cp and rename Query from MLDB

Author: Christopher J. Bailey

access.py

@@ -0,0 +1,200 @@
+"""
+=========================
+Methods to interact with the STORM database
+=========================
+
+"""
+# Author: Chris Bailey <cjb@cfin.au.dk>
+#
+# License: BSD (3-clause)
+
+
+import subprocess as subp
+from sys import exit as sysexit
+from getpass import getuser, getpass
+import os
+
+
+class Query():
+    """
+    Query object for communicating with the STORM database
+    """
+
+    def __init__(self, proj_code, stormdblogin='~/.stormdblogin', username=None, verbose=None):
+
+        if os.path.exists('/projects/' + proj_code):
+            pass
+        else:
+            print 'ERROR: Bad project code?'
+            sysexit(-1)
+        
+        try: 
+            with open(os.path.expanduser(stormdblogin)):
+                if verbose:
+                    print 'Reading login credentials from ' + stormdblogin
+                f = open(os.path.expanduser(stormdblogin))
+                self._login_code = f.readline()
+                f.close()
+        except IOError:
+            print 'Login credentials not found, please enter them here'
+            print 'WARNING: This might not work if you\'re in an IDE (e.g. spyder)!'
+            if username:
+                usr = username                
+            else:
+                usr = getuser()
+            
+            prompt = 'User \"%s\", please enter your password: ' % usr
+            pwd = getpass(prompt)
+            
+            url = 'login/username/' + usr + '/password/' + pwd
+            output = self._wget_system_call(url)
+            self._login_code = output
+            #stormdblogin='~/.stormdbdblogin'
+            print "Code generated, writing to %s" % stormdblogin
+            fout = open(os.path.expanduser(stormdblogin), 'w')
+            fout.write(self._login_code)
+            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:
+            print "Something is wrong, database answers as follows (dying...):"
+            print stdout
+            return -1
+            
+        return 0
+
+    def _wget_system_call(self, url, verbose=False):
+        cmd = self._wget_cmd + url
+
+        if verbose:
+            print cmd
+        
+        pipe = subp.Popen(cmd, stdout=subp.PIPE, stderr=subp.PIPE, shell=True)
+        output, stderr = pipe.communicate()
+        #output = subp.call([cmd,opts], shell=True)
+    
+        if self._wget_error_handling(output) < 0:
+            sysexit(-1)        
+    
+        return output
+
+    def get_subjects(self, subj_type='included', verbose=False):
+        
+        if subj_type == 'all':  # Doesn't work yet!
+            scode = 'subjectswithcode'
+        elif subj_type == 'included':
+            scode = 'subjectswithcode'
+        elif subj_type == 'excluded':
+            scode = 'excludedsubjectswithcode'
+        else:
+            scode = 'subjectswithcode'
+
+        url = scode + '?' + self._login_code + '\\&projectCode=' + self.proj_code
+        output = self._wget_system_call(url)
+    
+        # Split at '\n'
+        subj_list = output.split('\n')
+        # Remove any empty entries!
+        subj_list = [x for x in subj_list if x]
+        
+        if verbose:
+            print "Found following subjects:"
+            print subj_list
+            
+        return subj_list
+
+    def get_studies(self, subj_id, modality=None, unique=True, verbose=False):
+        
+        url = 'studies?' + self._login_code + '\\&projectCode=' + self.proj_code + '\\&subjectNo=' + subj_id
+        output = self._wget_system_call(url)
+    
+        # Split at '\n'
+        stud_list = output.split('\n')
+        # Remove any empty entries!
+        stud_list = [x for x in stud_list if x]
+    
+        if modality:
+            for study in 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 we get this far, no studies found with the desired modality    
+            if verbose:
+                print "No studies found with the desired modality"
+            return None
+            
+        else:    
+            return stud_list
+
+    def get_series(self, subj_id, study, modality, verbose=False):
+        
+        url = 'series?' + self._login_code + '\\&projectCode=' + self.proj_code + '\\&subjectNo=' + \
+              subj_id + '\\&study=' + study + '\\&modality=' + modality
+        output = self._wget_system_call(url, verbose=verbose)
+    
+        # Split at '\n'
+        series_list = output.split('\n')
+        # Remove any empty entries!
+        series_list = [x for x in series_list if x]
+    
+        # Return a 2D list with series number (as string) in 1st column and name as 2nd column
+        series_list_2d = [x.split(' ') for x in series_list]
+    
+        if verbose:
+            print "Found following series:"
+            print series_list_2d
+
+        return series_list_2d
+
+    def get_files(self, subj_id, study, modality, series, verbose=False):
+        # NB: Series can be either just the number (1) or number.name (001.VS_1b_1)     
+
+        url = 'files?' + self._login_code + '\\&projectCode=' + self.proj_code + \
+              '\\&subjectNo=' + subj_id + '\\&study=' + study + '\\&modality=' + \
+              modality + '\\&serieNo=' + series
+        output = self._wget_system_call(url)
+    
+        # Split at '\n'
+        file_list = output.split('\n')
+        # Remove any empty entries!
+        file_list = [x for x in file_list if x]
+    
+        if verbose:
+            print "Found following files:"
+            print file_list
+
+        return file_list
+            
+    def __str__(self):
+        print "Print not implemented yet!"
+
+
+if __name__ == '__main__':
+    
+    #test code
+
+    project_code = 'MEG_service'
+    
+    Q = Query(proj_code=project_code)
+    print Q