Merge pull request #14 from bmatern/master

more embl-ena changes

saddlebags/AlleleSubMainGui.py

@@ -66,9 +66,9 @@ def initialize(self):
 
         # Make a frame for the more-info buttons
         self.moreInfoFrame = Tkinter.Frame(self)
-        Tkinter.Button(self.moreInfoFrame, text='Generate an EMBL-ENA submission', command=lambda: self.openAlleleSubGUI('EMBL')).grid(row=0, column=0)
+        Tkinter.Button(self.moreInfoFrame, text='Begin an EMBL-ENA submission', command=lambda: self.openAlleleSubGUI('EMBL')).grid(row=0, column=0)
         #TODO Enable IMGT
-        Tkinter.Button(self.moreInfoFrame, text='Generate an IPD-IMGT/HLA submission', command=lambda: self.openAlleleSubGUI('IMGT'), state=DISABLED).grid(row=0, column=1)
+        Tkinter.Button(self.moreInfoFrame, text='Begin an IPD-IMGT/HLA submission', command=lambda: self.openAlleleSubGUI('IMGT'), state=DISABLED).grid(row=0, column=1)
         Tkinter.Button(self.moreInfoFrame, text='    How to use this tool     ', command=self.howToUse).grid(row=1, column=0)
         Tkinter.Button(self.moreInfoFrame, text='Contacting and Citing MUMC', command=self.contactInformation).grid(row=1, column=1)
         self.moreInfoFrame.pack()

saddlebags/EmblSubGui.py

@@ -99,7 +99,6 @@ def __init__(self, root):
         self.featureInputGuiObject.pack(expand=True, fill='both') 
         self.featureInputFrame.pack(expand=True, fill='both')
 
-
         # Create  Frame for "Generate Submission" button.
         self.submButtonFrame = Tkinter.Frame(self)
         self.submissionOptionsButton = Tkinter.Button(self.submButtonFrame, text='1) Submission Options', command=self.chooseSubmissionOptions)
@@ -138,7 +137,7 @@ def __init__(self, root):
         self.uploadSubmissionFrame = Tkinter.Frame(self)        
         self.saveSubmissionButton = Tkinter.Button(self.uploadSubmissionFrame, text='4) Save Submission to My Computer', command=self.saveSubmissionFile)
         self.saveSubmissionButton.pack(**button_opt)
-        self.uploadButton = Tkinter.Button(self.uploadSubmissionFrame, text='5) Upload Submission to EMBL', command=self.uploadSubmission)
+        self.uploadButton = Tkinter.Button(self.uploadSubmissionFrame, text='5) Upload Submission to EMBL-ENA', command=self.uploadSubmission)
         self.uploadButton.pack(**button_opt)
         self.exitButton = Tkinter.Button(self.uploadSubmissionFrame, text='Exit', command=self.saveAndExit)
         self.exitButton.pack(**button_opt)
@@ -147,7 +146,7 @@ def __init__(self, root):
         self.pack(expand=True, fill='both')
 
     def chooseSubmissionOptions(self):
-        print ('Opening the EMBL Submission Options Dialog')
+        print ('Opening the EMBL-ENA Submission Options Dialog')
 
         self.disableGUI()
 
@@ -217,7 +216,7 @@ def howToUse(self):
             + 'annotate your exons automatically.\n'
             + '4.) Push [Generate an EMBL-ENA submission]\n'
             + 'button to generate a submission.\n'
-            + '5.) Push [Upload Submission to EMBL]\n'
+            + '5.) Push [Upload Submission to EMBL-ENA]\n'
             + 'to submit the sequence\n'
             + 'using EMBL Webin REST interface\n\n'
 

saddlebags/EmblSubOptionsForm.py

@@ -28,7 +28,7 @@ def __init__(self, root):
         #Tkinter.Frame.__init__(self, root)
         VerticalScrolledFrame.__init__(self, root)
 
-        root.title("Choose EMBL Submission Options")
+        root.title("Choose EMBL-ENA Submission Options")
         self.parent = root
 
         # Assign the icon of this sub-window.
@@ -90,20 +90,20 @@ def __init__(self, root):
         self.testProductionFrame = Tkinter.Frame(self.interior)
 
         self.testProductionInstrText = Tkinter.StringVar()
-        self.testProductionInstrText.set('\nBy default, you submit to the EMBL test servers,\n'
+        self.testProductionInstrText.set('\nBy default, you submit to the EMBL-ENA test servers,\n'
             + 'where submissions are regularly deleted.\n'
-            + 'change this option if you want to submit to the live EMBL environment.\n'
+            + 'change this option if you want to submit to the live environment.\n'
             + 'Login Credentials will not be stored, but they will be sent\n'
-            + 'to EMBL via REST during allele submission.\n'
+            + 'to EMBL-ENA via REST during allele submission.\n'
             )
         self.alleleInstrLabel = Tkinter.Label(self.testProductionFrame, width=70, height=7, textvariable=self.testProductionInstrText).pack()#.grid(row=2, column=0)
 
         # 1 = Test.  0 = Production/live server
         self.chooseTestServersIntVar = IntVar()
         self.chooseTestServersIntVar.set(int(getConfigurationValue('test_submission')))
 
-        Radiobutton(self.testProductionFrame, text="Submit to EMBL TEST / DEMO environment.", variable=self.chooseTestServersIntVar, value=1).pack()
-        Radiobutton(self.testProductionFrame, text="Submit to EMBL LIVE / PROD environment.", variable=self.chooseTestServersIntVar, value=0).pack()
+        Radiobutton(self.testProductionFrame, text="Submit to EMBL-ENA TEST / DEMO environment.", variable=self.chooseTestServersIntVar, value=1).pack()
+        Radiobutton(self.testProductionFrame, text="Submit to EMBL-ENA LIVE / PROD environment.", variable=self.chooseTestServersIntVar, value=0).pack()
 
         self.testProductionFrame.pack()
 
@@ -129,7 +129,7 @@ def __init__(self, root):
 
         # TODO: Better instructions for how a user will use this?
         self.analysisMetadataInstrText = Tkinter.StringVar()
-        self.analysisMetadataInstrText.set('\nEMBL will store the sequence in an "Analysis" object.\n'
+        self.analysisMetadataInstrText.set('\nEMBL-ENA will store the sequence in an "Analysis" object.\n'
                 + 'You must specify an analysis Alias, Title, and\n'
                 + 'Description for every submitted sequence.\n'
                 + 'The Alias must be unique.\n'
@@ -166,15 +166,16 @@ def __init__(self, root):
         self.projectDetailsFrame = Tkinter.Frame(self.interior)
 
         self.alleleInstrText = Tkinter.StringVar()
-        self.alleleInstrText.set('\nEMBL requires that submissions are assigned to a Study/Project.\n'
+        self.alleleInstrText.set('\nEMBL-ENA requires that submissions are assigned to a Study/Project.\n'
             + 'You must either:\n\n'
-            + '1.) Provide an existing EMBL study/project accession #.\n'
+            + '1.) Provide an existing EMBL-ENA study/project accession #.\n'
             + 'This was provided in a previous submission, or you can see a list of\n'
             + 'your projects by logging into EMBL Webin. (ex. \'PRJEB01234\')\n'
             + '\n'
-            + '2.) Specify metadata for a new study at EMBL. Provide an Identifier,\n'
-            + 'Title, and short Abstract for the new Study, and I will create\n'
-            + 'it automatically. Study Identifier must be Unique.'
+            + '2.) Specify metadata for a new study at EMBL-ENA.\n'
+            + 'Provide an Identifier, Title, and short Abstract for the new Study,\n'
+            + 'and I will create it automatically.\n'
+            + 'Study Identifier must be Unique.'
             )
         self.alleleInstrLabel = Tkinter.Label(self.projectDetailsFrame, width=70, height=12, textvariable=self.alleleInstrText).pack()#.grid(row=2, column=0)
 
@@ -267,7 +268,7 @@ def loadOptions(self):
             elif (str(getConfigurationValue('choose_project')) == '2'):
                 self.chooseProjectIntVar.set(2)
             else:
-                raise Exception('Error loading EMBL submission options. Invalid Project choice:' + str(getConfigurationValue('choose_project')))
+                raise Exception('Error loading EMBL-ENA submission options. Invalid Project choice:' + str(getConfigurationValue('choose_project')))
 
         if getConfigurationValue('study_accession') is not None:
             self.inputStudyAccession.set(getConfigurationValue('study_accession'))