Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo…

…_queue_sharing

lib/galaxy/security/validate_user_input.py

@@ -9,15 +9,20 @@
 
 log = logging.getLogger( __name__ )
 
-VALID_PUBLICNAME_RE = re.compile( "^[a-z0-9\-]+$" )
-VALID_PUBLICNAME_SUB = re.compile( "[^a-z0-9\-]" )
+# Email validity parameters
+VALID_EMAIL_RE = re.compile( "[^@]+@[^@]+\.[^@]+" )
+EMAIL_MAX_LEN = 255
+
+# Public name validity parameters
 PUBLICNAME_MIN_LEN = 3
 PUBLICNAME_MAX_LEN = 255
-
-#  Basic regular expression to check email validity.
-VALID_EMAIL_RE = re.compile( "[^@]+@[^@]+\.[^@]+" )
+VALID_PUBLICNAME_RE = re.compile( "^[a-z0-9._\-]+$" )
+VALID_PUBLICNAME_SUB = re.compile( "[^a-z0-9._\-]" )
 FILL_CHAR = '-'
 
+# Password validity parameters
+PASSWORD_MIN_LEN = 6
+
 
 def validate_email( trans, email, user=None, check_dup=True ):
     """
@@ -27,9 +32,9 @@ def validate_email( trans, email, user=None, check_dup=True ):
     if user and user.email == email:
         return message
     if not( VALID_EMAIL_RE.match( email ) ):
-        message = "Please enter your real email address."
-    elif len( email ) > 255:
-        message = "Email address exceeds maximum allowable length."
+        message = "The format of the email address is not correct."
+    elif len( email ) > EMAIL_MAX_LEN:
+        message = "Email address cannot be more than %d characters in length." % EMAIL_MAX_LEN
     elif check_dup and trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first():
         message = "User with that email already exists."
     #  If the blacklist is not empty filter out the disposable domains.
@@ -48,13 +53,13 @@ def validate_publicname( trans, publicname, user=None ):
     if user and user.username == publicname:
         return ''
     if len( publicname ) < PUBLICNAME_MIN_LEN:
-        return "Public name must be at least %d characters in length" % ( PUBLICNAME_MIN_LEN )
+        return "Public name must be at least %d characters in length." % ( PUBLICNAME_MIN_LEN )
     if len( publicname ) > PUBLICNAME_MAX_LEN:
-        return "Public name cannot be more than %d characters in length" % ( PUBLICNAME_MAX_LEN )
+        return "Public name cannot be more than %d characters in length." % ( PUBLICNAME_MAX_LEN )
     if not( VALID_PUBLICNAME_RE.match( publicname ) ):
-        return "Public name must contain only lower-case letters, numbers and '-'"
+        return "Public name must contain only lower-case letters, numbers, '.', '_' and '-'."
     if trans.sa_session.query( trans.app.model.User ).filter_by( username=publicname ).first():
-        return "Public name is taken; please choose another"
+        return "Public name is taken; please choose another."
     return ''
 
 
@@ -67,15 +72,15 @@ def transform_publicname( trans, publicname, user=None ):
     elif publicname not in [ 'None', None, '' ]:
         publicname = publicname.lower()
         publicname = re.sub( VALID_PUBLICNAME_SUB, FILL_CHAR, publicname )
-        publicname = publicname.ljust( 4, FILL_CHAR )[:255]
+        publicname = publicname.ljust( PUBLICNAME_MIN_LEN + 1, FILL_CHAR )[:PUBLICNAME_MAX_LEN]
         if not trans.sa_session.query( trans.app.model.User ).filter_by( username=publicname ).first():
             return publicname
     return ''
 
 
 def validate_password( trans, password, confirm ):
-    if len( password ) < 6:
-        return "Use a password of at least 6 characters"
+    if len( password ) < PASSWORD_MIN_LEN:
+        return "Use a password of at least %d characters." % PASSWORD_MIN_LEN
     elif password != confirm:
-        return "Passwords do not match"
+        return "Passwords don't match."
     return ''

lib/galaxy/webapps/galaxy/controllers/mobile.py

@@ -67,7 +67,8 @@ def __login(self, trans, login="", password=""):
         #         kwd['email'] = autoreg[1]
         #         kwd['username'] = autoreg[2]
         #         params = util.Params( kwd )
-        #         message = validate_email( trans, kwd['email'] )
+        #         message = " ".join( [ validate_email( trans, kwd['email'] ),
+        #                               validate_publicname( trans, kwd['username'] ) ] ).rstrip()
         #         if not message:
         #             message, status, user, success = self.__register( trans, 'user', False, **kwd )
         #             if success:

lib/galaxy/webapps/galaxy/controllers/user.py

@@ -530,7 +530,8 @@ def __validate_login( self, trans, **kwd ):
             if autoreg[0]:
                 kwd['email'] = autoreg[1]
                 kwd['username'] = autoreg[2]
-                message = validate_email( trans, kwd['email'] )  # self.__validate( trans, params, email, password, password, username )
+                message = " ".join( [ validate_email( trans, kwd['email'] ),
+                                      validate_publicname( trans, kwd['username'] ) ] ).rstrip()
                 if not message:
                     message, status, user, success = self.__register( trans, 'user', False, **kwd )
                     if success:

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -993,7 +993,7 @@ def import_workflow( self, trans, cntrller='workflow', **kwd ):
                                     myexperiment_target_url=myexperiment_target_url )
 
     @web.expose
-    def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None ):
+    def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None ):
         user = trans.get_user()
         history = trans.get_history()
         if not user:
@@ -1014,7 +1014,9 @@ def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, dat
                 job_ids=job_ids,
                 dataset_ids=dataset_ids,
                 dataset_collection_ids=dataset_collection_ids,
-                workflow_name=workflow_name
+                workflow_name=workflow_name,
+                dataset_names=dataset_names,
+                dataset_collection_names=dataset_collection_names
             )
             # Index page with message
             workflow_id = trans.security.encode_id( stored_workflow.id )

lib/galaxy/workflow/extract.py

@@ -25,8 +25,8 @@
 WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored"
 
 
-def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None ):
-    steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids )
+def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None ):
+    steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids, dataset_names=dataset_names, dataset_collection_names=None )
     # Workflow to populate
     workflow = model.Workflow()
     workflow.name = workflow_name
@@ -52,7 +52,7 @@ def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None,
     return stored
 
 
-def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_collection_ids=None ):
+def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_collection_ids=None, dataset_names=None, dataset_collection_names=None ):
     # Ensure job_ids and dataset_ids are lists (possibly empty)
     if job_ids is None:
         job_ids = []
@@ -79,19 +79,27 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_
     steps_by_job_id = {}
     hid_to_output_pair = {}
     # Input dataset steps
-    for hid in dataset_ids:
+    for i, hid in enumerate( dataset_ids ):
         step = model.WorkflowStep()
         step.type = 'data_input'
-        step.tool_inputs = dict( name="Input Dataset" )
+        if dataset_names:
+            name = dataset_names[i]
+        else:
+            name = "Input Dataset"
+        step.tool_inputs = dict( name=name )
         hid_to_output_pair[ hid ] = ( step, 'output' )
         steps.append( step )
-    for hid in dataset_collection_ids:
+    for i, hid in enumerate( dataset_collection_ids ):
         step = model.WorkflowStep()
         step.type = 'data_collection_input'
         if hid not in summary.collection_types:
             raise exceptions.RequestParameterInvalidException( "hid %s does not appear to be a collection" % hid )
         collection_type = summary.collection_types[ hid ]
-        step.tool_inputs = dict( name="Input Dataset Collection", collection_type=collection_type )
+        if dataset_collection_names:
+            name = dataset_collection_names[i]
+        else:
+            name = "Input Dataset Collection"
+        step.tool_inputs = dict( name=name, collection_type=collection_type )
         hid_to_output_pair[ hid ] = ( step, 'output' )
         steps.append( step )
     # Tool steps

templates/user/info.mako

@@ -9,7 +9,7 @@
 
             function validateString(test_string, type) {
                 var mail_re = /^(([^<>()[\]\\.,;:\s@\"]+(\.[^<>()[\]\\.,;:\s@\"]+)*)|(\".+\"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/;
-                var username_re = /^[a-z0-9\-]{3,255}$/;
+                var username_re = /^[a-z0-9._\-]{3,255}$/;
                 if (type === 'email') {
                     return mail_re.test(test_string);
                 } else if (type === 'username'){
@@ -45,9 +45,9 @@
             original_username = $( '#name_input' ).val();
 
             $( '#login_info' ).bind( 'submit', function( e ) {
-                var error_text_email= 'Please enter your valid email address.';
-                var error_text_email_long= 'Email cannot be more than 255 characters in length.';
-                var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 2.';
+                var error_text_email = 'The format of the email address is not correct.';
+                var error_text_email_long = 'Email address cannot be more than 255 characters in length.';
+                var error_text_username_characters = "Public name must contain only lowercase letters, numbers, '.', '_' and '-'. It also must be between 3 and 255 characters in length.";
                 var email = $( '#email_input' ).val();
                 var name = $( '#name_input' ).val();
                 var validForm = true;
@@ -102,23 +102,23 @@
                         <input type="hidden" id="name_input" name="username" value="${username | h}"/>
                         ${username | h}
                         <div class="toolParamHelp" style="clear: both;">
-                            You cannot change your public name after you have created a repository in this tool shed.
+                            You cannot change your public name after you have created a repository in this Tool Shed.
                         </div>
                     %else:
                         <input type="text" id="name_input" name="username" size="40" value="${username | h}"/>
                         <div class="toolParamHelp" style="clear: both;">
-                            Your public name provides a means of identifying you publicly within this tool shed. Public
+                            Your public name provides a means of identifying you publicly within this Tool Shed. Public
                             names must be at least three characters in length and contain only lower-case letters, numbers,
-                            and the '-' character.  You cannot change your public name after you have created a repository
-                            in this tool shed.
+                            dots, underscores, and dashes ('.', '_', '-').  You cannot change your public name after you have created a repository
+                            in this Tool Shed.
                         </div>
                     %endif
                 %else:
                     <input type="text" id="name_input" name="username" size="40" value="${username | h}"/>
                     <div class="toolParamHelp" style="clear: both;">
                         Your public name is an identifier that will be used to generate addresses for information
                         you share publicly. Public names must be at least three characters in length and contain only lower-case
-                        letters, numbers, and the '-' character.
+                        letters, numbers, dots, underscores, and dashes ('.', '_', '-').
                     </div>
                 %endif
             </div>