsalogic.queries as queries
             user, _, passw = credentials.partition(":")
-            fields = xnat_search.get_fields_from_labels(labels,root_type)
-            query_results = xnat_search.search_for(host, 'xnat:mrScanData', query, fields, user, passw)
-            xnat_search.HOST = host
+            fields = type_reader.get_fields_from_labels(labels,root_type)
+            query_results = queries.search_for(host, 'xnat:mrScanData', query, fields, user, passw)
+            queries.HOST = host
 
             #TODO catch errors
 

xsa_skript.py

+import xsalogic.queries as queries
+
+def main(host, user, passw):
+    import distutils.core
+
+    root_element = 'xnat:mrScanData'
+    constraints = [
+        ('xnat:mrScanData/TYPE', 'LIKE', '%t1%'),
+        ('xnat:mrScanData/PARAMETERS_FLIP', '>=', '10'),
+        'AND',
+        [('xnat:mrScanData/PARAMETERS_TE', '>', '2.0'),
+         ('xnat:mrScanData/PARAMETERS_TE', '<', '2.0'),
+         'OR'
+         ]
+        ]
+
+    search_fields=[ 'xnat:mrScanData/TYPE',
+                    'xnat:mrSessionData/PROJECT',
+                    'xnat:mrSessionData/SUBJECT_ID',
+                    'xnat:mrSessionData/SESSION_ID',
+                    'xnat:mrScanData/ID'
+                    ]
+
+
+    results = queries.search_for(host, root_element, constraints,search_fields, user, passw)
+
+    print "Search results (%s):" % len(results)
+    print results
+
+    while True:
+        try:
+            is_downl = distutils.util.strtobool(raw_input("download? "))
+            break
+        except ValueError:
+            print "invalid character. Please use y or n."
+
+    if is_downl:
+        print "downloading files..."
+        queries.download_all(results, host)
+        print "finished"
+    else:
+        print "download canceled"
+
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description='search and download')
+    parser.add_argument('--host', type=str, help='hostname or ip-address (including port).', default="localhost:8080")
+    parser.add_argument('--user', type=str, help='user:passw', default=":")
+
+    args = parser.parse_args()
+
+    u,p = args.user.split(':')
+    main(args.host, u, p)

xsagtk/chart_view.py

@@ -108,10 +108,10 @@ class ComboBoxRootType(gtk.ComboBox):
             return None
 
     def show_data(self, root_type, data):
-        import xnat_search
+        import xsalogic.datatypereader as type_reader
         self.store.clear()
         for key in data.headers():
-            label = xnat_search.get_field_label(root_type, key)
+            label = type_reader.get_field_label(root_type, key)
             self.store.append([label, key])
 
 

xsagtk/query_view.py

@@ -26,9 +26,9 @@ class QueryView(gtk.VBox):
     def __init__(self, *args, **kwargs):
         super(QueryView, self).__init__(*args, **kwargs)
 
-        import xnat_search
-
+        import xsalogic.datatypereader as type_reader
         import gobject
+
         gobject.signal_new("send-query", QueryView, gobject.SIGNAL_RUN_FIRST,
         gobject.TYPE_NONE, (gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_STRING, gobject.TYPE_PYOBJECT, gobject.TYPE_PYOBJECT))
 
@@ -43,7 +43,7 @@ class QueryView(gtk.VBox):
 
         def changed_cb(combobox):
             selected =  combobox.get_selected_item()
-            fields = xnat_search.get_field_labels_required_of_type(selected)
+            fields = type_reader.get_field_labels_required_of_type(selected)
             self.treeView_search.set_root_type(selected)
             self.treeView_fields.show_fields(fields)
 
@@ -52,7 +52,7 @@ class QueryView(gtk.VBox):
         cell = gtk.CellRendererText()
         self.combobox.pack_start(cell)
         self.combobox.add_attribute(cell, 'text', 0)
-        for t in xnat_search.get_data_types():
+        for t in type_reader.get_data_types():
             self.combobox.append_text(t)
         hBox_root_type.pack_start(self.combobox, True, True,0)
 
@@ -339,21 +339,21 @@ class TreeViewQuery(gtk.TreeView):
         self.store.append(None, (self.inital_value, '', '', False, self.tooltip))
 
     def create_type_list(self):
-        import xnat_search
-        self.types = xnat_search.get_field_labels_of_type(self.root_type)
+        import xsalogic.datatypereader as type_reader
+        self.types = type_reader.get_field_labels_of_type(self.root_type)
 
     def create_method_list(self):
-        import xnat_search
-        self.methods = xnat_search.get_query_methods()
+        import xsalogic.queries as queries
+        self.methods = queries.get_query_methods()
 
     def create_operator_list(self):
-        import xnat_search
-        self.operators = xnat_search.get_operators()
+        import xsalogic.queries as queries
+        self.operators = queries.get_operators()
 
     def get_query(self, type):
-        import xnat_search
+        import xsalogic.datatypereader as type_reader
 
-        search_fields = xnat_search.get_fields_of_type(type)
+        search_fields = type_reader.get_fields_of_type(type)
         query = []
 
         def add_next_to_querry(iter):

xsagtk/results_view.py

@@ -21,7 +21,7 @@ class ResultsDownloadView(gtk.VBox):
 
         def event_clicked_download(button, *_):
             import gobject
-            import xnat_search
+            import xsalogic.queries as queries
             enabled = (d for d in self.treeViewResults.store if d[0])
             for d in enabled:
                 def stop_spinner(_row):
@@ -29,7 +29,7 @@ class ResultsDownloadView(gtk.VBox):
                     _row[0] = False # Checkbox to false
                 d[3] = 0
                 d[2] = True # Show Spinner
-                xnat_search.download_async(d[1], button.destination, cb=stop_spinner, cb_args=(d,))
+                queries.download_async(d[1], button.destination, cb=stop_spinner, cb_args=(d,))
 
         def event_clicked_toggle_selection(*_):
             self.treeViewResults.toggle_selection()
@@ -149,7 +149,7 @@ class TreeViewResults(gtk.TreeView):
 
             self.store.append(result)
 
-        import xnat_search
-        keys_ = list(xnat_search.get_field_label(root_type, key) for key in keys)
-        self.create_columns(keys_)    # TODO labels
+        import xsalogic.datatypereader as type_reader
+        keys_ = list(type_reader.get_field_label(root_type, key) for key in keys)
+        self.create_columns(keys_)
         self.set_model(self.store)

xsalogic/datatypereader.py

+# TODO nur einmal einlesen
+
+def get_data_types():
+    from os import listdir
+    from os.path import isfile, join
+    import json
+
+    DIR = 'datatypes/'
+    files = [ f for f in listdir(DIR) if isfile(join(DIR,f)) ]
+    result = []
+    for file in files:
+        with open(join(DIR,file)) as f:
+            try:
+                data=json.loads(f.read())['root-type']
+                result.append(data)
+            except ValueError:
+                pass
+    return result
+
+
+def get_field_labels_of_type(type):
+    result = []
+    fields = get_fields_of_type(type)
+    if fields is not None:
+        for f in fields:
+            result.append(f['label'])
+    return result
+
+def get_field_labels_required_of_type(type): # TODO rename
+    result = []
+    fields = get_fields_of_type(type)
+    if fields is not None:
+        for f in fields:
+            result.append((f['label'],f['required']))
+    return result
+
+
+def get_fields_of_type(type):
+    from os import listdir
+    from os.path import isfile, join
+    import json
+
+    DIR = 'datatypes/'
+    files = [ f for f in listdir(DIR) if isfile(join(DIR,f)) ]
+    for file in files:
+        with open(join(DIR,file)) as f:
+            try:
+                t = json.loads(f.read())
+                if t['root-type'] == type:
+                    return t['fields']
+            except ValueError:
+                pass
+
+
+def get_field_label(type, key):
+    fields = get_fields_of_type(type)
+    for f in fields:
+        if "key" in f and f["key"] == key:
+            return f["label"]
+    return key
+
+def get_fields_from_labels(labels, type):
+    result=[]
+    fields = get_fields_of_type(type)
+    if fields is not None:
+        for l in labels:
+            for f in fields:
+                if f['label'] == l:
+                    result.append(f['field'])
+                    break
+    return result

xnat_search.py → xsalogic/queries.py

 HOST = None
-
 from threading import Lock
 requests_lock = Lock()
 
-def main(host):
-    import distutils.core
-
-    root_element = 'xnat:mrScanData'
-    constraints = [
-        ('xnat:mrScanData/TYPE', 'LIKE', '%t1%'),
-        ('xnat:mrScanData/PARAMETERS_FLIP', '>=', '10'),
-        'AND',
-        [('xnat:mrScanData/PARAMETERS_TE', '>', '2.0'),
-         ('xnat:mrScanData/PARAMETERS_TE', '<', '2.0'),
-         'OR'
-         ]
-        ]
-
-
-
-    results = search_for(host, root_element, constraints)
-
-    print "Search results (%s):" % len(results)
-    print results
-
-    while True:
-        try:
-            is_downl = distutils.util.strtobool(raw_input("download? "))
-            break
-        except ValueError:
-            print "invalid character. Please use y or n."
-
-    if is_downl:
-        print "downloading files..."
-        download_all(results, host)
-        print "finished"
-    else:
-        print "download canceled"
-
-def read_json_from_file():
-    pass
-
-def get_data_types():
-    from os import listdir
-    from os.path import isfile, join
-    import json
-
-    DIR = 'datatypes/'
-    files = [ f for f in listdir(DIR) if isfile(join(DIR,f)) ]
-    result = []
-    for file in files:
-        with open(join(DIR,file)) as f:
-            try:
-                data=json.loads(f.read())['root-type']
-                result.append(data)
-            except ValueError:
-                pass
-    return result
-
-def get_field_labels_of_type(type):
-    result = []
-    fields = get_fields_of_type(type)
-    if fields is not None:
-        for f in fields:
-            result.append(f['label'])
-    return result
-
-def get_field_labels_required_of_type(type):
-    result = []
-    fields = get_fields_of_type(type)
-    if fields is not None:
-        for f in fields:
-            result.append((f['label'],f['required']))
-    return result
-
-def get_fields_of_type(type):
-    from os import listdir
-    from os.path import isfile, join
-    import json
-
-    DIR = 'datatypes/'
-    files = [ f for f in listdir(DIR) if isfile(join(DIR,f)) ]
-    for file in files:
-        with open(join(DIR,file)) as f:
-            try:
-                t = json.loads(f.read())
-                if t['root-type'] == type:
-                    return t['fields']
-            except ValueError:
-                pass
-
-def get_field_label(type, key):
-    fields = get_fields_of_type(type)
-    for f in fields:
-        if "key" in f and f["key"] == key:
-            return f["label"]
-    return key
-
-def get_fields_from_labels(labels, type):
-    result=[]
-    fields = get_fields_of_type(type)
-    if fields is not None:
-        for l in labels:
-            for f in fields:
-                if f['label'] == l:
-                    result.append(f['field'])
-                    break
-    return result
-
 def get_query_methods():
     return ["AND", "OR"]
 
 def get_operators():
     return ["LIKE", ">", "<", "<=", ">=", "="]
 
+def get_credentials(force=False,username="", password="" ):
+    if get_credentials.cache and not force:
+        return get_credentials.cache
+    from getpass import getpass
+    while not len(username):
+        username = raw_input("Username: ").strip()
+    while not len(password):
+        password = getpass().strip()
+    get_credentials.cache = username, password
+    return get_credentials()
+get_credentials.cache = None
+
+
+
 def download_all(results, host=None):
     for r in results:
         download(r, host)
@@ -129,7 +37,7 @@ def download(result, dest_folder='', host=None, cb=(lambda *_: None), cb_args=()
         host = HOST
     requests_lock.acquire()
     print(result)
-    subject = result['xnat_mrsessiondata_subject_id']
+    subject = result['xnat_mrsessiondata_subject_id']   #TODO download andere typen
     experiment = result['xnat_mrsessiondata_session_id']
     project = result['xnat_mrsessiondata_project']
     scan = result['id']
@@ -138,6 +46,33 @@ def download(result, dest_folder='', host=None, cb=(lambda *_: None), cb_args=()
     requests_lock.release()
     cb(*cb_args)
 
+def download_file(host, project, subject, experiment, scan, file_name):
+    import requests
+    from base64 import b64encode
+    from requests.auth import HTTPBasicAuth
+
+    if not file_name.endswith(".zip"):
+        file_name += ".zip"
+
+    url= "%s/data/archive/projects/%s/subjects/%s/experiments/%s/scans/%s/resources/DICOM/files?format=zip" % (host, project, subject, experiment, scan)
+
+    user, passw = get_credentials()
+
+    try:
+        with open(file_name, 'wb') as handle:
+            response = requests.get(url, stream=True, auth=HTTPBasicAuth(user, passw))
+            if not response.ok:
+                raise ValueError(response.status_code)
+            for block in response.iter_content(1024):
+                if not block:
+                    break
+                handle.write(block)
+    except IOError as e:
+        print "Error writing file %s, %s" % (file_name, e)
+    except ValueError as e:
+        print "Error downloading file %s, Status Code %s" % (url, e)
+
+
 def search_for(host, root_element, constraints, search_fields, user, passw):
     from pyxnat import Interface
     from pyxnat.core import errors
@@ -145,7 +80,6 @@ def search_for(host, root_element, constraints, search_fields, user, passw):
     from httplib2 import ServerNotFoundError
 
     get_credentials(username=user, password=passw, force=True)
-
     user, passw = get_credentials()
     tmp_dir=mkdtemp()
 
@@ -177,59 +111,3 @@ def search_for(host, root_element, constraints, search_fields, user, passw):
     except:
         pass
     return result
-
-
-def get_credentials(force=False,username="", password="" ):
-    if get_credentials.cache and not force:
-        return get_credentials.cache
-    from getpass import getpass
-    while not len(username):
-        username = raw_input("Username: ").strip()
-    while not len(password):
-        password = getpass().strip()
-    get_credentials.cache = username, password
-    return get_credentials()
-get_credentials.cache = None
-
-def download_file(host, project, subject, experiment, scan, file_name):
-    import requests
-    from base64 import b64encode
-    from requests.auth import HTTPBasicAuth
-
-    if not file_name.endswith(".zip"):
-        file_name += ".zip"
-
-    url= "%s/data/archive/projects/%s/subjects/%s/experiments/%s/scans/%s/resources/DICOM/files?format=zip" % (host, project, subject, experiment, scan)
-
-    user, passw = get_credentials()
-
-    try:
-        with open(file_name, 'wb') as handle:
-            response = requests.get(url, stream=True, auth=HTTPBasicAuth(user, passw))
-            if not response.ok:
-                raise ValueError(response.status_code)
-            for block in response.iter_content(1024):
-                if not block:
-                    break
-                handle.write(block)
-    except IOError as e:
-        print "Error writing file %s, %s" % (file_name, e)
-    except ValueError as e:
-        print "Error downloading file %s, Status Code %s" % (url, e)
-
-if __name__ == "__main__":
-    import argparse
-
-    parser = argparse.ArgumentParser(description='search and download')
-    parser.add_argument('--host', type=str, help='hostname or ip-address (including port).', default="localhost:8080")
-    parser.add_argument('--user', type=str, help='user:passw', default=":")
-
-    #TODO force download (boolean)
-    #TODO read constraints und root_element from file
-    #TODO GUI
-
-    args = parser.parse_args()
-
-    u,p = args.user.split(':')
-    get_credentials(username=u, password=p)
-    main(args.host)