Merge pull request #1 from cfin-tools/distribute

Distribute

Author: cjayb

setup.py

@@ -0,0 +1,42 @@
+import os
+from setuptools import setup, Command
+
+# Utility function to read the README file.
+# Used for the long_description.  It's nice, because now 1) we have a top level
+# README file and 2) it's easier to type in the README file than to put a raw
+# string in below ...
+def read(fname):
+    return open(os.path.join(os.path.dirname(__file__), fname)).read()
+
+class CleanCommand(Command):
+    """Custom clean command to tidy up the project root."""
+    user_options = []
+    def initialize_options(self):
+        pass
+    def finalize_options(self):
+        pass
+    def run(self):
+        os.system('rm -vrf ./build ./dist ./*.pyc ./*.tgz ./*.egg-info')
+
+setup(
+    name = "stormdb",
+    version = "0.1",
+    author = "Christopher Bailey",
+    author_email = "cjb@cfin.au.dk",
+    description = ("Access to StormDb @ CFIN"),
+    license = "BSD",
+    keywords = "code",
+    url = "https://github.com/cfin-tools/stormdb.git",
+    packages=['stormdb'],
+    long_description=read('README.md'),
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "Topic :: Utilities",
+        "License :: OSI Approved :: BSD License",
+    ],
+    cmdclass={
+        'clean': CleanCommand,
+    }
+
+)
+

__init__.py stormdb/__init__.py__init__.py renamed to stormdb/__init__.py

@@ -28,6 +28,10 @@ def __init__(self, proj_code, stormdblogin='~/.stormdblogin', username=None, ver
             print 'ERROR: Bad project code?'
             sysexit(-1)
 
+        self.proj_code = proj_code                   
+        self._server = 'http://hyades00.pet.auh.dk/modules/StormDb/extract/'
+        self._wget_cmd = 'wget -qO - test ' + self._server
+
         try: 
             with open(os.path.expanduser(stormdblogin)):
                 if verbose:
@@ -56,10 +60,6 @@ def __init__(self, proj_code, stormdblogin='~/.stormdblogin', username=None, ver
             fout.close()
             os.chmod(os.path.expanduser(stormdblogin), 0400)
 
-        self.proj_code = proj_code                   
-        self._server = 'http://hyades00.pet.auh.dk/modules/StormDb/extract/'
-        self._wget_cmd = 'wget -qO - test ' + self._server
-
     @staticmethod
     def _wget_error_handling(stdout):
         if 'error' in stdout:
@@ -120,32 +120,40 @@ def get_studies(self, subj_id, modality=None, unique=True, verbose=False):
         stud_list = [x for x in stud_list if x]
 
         if modality:
-            for study in stud_list:
+            for ii,study in enumerate(stud_list):
                 url = 'modalities?' + self._login_code + '\\&projectCode=' + self.proj_code + '\\&subjectNo=' + \
                       subj_id + '\\&study=' + study
                 output = self._wget_system_call(url).split('\n')
                 #print output, '==', modality
 
-                for entry in output:              
-                    if entry == modality:
-                        if unique:
-                            return study
-                            ### NB!! This only matches first hit! If subject contains several studies
-                            ### with this modality,
-                            ### only first one is returned... Fix me!
-                        else:
-                            # must re-write code a bit to accommodate the existence of
-                            # several studies containing the desired modality...
-                            print "Error: non-unique modalities not implemented yet!"
-                            sysexit(-1)
+                if modality in output:
+                    if unique:
+                        return study # NB: returns string! Should change to [study] to return list...
+                else:
+                    stud_list[ii] = None
+
+            stud_list = filter(None, stud_list)
+#                for entry in output:              
+#                    if entry == modality:
+#                        if unique:
+#                            return study
+#                            ### NB!! This only matches first hit! If subject contains several studies
+#                            ### with this modality,
+#                            ### only first one is returned... Fix me!
+#                    else:
+#                        stud_list = [x for x in stud_list if x 
+#                        else:
+#                            # must re-write code a bit to accommodate the existence of
+#                            # several studies containing the desired modality...
+#                            print "Error: non-unique modalities not implemented yet!"
+#                            sysexit(-1)
 
             # If we get this far, no studies found with the desired modality    
             if verbose:
                 print "No studies found with the desired modality"
-            return None
+                return None
 
-        else:    
-            return stud_list
+        return stud_list
 
     def get_series(self, subj_id, study, modality, verbose=False):