[galaxy-dev] [hg] galaxy 2453: Fixes and functional tests for uploading direc...

16 Jun 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/e899101e63d1
changeset: 2453:e899101e63d1
user:      Greg Von Kuster greg@bx.psu.edu
date:      Tue Jun 16 09:55:15 2009 -0400
description:
Fixes and functional tests for uploading directories of files from both the Admin view and the Libraries view ( requires new config setting ).
In addition to the config setting "library_import_dir" for the Admin view, the new config setting "user_library_import_dir" for the Libraries view will allow non-amin users to upload a directory of files.
The configured directory must contain sub-directories named the same as the non-admin user's Galaxy login ( email ).  The non-admin user is restricted to uploading files or sub-directories of files contained in their directoy.
10 file(s) affected in this change:
lib/galaxy/config.py
lib/galaxy/web/controllers/library_dataset.py
templates/admin/library/new_dataset.mako
templates/library/new_dataset.mako
test-data/users/test1@bx.psu.edu/1.fasta
test-data/users/test3@bx.psu.edu/run1/2.fasta
test/base/twilltestcase.py
test/functional/__init__.py
test/functional/test_security_and_libraries.py
universe_wsgi.ini.sample
diffs (1056 lines):
diff -r c44567359a03 -r e899101e63d1 lib/galaxy/config.py

--- a/lib/galaxy/config.py	Fri Jun 12 09:56:23 2009 -0400
+++ b/lib/galaxy/config.py	Tue Jun 16 09:55:15 2009 -0400
@@ -81,6 +81,9 @@
         self.library_import_dir = kwargs.get( 'library_import_dir', None )
         if self.library_import_dir is not None and not os.path.exists( self.library_import_dir ):
             raise ConfigurationError( "library_import_dir specified in config (%s) does not exist" % self.library_import_dir )
+        self.user_library_import_dir = kwargs.get( 'user_library_import_dir', None )
+        if self.user_library_import_dir is not None and not os.path.exists( self.user_library_import_dir ):
+            raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir )
         # Configuration options for taking advantage of nginx features
         self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
         self.nginx_upload_location = kwargs.get( 'nginx_upload_store', False )
diff -r c44567359a03 -r e899101e63d1 lib/galaxy/web/controllers/library_dataset.py
--- a/lib/galaxy/web/controllers/library_dataset.py	Fri Jun 12 09:56:23 2009 -0400
+++ b/lib/galaxy/web/controllers/library_dataset.py	Tue Jun 16 09:55:15 2009 -0400
@@ -1,4 +1,4 @@
-import os, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile
+import os, os.path, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile
 from galaxy.web.base.controller import *
 from galaxy import util, jobs
 from galaxy.datatypes import sniff
@@ -193,7 +193,7 @@
         file_format = params.get( 'file_format', 'auto' )
         data_file = params.get( 'file_data', '' )
         url_paste = params.get( 'url_paste', '' )
-        server_dir = params.get( 'server_dir', None )
+        server_dir = util.restore_text( params.get( 'server_dir', '' ) )
         if replace_dataset is not None:
             replace_id = replace_dataset.id
         else:
@@ -222,10 +222,17 @@
         elif upload_option == 'upload_directory':
             if server_dir in [ None, 'None', '' ]:
                 err_redirect = True
-                if trans.app.config.library_import_dir:
-                    msg = 'Select a server directory'
-                else:
-                    msg = '"library_import_dir" is not defined in the Galaxy configuration file'
+            # See if our request is from the Admin view or the Libraries view
+            if trans.request.browser_url.find( 'admin' ) >= 0:
+                import_dir = trans.app.config.library_import_dir
+                import_dir_desc = 'library_import_dir'
+            else:
+                import_dir = trans.app.config.user_library_import_dir
+                import_dir_desc = 'user_library_import_dir'
+            if import_dir:
+                msg = 'Select a directory'
+            else:
+                msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc
         if err_redirect:
             trans.response.send_redirect( web.url_for( controller=controller,
                                                        action='library_dataset_dataset_association',
@@ -264,7 +271,7 @@
                 created_ldda_ids = str( created_ldda.id )
             except Exception, e:
                 log.exception( 'exception in upload_dataset using file_name %s: %s' % ( str( file_name ), str( e ) ) )
-                return self.upload_empty( trans, controller, library_id, "Error:", str( e ) )
+                return self.upload_empty( trans, controller, library_id, folder_id, "Error:", str( e ) )
         elif url_paste not in [ None, "" ]:
             if url_paste.lower().find( 'http://' ) >= 0 or url_paste.lower().find( 'ftp://' ) >= 0:
                 url_paste = url_paste.replace( '\r', '' ).split( '\n' )
@@ -292,7 +299,7 @@
                             created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( created_ldda.id ) )
                         except Exception, e:
                             log.exception( 'exception in upload_dataset using url_paste %s' % str( e ) )
-                            return self.upload_empty( trans, controller, library_id, "Error:", str( e ) )
+                            return self.upload_empty( trans, controller, library_id, folder_id, "Error:", str( e ) )
             else:
                 is_valid = False
                 for line in url_paste:
@@ -318,13 +325,36 @@
                         created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( created_ldda.id ) )
                     except Exception, e:
                         log.exception( 'exception in add_file using StringIO.StringIO( url_paste ) %s' % str( e ) )
-                        return self.upload_empty( trans, controller, library_id, "Error:", str( e ) )
+                        return self.upload_empty( trans, controller, library_id, folder_id, "Error:", str( e ) )
         elif server_dir not in [ None, "", "None" ]:
-            full_dir = os.path.join( trans.app.config.library_import_dir, server_dir )
+            # See if our request is from the Admin view or the Libraries view
+            if trans.request.browser_url.find( 'admin' ) >= 0:
+                import_dir = trans.app.config.library_import_dir
+                import_dir_desc = 'library_import_dir'
+                full_dir = os.path.join( import_dir, server_dir )
+            else:
+                imrport_dir = trans.app.config.user_library_import_dir
+                import_dir_desc = 'user_library_import_dir'
+                # From the Libraries view, users are restricted to the directory named the same as
+                # their email within the configured user_library_import_dir.  If this directory contains
+                # sub-directories, server_dir will be the name of the selected sub-directory.  Otherwise
+                # server_dir will be the user's email address.
+                if server_dir == trans.user.email:
+                    full_dir = os.path.join( import_dir, server_dir )
+                else:
+                    full_dir = os.path.join( import_dir, trans.user.email, server_dir )
+            files = []
             try:
-                files = os.listdir( full_dir )
-            except:
-                log.debug( "Unable to get file list for configured library_import_dir %s" % full_dir )
+                for entry in os.listdir( full_dir ):
+                    # Only import regular files
+                    if os.path.isfile( os.path.join( full_dir, entry ) ):
+                        files.append( entry )
+            except Exception, e:
+                msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) )
+                return self.upload_empty( trans, controller, library_id, folder_id, "Error:", msg )
+            if not files:
+                msg = "The directory '%s' contains no valid files" % full_dir
+                return self.upload_empty( trans, controller, library_id, folder_id, "Error:", msg )
             for file in files:
                 full_file = os.path.join( full_dir, file )
                 if not os.path.isfile( full_file ):
@@ -346,7 +376,7 @@
                     created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( created_ldda.id ) )
                 except Exception, e:
                     log.exception( 'exception in add_file using server_dir %s' % str( e ) )
-                    return self.upload_empty( trans, controller, library_id, "Error:", str( e ) )
+                    return self.upload_empty( trans, controller, library_id, folder_id, "Error:", str( e ) )
         if created_ldda_ids:
             created_ldda_ids = created_ldda_ids.lstrip( ',' )
             return created_ldda_ids
@@ -425,11 +455,12 @@
         if chunk is None:
             temp.close()
         return False
-    def upload_empty( self, trans, controller, library_id, err_code, err_msg ):
+    def upload_empty( self, trans, controller, library_id, folder_id, err_code, err_msg ):
         msg = err_code + err_msg
         return trans.response.send_redirect( web.url_for( controller=controller,
-                                                          action='browse_library',
-                                                          id=library_id,
+                                                          action='library_dataset_dataset_association',
+                                                          library_id=library_id,
+                                                          folder_id=folder_id,
                                                           msg=util.sanitize_text( msg ),
                                                           messagetype='error' ) )
 class BadFileException( Exception ):
diff -r c44567359a03 -r e899101e63d1 templates/admin/library/new_dataset.mako
--- a/templates/admin/library/new_dataset.mako	Fri Jun 12 09:56:23 2009 -0400
+++ b/templates/admin/library/new_dataset.mako	Tue Jun 16 09:55:15 2009 -0400
@@ -2,13 +2,15 @@
 <%namespace file="/message.mako" import="render_msg" />
 <%namespace file="/admin/library/common.mako" import="render_available_templates" />
-<% import os %>
+<% import os, os.path %>
<b>Create new library datasets</b>
 <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">&#9660;</a>
 <div popupmenu="upload-librarydataset--popup">
     <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
-    <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
+    %if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ):
+        <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
+    %endif
     <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
 </div>
 <br/><br/>
@@ -26,135 +28,149 @@
     <div class="toolForm" id="new_dataset">
         %if upload_option == 'upload_file':
             <div class="toolFormTitle">Upload files</div>
-        %elif upload_option == 'upload_directory':
+        %else:
             <div class="toolFormTitle">Upload a directory of files</div>
         %endif
-        %if upload_option == 'upload_directory' and not trans.app.config.library_import_dir:
-            <p/>
-            "library_import_dir" is not defined in the Galaxy configuration file
-            <p/>
-        %else:
-            <div class="toolFormBody">
-                <form name="tool_form" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id )}" enctype="multipart/form-data" method="post">
-                    <input type="hidden" name="folder_id" value="${folder_id}"/>
-                    <input type="hidden" name="upload_option" value="${upload_option}"/>
-                    %if replace_dataset:
-                        <input type="hidden" name="replace_id" value="${replace_dataset.id}"/>
-                        <div class="form-row">
-                            You are currently selecting a new file to replace '<a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'.
-                            <div style="clear: both"></div>
-                        </div>
-                    %endif
-                    %if upload_option == 'upload_file':
-                        <div class="form-row">
-                            <label>File:</label>
-                            <div style="float: left; width: 250px; margin-right: 10px;">
-                                <input type="file" name="file_data"/>
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                        <div class="form-row">
-                            <label>URL/Text:</label>
-                            <div style="float: left; width: 250px; margin-right: 10px;">
-                                <textarea name="url_paste" rows="5" cols="35"></textarea>
-                            </div>
-                            <div class="toolParamHelp" style="clear: both;">
-                                Specify a list of URLs (one per line) or paste the contents of a file.
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                    %elif upload_option == 'upload_directory':
-                        <div class="form-row">
-                            <label>Server Directory</label>
-                            <div style="float: left; width: 250px; margin-right: 10px;">
-                                <select name="server_dir">
-                                    <option>None</option>
-                                    %for dir in os.listdir( trans.app.config.library_import_dir ):
-                                        <option>${dir}</option>
-                                    %endfor
-                                </select>
-                            </div>
-                            <div class="toolParamHelp" style="clear: both;">
-                                Upload all files in a subdirectory of <strong>${trans.app.config.library_import_dir}</strong> on the Galaxy server.
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                    %endif
+        <div class="toolFormBody">
+            <form name="tool_form" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id )}" enctype="multipart/form-data" method="post">
+                <input type="hidden" name="folder_id" value="${folder_id}"/>
+                <input type="hidden" name="upload_option" value="${upload_option}"/>
+                %if replace_dataset:
+                    <input type="hidden" name="replace_id" value="${replace_dataset.id}"/>
                     <div class="form-row">
-                        <label>Convert spaces to tabs:</label>
+                        You are currently selecting a new file to replace '<a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'.
+                        <div style="clear: both"></div>
+                    </div>
+                %endif
+                %if upload_option == 'upload_file':
+                    <div class="form-row">
+                        <label>File:</label>
                         <div style="float: left; width: 250px; margin-right: 10px;">
-                            <div>
-                                <input type="checkbox" name="space_to_tab" value="Yes"/>Yes
-                            </div>
-                        </div>
-                        <div class="toolParamHelp" style="clear: both;">
-                            Use this option if you are manually entering intervals.
+                            <input type="file" name="file_data"/>
                         </div>
                         <div style="clear: both"></div>
                     </div>
                     <div class="form-row">
-                        <label>File Format:</label>
+                        <label>URL/Text:</label>
                         <div style="float: left; width: 250px; margin-right: 10px;">
-                            <select name="file_format">
-                                <option value="auto" selected>Auto-detect</option>
-                                %for file_format in file_formats:
-                                    <option value="${file_format}">${file_format}</option>
-                                %endfor
-                            </select>
+                            <textarea name="url_paste" rows="5" cols="35"></textarea>
+                        </div>
+                        <div class="toolParamHelp" style="clear: both;">
+                            Specify a list of URLs (one per line) or paste the contents of a file.
                         </div>
                         <div style="clear: both"></div>
                     </div>
+                %elif upload_option == 'upload_directory':
                     <div class="form-row">
-                        <label>Genome:</label>
+                        <%
+                            # See if we have any contained sub-directories, if not the only option
+                            # in the server_dir select list will be library_import_dir
+                            contains_directories = False
+                            for entry in os.listdir( trans.app.config.library_import_dir ):
+                                if os.path.isdir( os.path.join( trans.app.config.library_import_dir, entry ) ):
+                                    contains_directories = True
+                                    break
+                        %>
+                        <label>Server Directory</label>
                         <div style="float: left; width: 250px; margin-right: 10px;">
-                            <select name="dbkey">
-                                %for dbkey in dbkeys:
-                                    %if dbkey[1] == last_used_build:
-                                        <option value="${dbkey[1]}" selected>${dbkey[0]}</option>
-                                    %else:
-                                        <option value="${dbkey[1]}">${dbkey[0]}</option>
-                                    %endif
-                                %endfor
+                            <select name="server_dir">
+                                %if contains_directories:
+                                    <option>None</option>
+                                    %for entry in os.listdir( trans.app.config.library_import_dir ):
+                                        ## Do not include entries that are not directories
+                                        %if os.path.isdir( os.path.join( trans.app.config.library_import_dir, entry ) ):
+                                            <option>${entry}</option>
+                                        %endif
+                                    %endfor
+                                %else:
+                                    <option>${trans.app.config.library_import_dir}</option>
+                                %endif
                             </select>
+                        </div>
+                        <div class="toolParamHelp" style="clear: both;">
+                            %if contains_directories:
+                                Upload all files in a sub-directory of <strong>${trans.app.config.library_import_dir}</strong> on the Galaxy server.
+                            %else:
+                                Upload all files in <strong>${trans.app.config.library_import_dir}</strong> on the Galaxy server.
+                            %endif
                         </div>
                         <div style="clear: both"></div>
                     </div>
-                    <div class="form-row">
-                        <label>Message:</label>
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            <textarea name="message" rows="3" cols="35"></textarea>
-                        </div>
-                        <div class="toolParamHelp" style="clear: both;">
-                            This information will be displayed in the "Information" column for this dataset in the library browser
-                        </div>
-                        <div style="clear: both"></div>
-                    </div>
-                    <div class="form-row">
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            <label>Restrict dataset access to specific roles:</label>
-                            <select name="roles" multiple="true" size="5">
-                                %for role in roles:
-                                    <option value="${role.id}">${role.name}</option>
-                                %endfor
-                            </select>
-                        </div>
-                        <div class="toolParamHelp" style="clear: both;">
-                            Multi-select list - hold the appropriate key while clicking to select multiple roles.  More restrictions can be applied after the upload is complete.  Selecting no roles makes a dataset public.
+                %endif
+                <div class="form-row">
+                    <label>Convert spaces to tabs:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <div>
+                            <input type="checkbox" name="space_to_tab" value="Yes"/>Yes
                         </div>
                     </div>
+                    <div class="toolParamHelp" style="clear: both;">
+                        Use this option if you are manually entering intervals.
+                    </div>
                     <div style="clear: both"></div>
-                    <% folder = trans.app.model.LibraryFolder.get( folder_id ) %>
-                    %if folder.library_folder_info_template_associations:
-                        ${render_available_templates( folder, library_id, restrict=True, upload=True )}
-                    %else:
-                        ${render_available_templates( folder, library_id, restrict=False, upload=True )}
-                    %endif
-                    <div class="form-row">
-                        <input type="submit" class="primary-button" name="new_dataset_button" value="Upload to library"/>
+                </div>
+                <div class="form-row">
+                    <label>File Format:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <select name="file_format">
+                            <option value="auto" selected>Auto-detect</option>
+                            %for file_format in file_formats:
+                                <option value="${file_format}">${file_format}</option>
+                            %endfor
+                        </select>
                     </div>
-                </form>
-            </div>
-        %endif
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Genome:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <select name="dbkey">
+                            %for dbkey in dbkeys:
+                                %if dbkey[1] == last_used_build:
+                                    <option value="${dbkey[1]}" selected>${dbkey[0]}</option>
+                                %else:
+                                    <option value="${dbkey[1]}">${dbkey[0]}</option>
+                                %endif
+                            %endfor
+                        </select>
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Message:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <textarea name="message" rows="3" cols="35"></textarea>
+                    </div>
+                    <div class="toolParamHelp" style="clear: both;">
+                        This information will be displayed in the "Information" column for this dataset in the library browser
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <label>Restrict dataset access to specific roles:</label>
+                        <select name="roles" multiple="true" size="5">
+                            %for role in roles:
+                                <option value="${role.id}">${role.name}</option>
+                            %endfor
+                        </select>
+                    </div>
+                    <div class="toolParamHelp" style="clear: both;">
+                        Multi-select list - hold the appropriate key while clicking to select multiple roles.  More restrictions can be applied after the upload is complete.  Selecting no roles makes a dataset public.
+                    </div>
+                </div>
+                <div style="clear: both"></div>
+                <% folder = trans.app.model.LibraryFolder.get( folder_id ) %>
+                %if folder.library_folder_info_template_associations:
+                    ${render_available_templates( folder, library_id, restrict=True, upload=True )}
+                %else:
+                    ${render_available_templates( folder, library_id, restrict=False, upload=True )}
+                %endif
+                <div class="form-row">
+                    <input type="submit" class="primary-button" name="new_dataset_button" value="Upload to library"/>
+                </div>
+            </form>
+        </div>
     </div>
 %elif upload_option == 'import_from_history':
     <div class="toolForm">
diff -r c44567359a03 -r e899101e63d1 templates/library/new_dataset.mako
--- a/templates/library/new_dataset.mako	Fri Jun 12 09:56:23 2009 -0400
+++ b/templates/library/new_dataset.mako	Tue Jun 16 09:55:15 2009 -0400
@@ -2,13 +2,15 @@
 <%namespace file="/message.mako" import="render_msg" />
 <%namespace file="/library/common.mako" import="render_available_templates" />
-<% import os %>
+<% import os, os.path %>
<b>Create new library datasets</b>
 <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">&#9660;</a>
 <div popupmenu="upload-librarydataset--popup">
     <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a>
-    <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
+    %if trans.app.config.user_library_import_dir and os.path.exists( os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) ):
+        <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a>
+    %endif
     <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a>
 </div>
 <br/><br/>
@@ -31,135 +33,153 @@
     <div class="toolForm" id="new_dataset">
         %if upload_option == 'upload_file':
             <div class="toolFormTitle">Upload files</div>
-        %elif upload_option == 'upload_directory':
+        %else:
             <div class="toolFormTitle">Upload a directory of files</div>
         %endif
-        %if upload_option == 'upload_directory' and not trans.app.config.library_import_dir:
-            <p/>
-            "library_import_dir" is not defined in the Galaxy configuration file
-            <p/>
-        %else:
-            <div class="toolFormBody">
-                <form name="tool_form" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id )}" enctype="multipart/form-data" method="post">
-                    <input type="hidden" name="folder_id" value="${folder_id}"/>
-                    <input type="hidden" name="upload_option" value="${upload_option}"/>
-                    %if replace_dataset:
-                        <input type="hidden" name="replace_id" value="${replace_dataset.id}"/>
-                        <div class="form-row">
-                            You are currently selecting a new file to replace '<a href="${h.url_for( controller='library', action='library_dataset', id=replace_dataset.id )}">${replace_dataset.name}</a>'.
-                            <div style="clear: both"></div>
-                        </div>
-                    %endif
-                    %if upload_option == 'upload_file':
-                        <div class="form-row">
-                            <label>File:</label>
-                            <div style="float: left; width: 250px; margin-right: 10px;">
-                                <input type="file" name="file_data"/>
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                        <div class="form-row">
-                            <label>URL/Text:</label>
-                            <div style="float: left; width: 250px; margin-right: 10px;">
-                                <textarea name="url_paste" rows="5" cols="35"></textarea>
-                            </div>
-                            <div class="toolParamHelp" style="clear: both;">
-                                Specify a list of URLs (one per line) or paste the contents of a file.
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                    %elif upload_option == 'upload_directory':
-                        <div class="form-row">
-                            <label>Server Directory</label>
-                            <div style="float: left; width: 250px; margin-right: 10px;">
-                                <select name="server_dir">
-                                    <option>None</option>
-                                    %for dir in os.listdir( trans.app.config.library_import_dir ):
-                                        <option>${dir}</option>
-                                    %endfor
-                                </select>
-                            </div>
-                            <div class="toolParamHelp" style="clear: both;">
-                                Upload all files in a subdirectory of <strong>${trans.app.config.library_import_dir}</strong> on the Galaxy server.
-                            </div>
-                            <div style="clear: both"></div>
-                        </div>
-                    %endif
+        <div class="toolFormBody">
+            <form name="tool_form" action="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id )}" enctype="multipart/form-data" method="post">
+                <input type="hidden" name="folder_id" value="${folder_id}"/>
+                <input type="hidden" name="upload_option" value="${upload_option}"/>
+                %if replace_dataset:
+                    <input type="hidden" name="replace_id" value="${replace_dataset.id}"/>
                     <div class="form-row">
-                        <label>Convert spaces to tabs:</label>
+                        You are currently selecting a new file to replace '<a href="${h.url_for( controller='library', action='library_dataset', id=replace_dataset.id )}">${replace_dataset.name}</a>'.
+                        <div style="clear: both"></div>
+                    </div>
+                %endif
+                %if upload_option == 'upload_file':
+                    <div class="form-row">
+                        <label>File:</label>
                         <div style="float: left; width: 250px; margin-right: 10px;">
-                            <div>
-                                <input type="checkbox" name="space_to_tab" value="Yes"/>Yes
-                            </div>
-                        </div>
-                        <div class="toolParamHelp" style="clear: both;">
-                            Use this option if you are manually entering intervals.
+                            <input type="file" name="file_data"/>
                         </div>
                         <div style="clear: both"></div>
                     </div>
                     <div class="form-row">
-                        <label>File Format:</label>
+                        <label>URL/Text:</label>
                         <div style="float: left; width: 250px; margin-right: 10px;">
-                            <select name="file_format">
-                                <option value="auto" selected>Auto-detect</option>
-                                %for file_format in file_formats:
-                                    <option value="${file_format}">${file_format}</option>
-                                %endfor
-                            </select>
+                            <textarea name="url_paste" rows="5" cols="35"></textarea>
+                        </div>
+                        <div class="toolParamHelp" style="clear: both;">
+                            Specify a list of URLs (one per line) or paste the contents of a file.
                         </div>
                         <div style="clear: both"></div>
                     </div>
+                %elif upload_option == 'upload_directory':
                     <div class="form-row">
-                        <label>Genome:</label>
+                        <%
+                            # Directories of files from the Libraries view are restricted to a
+                            # sub-directory named the same as the current user's email address
+                            # contained within the configured setting for user_library_import_dir
+                            user_library_import_dir = os.path.join( trans.app.config.user_library_import_dir, trans.user.email )
+                            # See if we have any contained sub-directories, if not the only option
+                            # in the server_dir select list will be user_library_import_dir
+                            contains_directories = False
+                            for entry in os.listdir( user_library_import_dir ):
+                                if os.path.isdir( os.path.join( user_library_import_dir, entry ) ):
+                                    contains_directories = True
+                                    break
+                        %>
+                        <label>Server Directory</label>
                         <div style="float: left; width: 250px; margin-right: 10px;">
-                            <select name="dbkey">
-                                %for dbkey in dbkeys:
-                                    %if dbkey[1] == last_used_build:
-                                        <option value="${dbkey[1]}" selected>${dbkey[0]}</option>
-                                    %else:
-                                        <option value="${dbkey[1]}">${dbkey[0]}</option>
-                                    %endif
-                                %endfor
+                            <select name="server_dir">
+                                %if contains_directories:
+                                    <option>None</option>
+                                    %for entry in os.listdir( user_library_import_dir ):
+                                        ## Do not include entries that are not directories
+                                        %if os.path.isdir( os.path.join( user_library_import_dir, entry ) ):
+                                            <option>${entry}</option>
+                                        %endif
+                                    %endfor
+                                %else:
+                                    <option>${trans.user.email}</option>
+                                %endif
                             </select>
+                        </div>
+                        <div class="toolParamHelp" style="clear: both;">
+                            %if contains_directories:
+                                Upload all files in a subdirectory of <strong>${user_library_import_dir}}</strong> on the Galaxy server.
+                            %else:
+                                Upload all files in <strong>${user_library_import_dir}}</strong> on the Galaxy server.
+                            %endif
                         </div>
                         <div style="clear: both"></div>
                     </div>
-                    <div class="form-row">
-                        <label>Message:</label>
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            <textarea name="message" rows="3" cols="35"></textarea>
-                        </div>
-                        <div class="toolParamHelp" style="clear: both;">
-                            This information will be displayed in the "Information" column for this dataset in the library browser
-                        </div>
-                        <div style="clear: both"></div>
-                    </div>
-                    <div class="form-row">
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            <label>Restrict dataset access to specific roles:</label>
-                            <select name="roles" multiple="true" size="5">
-                                %for role in roles:
-                                    <option value="${role.id}">${role.name}</option>
-                                %endfor
-                            </select>
-                        </div>
-                        <div class="toolParamHelp" style="clear: both;">
-                            Multi-select list - hold the appropriate key while clicking to select multiple roles.  More restrictions can be applied after the upload is complete.  Selecting no roles makes a dataset public.
+                %endif
+                <div class="form-row">
+                    <label>Convert spaces to tabs:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <div>
+                            <input type="checkbox" name="space_to_tab" value="Yes"/>Yes
                         </div>
                     </div>
+                    <div class="toolParamHelp" style="clear: both;">
+                        Use this option if you are manually entering intervals.
+                    </div>
                     <div style="clear: both"></div>
-                    <% folder = trans.app.model.LibraryFolder.get( folder_id ) %>
-                    %if folder.library_folder_info_template_associations:
-                        ${render_available_templates( folder, library_id, restrict=True, upload=True )}
-                    %else:
-                        ${render_available_templates( folder, library_id, restrict=False, upload=True )}
-                    %endif
-                    <div class="form-row">
-                        <input type="submit" class="primary-button" name="new_dataset_button" value="Upload to library"/>
+                </div>
+                <div class="form-row">
+                    <label>File Format:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <select name="file_format">
+                            <option value="auto" selected>Auto-detect</option>
+                            %for file_format in file_formats:
+                                <option value="${file_format}">${file_format}</option>
+                            %endfor
+                        </select>
                     </div>
-                </form>
-            </div>
-        %endif
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Genome:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <select name="dbkey">
+                            %for dbkey in dbkeys:
+                                %if dbkey[1] == last_used_build:
+                                    <option value="${dbkey[1]}" selected>${dbkey[0]}</option>
+                                %else:
+                                    <option value="${dbkey[1]}">${dbkey[0]}</option>
+                                %endif
+                            %endfor
+                        </select>
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Message:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <textarea name="message" rows="3" cols="35"></textarea>
+                    </div>
+                    <div class="toolParamHelp" style="clear: both;">
+                        This information will be displayed in the "Information" column for this dataset in the library browser
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <label>Restrict dataset access to specific roles:</label>
+                        <select name="roles" multiple="true" size="5">
+                            %for role in roles:
+                                <option value="${role.id}">${role.name}</option>
+                            %endfor
+                        </select>
+                    </div>
+                    <div class="toolParamHelp" style="clear: both;">
+                        Multi-select list - hold the appropriate key while clicking to select multiple roles.  More restrictions can be applied after the upload is complete.  Selecting no roles makes a dataset public.
+                    </div>
+                </div>
+                <div style="clear: both"></div>
+                <% folder = trans.app.model.LibraryFolder.get( folder_id ) %>
+                %if folder.library_folder_info_template_associations:
+                    ${render_available_templates( folder, library_id, restrict=True, upload=True )}
+                %else:
+                    ${render_available_templates( folder, library_id, restrict=False, upload=True )}
+                %endif
+                <div class="form-row">
+                    <input type="submit" class="primary-button" name="new_dataset_button" value="Upload to library"/>
+                </div>
+            </form>
+        </div>
     </div>
 %elif upload_option == 'import_from_history':
     <div class="toolForm">
diff -r c44567359a03 -r e899101e63d1 test-data/users/test1@bx.psu.edu/1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/users/test1@bx.psu.edu/1.fasta	Tue Jun 16 09:55:15 2009 -0400
@@ -0,0 +1,2 @@
+>hg17
+gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaaactttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa----------------------------------------------
 ----ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaactattcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctccctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccgtggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttccc
 aaataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatcttcataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacagattgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcagaataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcggggtcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagtaggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaaggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgcaatggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggtggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactgttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagacccttatcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccctcaccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacagtactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtactctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaaatattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagcatgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcatta
 ccaaacccggcagtgg-caggctcggttcaccaacgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGGAGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg-------------------ggttcctagcccattgctattcctt----accagctgtggattctaaggaaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaacaaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATACAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACATCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGACCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGAGCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTCTCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGGAGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGT
 CCAGGGCCGTCGG-----------GGCCGAGTCCCGATTCGCTCCCACCCCGAAGCCGCGCCAGGACCAACGAGGGCGCAGCCGTATGCCCCAGCCCGCTCCGCGGAGCCCCTCACAGCCAcccccgccccgaccgcgccccgcgcggcTCGAAGCACCTTCCCAAGGGGCTGGTCCTTGC----------GCCATAGTCGCGCCGGAGCCTCTGGAGGGACATCAAGGATTTCTC-GCTCCTACCAGCCACCCCCAAATTTTTGGGAGGTACCCAAGGGTGCGCGCGTGGCTCCTGGCGCGCCGAGGCCCTCCCTCGAGGCCCCGCGAGGTGCACACTGC---------GGGCCCAGGGCTAGCAGCCGCCCGGCACGTCGCTACCCTGAGGGGCGGGGCGGGAGCTGGCGCTAGAAATGCGCCGGGGCCTGCGGGGCAGTTGCGCAAGTTGTGATCGGGCCGCTATAAGAGGGGCGGGCAGGCATGGAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCC-CGGCGCGCTCCTTCCTCCTTCTCTGCTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATCCCGGGGAAACTGAGTCAGG-AGGGATGCAGGGCGGATGGCTTAGTTCTGGACTATGATAGCTTTGTACCGAG-----TTCTAGCCAGATAGAAGGTTACCGGGAGCTGGGGAGCGTTGGATTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCA------GGACCTTGCAGAACCAGCCAGGTCCCTGGGAGACTGTCAGACCCACCAACCTGGTGGCATTCGCAGAGCTGAGATGCATTGGAAATTGCCTTGGGCACATCCCCAAAGATCAGGATGTCCCACCCCAGTCTGAAGGAGA---TAAAGTTGGGGGTAGGAGAGACGCAG-ATGCAAGTGATCAGTCTC---AGTCCCAGACATTGCCTTGCTCTGCGGGTAGGAAT
 TCAGGATTCATTTTCCAGGGAAG--------TTCCTGACCTCTGAATGAGAGGGGCTGTGTAAGGCCAATGCCTGGG-AGGAAGGCAAGGATGAGTAGAGGTGGGGGGAAACAAGTGTCAGGAAGA--------------------------------------------CTCAAA---------ATCTTC--------------------------------------------------------------CAGAGAAATTGT-----GCAGGGTCTTACCAGATCTGTCCTCAAAGCCATGCAAATTGCCTTCTTTGCAATGCAT-ACAATGAGGTGTCTCTGGGGGTCAGAACTGG-----------------------TTATTAGGGAACTTCTAGCCAGGACTGCTAAATACGCGCTGTTGG---------CCCACCAGGCTCACCTATAGCCT-TCCTTCAGTCTGGGCTTGGTTTGGATTTCACTGTGGGTGCCATCGCCTTTACACTCCTGTTTCTATAGTTTAAAGATAGTGGTGCTTTGGGAAAG---TGACTCCTTAAATACAGTTAGGTCCAAGTGA-GACAAGTGGCCTGGCTGTCATTTCAGAATAGCAGCTTCCAAGAGG----------TGATTAATTTCTGTTGGAAGGGTGAT-CTTTGGGGAGGT--GGGTGAAGAGCAGAGACTTGGTGGTACCGTTCCAGGAGCACAGGCTCTCT-----TCCTTTGCA--GTGCAGAATGACCTCTGGCAGCCGGAGTTGTGTTTGTT--------CTGTAGGATTCTGAGGTGGGCCATGGGCAGCTGGAACTGGG-----GAATTTTGCCAATCTCTTTCATATTAGGATTGTCTGCAGAACCAGATATGGAGG------CTTCTAGCAACGTGAGTGCTCCTGTTCTAATGCCCTTAGAAACAAGAAGGCCACACTGATCATTTCTCTCACTTAGGCAGGGAG
 ACAAGGCAAGAGAGAAACAGT-----------------GGATGC--TTTTAGGTTCTTTCCCTTCCCAAGCAGTTGTGGACATTGGGCTGA-GGGGAACATTTCCACATTGGCTAAAGGAGCGTCCTCCTCATATTTTGTACATTTTATACCCAA--AATAA-CTCTTCTTGGTATTT-GGGGAAATATTTTCCTCCCCGTCC------------ATTCCAGGAAATGGCTCCAAGTGCCAAGGACAGAGCCAGGGAAGTTGCAATGAATTCCTGCCCGTCAGCCCCAGGCAGATGCCTTGCACGTCTGAGTGGCCCATGCAGAGCGTGGAGGTGGCCGCC----------------ACGGAACC-TGGGTCAATGT-CCCACCCCCG----CTTAGATGCCA-CCAGGGG--CGTGGGAGCCAAGGAG--AGAAGAGGGGCTCCAGGAAGGTAGAGTCCTTGTGTCTTGTGCATCTGTGAACAGCACTGGTATGATTTAAAGGAAAATTGAGCCAAATTTTCCGGCAGTCAGTT-----ACCCCATCCCCACCGGGGTAGGAGTCTGGCAGCCGCAGCTCCATTCTGGCCAGTCGGCAGAGAGCCTTGAAATTCTTCTTTGTCCACACAGTTGTCTCAGAGAAACAG--AGAGGTT-GTTTCTGCTTAAAAACAACACACTTGGTGTCTGGGCCCACAGACTCCTTTGCACTTATTCCACGTGTGACAGCCAATGTGCCTCGTTGCTTAGCAGACAGCATGTTACCGTCTTTCCTGCTCAGTTTGTTAG--------------CTCTATGGAATGGAATTTATAATCAATGCCCATACCAACATTTCACTAATATCATAGGAGATTTAGTCTCCATCTGGGTGTACATTACATTTGC--TCTGGGG-TGCTCCAGGC--TGGGGGGTTGCCAAGGAAGAGAAGAGAAACCGCAGAGAAGAC---GGGAGGGCAGGGCAGGGGTCTCTG
 AGAAGGGGAGGGGTCCCAGAGTGCAGGAGCAGGAGCCAGGCTC---------ATGAAAGGGGCCACGGGCGGGAGTATCCAGGGACGGCAGTCAAGATGGAGCACAGCTTAGG--AAGCTGAAGGGAATCCTGGCCCACCTGGGTGCTAGAGGGCACATAGGAAGTGCAGGAAGCAGACCAAGGTCCCCAAGAGAGGGAGACCTGGACGCTGAAGCATTTTCTGTCTTTATTAAG-------------ACAACTCCGTAAGAATTCCTGCTGGGCCAAAGTGAATTCTAGGATGCGACTTTAAGATGGGAGCAAGCGAACCATTGAGGAGGCAGGTTACCCTAGTTAGCCAATGCAGATCGAGAATGGGAAATCTTTCatttattcatgcaacagatatttaacgaagccctgccgtgttccaggcctgtgatagatgctggaacaggtacagaga----------tAc-------aggtgtcattaattgatcaggg--caacctctc---cttctgagt--cttgctggagcttcagatgc-ccctcacacagagctcgagggagcctc-aacaattgatcagaagtcaggcaccatggctcacgcatataatcccagcactttgggaggccaaggcaggtggatcactggagcccaggagttccagatcagctggggcaacatggcaaaaccccatctctattaaaaaaaaaaaaagtaactggatgtgatggtacacacctgtagtcccagctacttgggaggctgagaggtgggagaattgcttgagcccgggaagtcgggggtccagtgagccttgatcacaccactgcactccagcctgagtgacagagcaagaccctgacacacacacacacacacacacacacacacacacagattagagctgaaacaggagtagaaacctatctg-tatctctgATGA-GATCAGATC---------TTTCTGATGAACAGAAAGAATG
 TAACCCCTGTACTCACACCCTCTCTGCTGGTTACATATGTTAACACGATTTCTCAAATGAGGCTTTTGGTTGCAAATAAGAGAAAATCACTCACGCT-GGCCCTGTG--TTTTTCAAATTGTTTATTGTGATCAACATTTGAAAAAAGAGCCGAGACTCTCAAGAGTGCATTACCCACGGTAAGGGTGAATTTT-ACTTCTTGACACTTATTTCTCTTACATGTATCTATCTGTCTC-----AAATGAAAAATATATTTAGAAAGTTGAAAGCTATCCAAGTGAGTATAAGAAAAGAGTATCTCACCCTGAAGGCTAAGGACAGGGAGGGC---------------------------CACCAGGCCTCACGAGGACCCAGGAACCACAAAGAAGGCT-AGGAAGGAGCACAGGCGGTGACCATACTCTGGCTCAGTGGCTATGTGGGCTCTGGTCTCTCTCAGCTGTTCCATGCATATGAGGCCAAATGTGGCTACCCTAGAGCTTCTGAGCCCTCAACAGAGATGAACTGGACTCTCTGCAGCCCCACTCTAAATTCCTAAGAGAGAAGTTGATTGACCCAATCAGGGTCAGGAGAAGGAAGGGAGGAGGAAAGGGAGGAGAGAAGAGCCTCTTCGTCTCTTGCCTACCACTGGCCAGGCAATTGTAGCCAAGGGGGCTGGAGTGTAAATGCAAACATAGCCATCAAGGGTtgtgtatgtgtgtgtgtgtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGA-TCTCCCAGGAGGTCCCTACTAAACAGACTTAAGCCCGCAAAATTTTAGCTCTCCAGCCTCACACACTCCACCCCTCTACCATATTGAATCTTCCCAAACCAACTATGGCTTTCCCTAACTCCGGAGc------ttggcctggaatgccctgcttcccctctttcccctggggaacgcctgtccttcaggcctcagttcacacactgcctcccttgca
 aagctctccTCCCATCCCCGGAGTCCCT--CTTCCCCTTTGTTCTTTGGGTTCTATGCTTCTTCCCTCATAACTCCCACCAGGTTGTGTTAAAATGAGTTGTTCAAGGTCCTGTCTGTTCCACTAGATTCTGAGCAACTTGGAGAACGAAGATCCAAACTTCGCTGCCTTTATTTCCTCCTTTGTTCTTTTCTCATCCCCAAGTCCCTTCCAACTTGGAGTTATgaagaaaggaaggaaggaagggtgggagggaagaaCAGGAGGGGATCCCACAGG-AGAATGTGTATAGGGAGAGGACTCAGACTAGCTAAAGCTTTTCCCTCATAATTAATAGCAAATACCATGTTACCTGAATTTAATTCACAGTAGCATACAAAAGACTCGCTTTGTTCT-------CCCCA---------TTGATGTCATCAGAGG--------------------GCTGTGGG--------------CAGGCCTAATCTTGGCTCAGGAGGCCCTCCAGCCTGGATCTAAAGAGCAGCAGATGggccaggctcggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcacgaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaaaattagccaggtgcggtggtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaaataaaGAGGAGCACACATCTCTGCCCATCCTAACTCCCACTTTGACATTGAGGTCCCCAGGATGGAGGGTCTGCCTCCATCTGCCTTGTCCCCTG-CAATGGTGGGAAGGTGATGGAGCTCAAGTCTAGAGGCCACC
 AGCTTCTTAGGGAGG--TAGGAGGTG---------------GAGGGTGGGGTGC-GGGCCCTGCACACAACTGCCAAGTGAGGATGGGGGTGGG-GTCCACCTGAGGATAAGTAACAGTGAGGCTGGTGCAGAGGACCCAGGTGGAGGTAGACAGCAGAATTTGTGGTGGGGT--GGATGGCAC-ATTATATAAGCCTCTCTTGC------TGCCCTGT---TTACTGAGATTGTTTCAttatcttttttggcttttgtttttaagagatggggtcttgctgtgtcacacaggctggagtgcactgtgtgatcatacctcactgcagcctcgacatcctgggctcaggcaaacctcccaccttggcctcccaagtagctgggaccacaagcgtttgccaccacactcagctatttttatttttattttta--ttttttttagagatggggtcttgctgtgtcgcccaggctggtcttgaactcctgggctcaagcgatcctcctgccttggcctcccaaagccctgggattataggctgagccaccacacccagccACATTTCATCTGTGCAGCTCCAGGGGCTCCACATTCT-ACTCTTCTCATTTCTTCTCCAGGGTACCC----------ATGGCAAGGGATGAGGGT--AGAAGATGGGGCA--GCCAGGCCTTGATTAAAGGAGAAGGAAGGCAGCCTGTGGAGAGG---GCAGCC---C---AGGGAG---TGCAGAGAGAAGTGGGCCATGAGGGAGA---CAGCAGAGTGCAGGCTGCGTCC---CAAATGAGCATACAGCCCACTGTGAGCCCACC--ATCTTCCTAGA-GA--CCCCTCTCCTCTCC-AGGAGCTGCTTCAGTAGCACTCA---------GAGGAAAGAATGATGC--------TGTATCAACATTTCAGCAGCTCATCTTTTAACTCTAAGAAAATGGCAGCTCCTAAATGTTCAA--AACTGCTTTG
 GAAACTTCT---GGAGAGAGGTTTTGCAGCTCAGGCAGACAGCTGATCGCGGCCTTTCTTCCACCCCAACCCATGCTCTCCCCATGCT--CTCCTGCCACAGCTGCAGCGGGCCCCTGGGTCCTACATTTGCAG-CCCTTTGTCTCTGAGCT-----CAGACTTCCAATTCCAAGCGGCAGCTGGGCAGGCTCACCAGCATGT---CCAGCCAGTACTAGGACATCAGCAGGAGC----CCAACCACCTCTTTCCAAAATCTCTCCTCATGTCTCTCCTAGTTTCCATCTCCATCCTTCTAGTCAGCCAGGCTGAAAACATT-----------------TGCTCCTCAGGGTGCAGAAGGGAAAGCTTTGCCTCCCTTCCTGGTGCTCACTGCCCCTGCGATTCCAGCCCAAGCCCTCCCCGGCTCCTCACC----------CTGGTGTCAGCTGGAAGCCACCATCTCCTAAACCCACCTGtgttcttccacctctgc--------cagggctgc-cctctcctccaccttcacaaactcaattcctacccattctcaggtcccttatcaaatgccatctcctccatgatgcctccctgattccccTGCTGGAaataatggtgataacagctaag--gcattggggttggctacgtgccaggcaaggagttggcactttacatgctttatctcatttcagccacataacatcgacaggt-ggcattatgattcatatcatccccatctgatagccaggaaaactgagtcccagagaggttagc-cactttcctagggccCTGTGCTCTGACTCAAGCATAGCTCTGAGGAACTCTAGCATTCATCAGTTTAAGCACCATGACTTTCTTTGCTGAGTCACCCAAGGCAT-TTCTTCATTTAAATGTTCTTCCTTGGCCAGGCGCAGTGGCTCAggcccaatgcggtggctcacgcctgtaatctcaacactttgggaggccgaggtggg
 cagataatctgaggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatacaaaaaaatgaggctgggcgtgatgactcacacctgtaatcccagcactttgggaggccaaggcaggtggattacatgaggtcaggagttcgagaccagcctggccaacatggtgaaatcctatctctattaaaaatacaaaaaattagccaggcatggtggcaggcacctgtaatcccagctacttgggaggctgaggcaggaaaatggcttgaacccgggaggtggaggttgcagtgagccaaggttgcaccattgcactccagcctgggcaaaaagagggaaacatcgtctaaaaaagaaaaaaaaaaaattagccaggctgggtggtgcatgcccgtaattccagctactcaggaggatgaagcaagagaattgcttgaacccaggaggcagagattacagtgagctgagatcacaacactgcactccagcctaggtaaagaacaagactccatctcaaaaataaataaataaaaataaaTGTTCTTCCTTGCAATGAAGTTAAATATGTAAATTCTCAAACCAGTTGCTTAAGGGCACAGTTTTGTTCTTTACCTATATTTTTAACAAATATTTTATGTAAGTAGTTGAC-AAAATCAAATACTGT-GTACACTACCGAGGCTTCCCTGGGAAAGCCATCAG-CCTCTGCCCCATCCCTTCCCACTCCTGATT-CCACTTTCCTGTGTTTCCATATCTTTTTCATGTCTGTTTCTGGCCCACAGTGGGCGATCAATACATGTTAGCCACCAACCATCAAACCTATATTGAGTAATTATGGTATGTCAGGCACTATGCTCAATGAAATTGTAttaggcttgtacaaaagtaattgtggtttttaagagtaatggcaaaaacggcagttactttcgcaccaacTATTTGCTGCCTTGAATTATTCCTCCTCTC-C
 TCATCCCTAAACCCTGCTCCTCCCAGCCATTCTTCCTCCCCTTCTTGGGCCATGGCCAGGCCCCACCCAGGTACTAAGACTCAGGTGAACCAAGGAAGACTTAATGCCCACTCTTTTCTGATGCCCATGTT--GGCATGTGTTAAGtcggttagcattaagtttggctgcatttagcagagacccaaaagaacagtgccttttaaaaggcagaggttatgtctctcacacacacccagcacaagtccaag-------------------------accagcatggcatctcagctccatcaa--cctcaggaaccgagctcctgcagctccctgccctgcagttgataaggtgaggtctttgtcctcctggttcaagatggtgctagaatgttggctaccatatctatagtccaggcatcagaatggagcaagggatgaaaaaggaagagatgaaggcacacgacaggttcctgagagctggcacaggacacttctgcttatatttcactggccagaacttagtcacatggtcacacctagttgggagactctgagaagtaa----agtatttattctagatggccatatccctacc-taagacttggagttttctatgactggggaagaacggaagacaagatattgggaaagactagcagcctctactaAAAGGGTGATCtgtgttgatgtgcgtgtgtgtgtgatgtttgtatg---agcatgtgtgt-tatgtgttgt--gtgtTGGTGGGGCA--GATTCTTGCGAGCACTTTGGTCTCAGATGGACCTGCTACCAGTTCTCTCTGCAGACCCCCATAGGTTTCTCCTAAACCTGGCCT-CTCCTATTAGGCAGCCTTACTCAGCGGCAGCTTCTCAGCTCCATGTTTTCAAGGAACCACAATTTATTTCCAGCATCCACTGAAGCATATTATCAGTGGTGATAGAGGGGGCTTGTAAAACTGTTTTTCCACTTAGGTATTAGA
 GGGTGGCCATTATTTGAGAGTGAC-----TATGACCACAGTTAATCTGGTAATAAATTCTCTTGGGTAGGAGGGGGAAAGGAAAGGATGCTTTAAGGAAGCATCTTGCCAGGAGACACAAAGCTAACAAGAGTGGAGCCTGCAG----------------------------CTGGAGCCGCAGAGCCTAATCACTACACCCGCCCATCTCTGCTAGGGTTTCATGACTTCGTATCGGGGATTAGCAGTATTTAACTCTGTTGCACAAACATTTGGTGTA-----TTATTCAGGTAACAAGTAGCTAATAGAGGAAGTTTTACTTTTTTAAGACATAA--------------------ATTTGCCTTTTCCCAAATTACTTGGTACATAGTAC-TTTTCATGTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTCCAGAGCAGGGTATTTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTG-----TGATTTGGGCTTTTCCTTAAATCCTTGA-----GGAGCTGGA---GGGGTGGGTGGCTCGCACTCCTGCTTTctgg---------atctgaatc--------------ctgactctgtcatggacctgtt-tgactttgggcaagttgactcctattcctgagccccatat-ttttctcttctgtgaaattcagattaaaaA-AACATGGCTTTGATCAAACATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAG-AAATGAATCCTACTAATATTGCCATCTATGGACAGAAAATGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGAGATTAATTTTACTGCCATCTCCAGAACCGTCATCCTAATATTTACTTACAT-TTTATTATTATTTCAGGCTCATGCACATATACTTAGCATGGATCATTGGCCACAGACTCGCA
 TACATTTAACTTTATTACCTTT-TGCCTCATGTATCTCATTAAAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCAAGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgc--tctctcccgccaccatgtctttataccccctgatttctcagccact-atggcaaccactttctactcttagtagcccatatttag--tccaatccccagctcaggagacacttcttccaggg--agccccctgtgccttccagtagtatcttgtacctgccctttttgcaaagctctttcctcctggcttagaatggcccattgacctgtttgtttctcctattaaactgtaagccactcgagggtagagagcatctgttgttcaccattgcatcctcggtgctgagcactgcgtctgacatattatttagaaggtcagtaagtgctagtgggatTCAGGCTCCCAGTGGGTGGGAGAGAAAGGACGTAAGGAAGCAAGTGGTAAAGGCCCTCACAGA-GTATCAGCAGGCTGGTGTGA-GGGAGAAATGCAGAGGATGGGTGAGTAGCA-----TAATCGCTAATGAT-AGGGTAATGATAGAGCACATTTCACAACACCTTt-aagccctttcacgtgcatcagataatttgatcctcataaaagcctagagatagatatattacagg-gatgaaggtggagtattttgtggttatgtgatatg-tttaaaattatgcagtgagtaaatgactgggttcaaaccagaccttaaaagtctgttatctttccCTCG-AGCATGCAATGAAGTCTACATCATCCCTACCATGTCCATTTGATCACACCCTGGCCTCACAGCTCTGTGGTCTACAGGATACCTCATGGTGGTTTTATTGACCAGACAATAATCCTCTTTCTAAGGGGATGCATTTCATTAATACATATGTAGATCATGAATTGTC
 TTTGACTTTGAGGGGATGGTAGC----CAGAGCAGAAAGCAAAGCTGATTTTCATCCCCGTCTGGTAATGTGGTTGGTAATGTGAAGA-TGGGTGTATTCTGAGATACCGGCTCCTTGCAGTGTGTGGTTCCTTCTGTTTTCAGGCCC------AAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACGGTAAGGAG---AGTATGCGGGGACAAA---GTAGAACTGCAGCCAGCCCAGCACTGGCTCCTAGTGGCACT-GGACC-CAGATAGtccaagaaacatttattgaacgcctcctgaatgccaggcacctactggaagctgagaaGGATTTGAAAGCACAGGGC-TCCACTCTTTCTGGTTGTTTCTTTTGGCCCCTCTGCCTGCTGAGATTCCAGGGGTTAGTGG--------------------------------------------------------TTCTAATTCTAAACCACTCCAAGAACATTTGATTTTGCTACATGTTTCCATTTAAAAATCATAGGATTTGggctgggtgtggtggcttgtacctgtcatcccagcactttgggaggccaaagcaggaggatcattcgagcccaagagttcgagaccagcctgggcagcatagggagaccccatctctacaaaaataataaaaaatgttagctgggcatggtggtgtgtacctgtggtcccagctaggggaggctgagatggaaggatcacctgagcctgggaggttgaggctgcagtgggccctgatcatgccaccgtgctccagcctgggtgacagagtgagaccttgtctcaaaataaataaataaataaataaaAGTCATAGGA
 TTTgatcaggcatgatgggtcacatctgtaagcccattgctttaggaggccaaggtaggaggatcagttgaggccaggagttcaagaccagcctgggcaacatggcaagacctctctctctaatttttaaaaaaataaaaaTTAAAGATAAGAAAAAAATCATAGGATTCTCATGAGGCCTCACGTGCTTATTTTCAACCTACCAAGGGGAAACCCAGGCCTCAGCGATTAGCTGAGC----------CACATGCAGGCACAG------------------------CCACTG-----TCTCTTTCCTTCCTGTCCCCTCTGTCCCCACCTTCTGCGCTCGCCTTCCTCCCTGACTTCACTTCCTTGAATCTTAGTGCCTACGACCAGAGGGAGCTGTGAAGTTCCTTG----TGTCCCATTGGCAGGAA-CAAGACCCCCAGAAGCATCTCCTCAGGGC------CTCTA-----TCCCATCTC-TAGATGTGCTTGTCATTAGG-Gttct-------------tgtagttccagctgatctctggccctgccgctcaaagatacccaaaagagcgagtctaccctttttcacattcaaccctctactgatttgcaaatagcagtcagtgcccaccctggtcttttctctggggtccagcaggcctagaccttcagccattttcctgatgaGGTCTGTAtttgaaattaggaagattaagtttgaatcttcacacttctgat----gtctgtgagatcttcagcaagttccttact--gtctttaagccttgt-tttcatcatctggataatggggatatcacacacta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCCCCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA-GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAA
 GATGGCTCAGAACTAGATAGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaaaaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCCCACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGTCAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACTGGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTACGGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCGGCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGAGGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGTTCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAGGGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTGGCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAGGAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCGA--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGTCTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGACCTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTCCAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCTGGCCTTCTCTA
 AGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCTGGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCAGGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGAAGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCCAGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGACTCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAAGATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGGCTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCCTCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCAGGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGGTTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTCCC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATGGATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCTCCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTTGAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCAGTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTGCAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTA
 TTTTAAAA---AGATTTGTTTTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGGGAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAGTGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA------------TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTTCTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTCCGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGATCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCTGGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTCTTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTTTACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACTGCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGGTCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTTTTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagctcacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCAAACC-GCAC
 TCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCAAATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCAGGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggcatcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaatttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCA
diff -r c44567359a03 -r e899101e63d1 test-data/users/test3@bx.psu.edu/run1/2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/users/test3@bx.psu.edu/run1/2.fasta	Tue Jun 16 09:55:15 2009 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt
+tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac
+cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg
+aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg
+gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt
+tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac
+ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt
+ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt
+tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa
+aacaattcta atggtcaaaa a
\ No newline at end of file
diff -r c44567359a03 -r e899101e63d1 test/base/twilltestcase.py
--- a/test/base/twilltestcase.py	Fri Jun 12 09:56:23 2009 -0400
+++ b/test/base/twilltestcase.py	Tue Jun 16 09:55:15 2009 -0400
@@ -1150,7 +1150,6 @@
         tc.fv( "1", "file_format", file_format )
         tc.fv( "1", "dbkey", dbkey )
         tc.fv( "1", "message", message.replace( '+', ' ' ) )
-        library_dir = "%s" % self.file_dir
         tc.fv( "1", "server_dir", "library" )
         tc.submit( "new_dataset_button" )
         check_str = "Added 3 dataset versions to the library dataset '%s' in the folder '%s'." % ( ldda_name, folder_name )
@@ -1167,34 +1166,55 @@
             check_str = "Added 1 datasets to the folder '%s' ( each is selected )." % folder_name
         self.check_page_for_string( check_str )
         self.home()
-    def add_datasets_from_library_dir( self, library_id, folder_id, folder_name, file_format='auto', dbkey='hg18', roles_tuple=[],
-                                       message='', root=False, check_template_str1='', check_template_str2='', check_template_str3='' ):
+    def add_dir_of_files_from_admin_view( self, library_id, folder_id, file_format='auto', dbkey='hg18', roles_tuple=[],
+                                          message='', check_str_after_submit='', check_str1='', check_str2='', check_str3='' ):
         """Add a directory of datasets to a folder"""
         # roles is a list of tuples: [ ( role_id, role_description ) ]
         self.home()
         self.visit_url( "%s/admin/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s" % ( self.url, library_id, folder_id ) )
         self.check_page_for_string( 'Upload a directory of files' )
         # If we've been sent some template labels, make sure they are included in the upload form
-        if check_template_str1:
-            self.check_page_for_string( check_template_str1 )
-        if check_template_str2:
-            self.check_page_for_string( check_template_str2 )
-        if check_template_str3:
-            self.check_page_for_string( check_template_str3 )
+        if check_str1:
+            self.check_page_for_string( check_str1 )
+        if check_str2:
+            self.check_page_for_string( check_str2 )
+        if check_str3:
+            self.check_page_for_string( check_str3 )
         tc.fv( "1", "folder_id", folder_id )
         tc.fv( "1", "file_format", file_format )
         tc.fv( "1", "dbkey", dbkey )
         tc.fv( "1", "message", message.replace( '+', ' ' ) )
-        library_dir = "%s" % self.file_dir
         tc.fv( "1", "server_dir", "library" )
         for role_tuple in roles_tuple:
             tc.fv( "1", "roles", role_tuple[1] ) # role_tuple[1] is the role name
         tc.submit( "new_dataset_button" )
-        if root:
-            check_str = "Added 3 datasets to the library '%s' ( each is selected )." % folder_name
-        else:
-            check_str = "Added 3 datasets to the folder '%s' ( each is selected )." % folder_name
-        self.check_page_for_string( check_str )
+        if check_str_after_submit:
+            self.check_page_for_string( check_str_after_submit )
+        self.home()
+    def add_dir_of_files_from_libraries_view( self, library_id, folder_id, selected_dir, file_format='auto', dbkey='hg18', roles_tuple=[],
+                                              message='', check_str_after_submit='', check_str1='', check_str2='', check_str3='' ):
+        """Add a directory of datasets to a folder"""
+        # roles is a list of tuples: [ ( role_id, role_description ) ]
+        self.home()
+        self.visit_url( "%s/library/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s" % ( self.url, library_id, folder_id ) )
+        self.check_page_for_string( 'Upload a directory of files' )
+        # If we've been sent some template labels, make sure they are included in the upload form
+        if check_str1:
+            self.check_page_for_string( check_str1 )
+        if check_str2:
+            self.check_page_for_string( check_str2 )
+        if check_str3:
+            self.check_page_for_string( check_str3 )
+        tc.fv( "1", "folder_id", folder_id )
+        tc.fv( "1", "file_format", file_format )
+        tc.fv( "1", "dbkey", dbkey )
+        tc.fv( "1", "message", message.replace( '+', ' ' ) )
+        tc.fv( "1", "server_dir", selected_dir )
+        for role_tuple in roles_tuple:
+            tc.fv( "1", "roles", role_tuple[1] ) # role_tuple[1] is the role name
+        tc.submit( "new_dataset_button" )
+        if check_str_after_submit:
+            self.check_page_for_string( check_str_after_submit )
         self.home()
     def delete_library_item( self, library_id, library_item_id, library_item_name, library_item_type='library_dataset' ):
         """Mark a library item as deleted"""
diff -r c44567359a03 -r e899101e63d1 test/functional/__init__.py
--- a/test/functional/__init__.py	Fri Jun 12 09:56:23 2009 -0400
+++ b/test/functional/__init__.py	Tue Jun 16 09:55:15 2009 -0400
@@ -80,6 +80,7 @@
                                    allow_user_deletion = True,
                                    admin_users = 'test@bx.psu.edu',
                                    library_import_dir = galaxy_test_file_dir,
+                                   user_library_import_dir = os.path.join( galaxy_test_file_dir, 'users' ),
                                    global_conf = { "__file__": "universe_wsgi.ini.sample" } )
log.info( "Embedded Universe application started" )
diff -r c44567359a03 -r e899101e63d1 test/functional/test_security_and_libraries.py
--- a/test/functional/test_security_and_libraries.py	Fri Jun 12 09:56:23 2009 -0400
+++ b/test/functional/test_security_and_libraries.py	Tue Jun 16 09:55:15 2009 -0400
@@ -1396,28 +1396,26 @@
                         ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) )
         self.check_page_for_string( 'This is an expired version of this library dataset' )
         self.home()
-    def test_185_upload_datasets_from_library_dir( self ):
-        """Testing uploading 3 datasets from a library directory to a root folder"""
+    def test_185_upload_directory_of_files_from_admin_view( self ):
+        """Testing uploading a directory of files to a root folder from the Admin view"""
         message = 'This is a test for uploading a directory of files'
         roles_tuple = [ ( str( role_one.id ), role_one.name ) ]
+        check_str = "Added 3 datasets to the library '%s' ( each is selected )." % library_one.root_folder.name
         ## TODO: temporarily eliminating templates until we have the new forms features done
         """
-        self.add_datasets_from_library_dir( str( library_one.id ),
+        self.add_dir_of_files_from_admin_view( str( library_one.id ),
                                             str( library_one.root_folder.id ),
-                                            library_one.root_folder.name,
                                             roles_tuple=roles_tuple,
                                             message=message.replace( '+', ' ' ),
-                                            root=True,
+                                            check_str=check_str,
                                             check_template_str1='wind',
                                             check_template_str2='bag',
                                             check_template_str3='Fubar' )
         """
-        self.add_datasets_from_library_dir( str( library_one.id ),
-                                            str( library_one.root_folder.id ),
-                                            library_one.root_folder.name,
-                                            roles_tuple=roles_tuple,
-                                            message=message.replace( '+', ' ' ),
-                                            root=True )
+        self.add_dir_of_files_from_admin_view( str( library_one.id ),
+                                               str( library_one.root_folder.id ),
+                                               roles_tuple=roles_tuple,
+                                               message=message.replace( '+', ' ' ) )
         self.home()
         self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) )
         self.check_page_for_string( admin_user.email )
@@ -1531,7 +1529,48 @@
                     pass
         check_edit_page2( latest_3_lddas )
         self.home()
-    def test_195_mark_group_deleted( self ):
+    def test_195_upload_directory_of_files_from_libraries_view( self ):
+        """Testing uploading a directory of files to a root folder from the Libraries view"""
+        # admin_user will not have the option sto upload a directory of files from the
+        # Libraries view since a sub-directory named the same as their email is not contained
+        # in the configured user_library_import_dir.  However, since members of role_one have
+        # the LIBRARY_ADD permission, we can test this feature as regular_user1 or regular_user3
+        self.logout()
+        self.login( email=regular_user1.email )
+        message = 'Uploaded all files in test-data/users/test1...'
+        # Since regular_user1 does not have any sub-directories contained within her configured
+        # user_library_import_dir, the only option in her server_dir select list will be the
+        # directory named the same as her email
+        check_str_after_submit = "Added 1 datasets to the library '%s' ( each is selected )." % library_one.root_folder.name
+        self.add_dir_of_files_from_libraries_view( str( library_one.id ),
+                                                   str( library_one.root_folder.id ),
+                                                   regular_user1.email,
+                                                   check_str_after_submit=check_str_after_submit,
+                                                   message=message.replace( '+', ' ' ) )
+        self.home()
+        self.visit_page( 'library/browse_library?id=%s' % ( str( library_one.id ) ) )
+        self.check_page_for_string( regular_user1.email )
+        self.check_page_for_string( message )
+        self.logout()
+        self.login( regular_user3.email )
+        message = 'Uploaded all files in test-data/users/test3.../run1'
+        # Since regular_user2 has a subdirectory contained within her configured user_library_import_dir,
+        # she will have a "None" option in her server_dir select list
+        check_str1 = '<option>None</option>'
+        self.add_dir_of_files_from_libraries_view( str( library_one.id ),
+                                                   str( library_one.root_folder.id ),
+                                                   'run1',
+                                                   check_str_after_submit=check_str_after_submit,
+                                                   check_str1=check_str1,
+                                                   message=message.replace( '+', ' ' ) )
+        self.home()
+        self.visit_page( 'library/browse_library?id=%s' % ( str( library_one.id ) ) )
+        self.check_page_for_string( regular_user3.email )
+        self.check_page_for_string( message )
+        self.home()
+        self.logout()
+        self.login( email=admin_user.email )
+    def test_200_mark_group_deleted( self ):
         """Testing marking a group as deleted"""
         self.home()
         self.visit_url( '%s/admin/groups' % self.url )
@@ -1545,13 +1584,13 @@
             raise AssertionError( '%s incorrectly lost all members when it was marked as deleted.' % group_two.name )
         if not group_two.roles:
             raise AssertionError( '%s incorrectly lost all role associations when it was marked as deleted.' % group_two.name )
-    def test_200_undelete_group( self ):
+    def test_205_undelete_group( self ):
         """Testing undeleting a deleted group"""
         self.undelete_group( str( group_two.id ), group_two.name )
         group_two.refresh()
         if group_two.deleted:
             raise AssertionError( '%s was not correctly marked as not deleted.' % group_two.name )
-    def test_205_mark_role_deleted( self ):
+    def test_210_mark_role_deleted( self ):
         """Testing marking a role as deleted"""
         self.home()
         self.visit_url( '%s/admin/roles' % self.url )
@@ -1565,10 +1604,10 @@
             raise AssertionError( '%s incorrectly lost all user associations when it was marked as deleted.' % role_two.name )
         if not role_two.groups:
             raise AssertionError( '%s incorrectly lost all group associations when it was marked as deleted.' % role_two.name )
-    def test_210_undelete_role( self ):
+    def test_215_undelete_role( self ):
         """Testing undeleting a deleted role"""
         self.undelete_role( str( role_two.id ), role_two.name )
-    def test_215_mark_dataset_deleted( self ):
+    def test_220_mark_dataset_deleted( self ):
         """Testing marking a library dataset as deleted"""
         self.home()
         self.delete_library_item( str( library_one.id ), str( ldda_two.library_dataset.id ), ldda_two.name, library_item_type='library_dataset' )
@@ -1581,13 +1620,13 @@
         except:
             pass
         self.home()
-    def test_220_display_deleted_dataset( self ):
+    def test_225_display_deleted_dataset( self ):
         """Testing displaying deleted dataset"""
         self.home()
         self.visit_url( "%s/admin/browse_library?id=%s&show_deleted=True" % ( self.url, str( library_one.id ) ) )
         self.check_page_for_string( ldda_two.name )
         self.home()
-    def test_225_hide_deleted_dataset( self ):
+    def test_230_hide_deleted_dataset( self ):
         """Testing hiding deleted dataset"""
         self.home()
         self.visit_url( "%s/admin/browse_library?id=%s&show_deleted=False" % ( self.url, str( library_one.id ) ) )
@@ -1597,7 +1636,7 @@
         except:
             pass
         self.home()
-    def test_230_mark_folder_deleted( self ):
+    def test_235_mark_folder_deleted( self ):
         """Testing marking a library folder as deleted"""
         self.home()
         self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
@@ -1609,7 +1648,7 @@
         except:
             pass
         self.home()
-    def test_230_mark_folder_undeleted( self ):
+    def test_240_mark_folder_undeleted( self ):
         """Testing marking a library folder as undeleted"""
         self.home()
         self.undelete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' )
@@ -1624,7 +1663,7 @@
         except:
             pass
         self.home()
-    def test_235_mark_library_deleted( self ):
+    def test_245_mark_library_deleted( self ):
         """Testing marking a library as deleted"""
         self.home()
         # First mark folder_two as deleted to further test state saving when we undelete the library
@@ -1648,7 +1687,7 @@
         except:
             pass
         self.home()
-    def test_245_purge_user( self ):
+    def test_250_purge_user( self ):
         """Testing purging a user account"""
         self.mark_user_deleted( user_id=regular_user3.id, email=regular_user3.email )
         regular_user3.refresh()
@@ -1680,7 +1719,7 @@
             role = galaxy.model.Role.get( ura.role_id )
             if role.type != 'private':
                 raise AssertionError( 'UserRoleAssociations for user %s are not related with the private role.' % regular_user3.email )
-    def test_250_manually_unpurge_user( self ):
+    def test_255_manually_unpurge_user( self ):
         """Testing manually un-purging a user account"""
         # Reset the user for later test runs.  The user's private Role and DefaultUserPermissions for that role
         # should have been preserved, so all we need to do is reset purged and deleted.
@@ -1688,7 +1727,7 @@
         regular_user3.purged = False
         regular_user3.deleted = False
         regular_user3.flush()
-    def test_255_purge_group( self ):
+    def test_260_purge_group( self ):
         """Testing purging a group"""
         group_id = str( group_two.id )
         self.mark_group_deleted( group_id, group_two.name )
@@ -1703,7 +1742,7 @@
             raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_id )
         # Undelete the group for later test runs
         self.undelete_group( group_id, group_two.name )
-    def test_260_purge_role( self ):
+    def test_265_purge_role( self ):
         """Testing purging a role"""
         role_id = str( role_two.id )
         self.mark_role_deleted( role_id, role_two.name )
@@ -1728,14 +1767,14 @@
         dp = galaxy.model.DatasetPermissions.filter( galaxy.model.DatasetPermissions.table.c.role_id == role_id ).all()
         if dp:
             raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_id )
-    def test_265_manually_unpurge_role( self ):
+    def test_270_manually_unpurge_role( self ):
         """Testing manually un-purging a role"""
         # Manually unpurge, then undelete the role for later test runs
         # TODO: If we decide to implement the GUI feature for un-purging a role, replace this with a method call
         role_two.purged = False
         role_two.flush()
         self.undelete_role( str( role_two.id ), role_two.name )
-    def test_270_purge_library( self ):
+    def test_275_purge_library( self ):
         """Testing purging a library"""
         self.home()
         self.delete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' )
@@ -1771,7 +1810,7 @@
                     raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted.' % \
                                           ( str( library_dataset.id ), library_dataset.name ) )
         check_folder( library_one.root_folder )
-    def test_275_reset_data_for_later_test_runs( self ):
+    def test_280_reset_data_for_later_test_runs( self ):
         """Reseting data to enable later test runs to pass"""
         ##################
         # Eliminate all non-private roles
diff -r c44567359a03 -r e899101e63d1 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample	Fri Jun 12 09:56:23 2009 -0400
+++ b/universe_wsgi.ini.sample	Tue Jun 16 09:55:15 2009 -0400
@@ -55,9 +55,13 @@
 # Galaxy session security
 id_secret = changethisinproductiontoo
-# Files in directories under this directory can be directly imported through
-# the library admin's "add dataset" tool
+# Directories of files contained in the following directory can be uploaded to a library from the Admin view
 #library_import_dir = /var/opt/galaxy/import
+# The following can be configured to allow non-admin users to upload a directory of files.  The
+# configured directory must contain sub-directories named the same as the non-admin user's Galaxy
+# login ( email ).  The non-admin user is restricted to uploading files or sub-directories of files
+# contained in their directory.
+# user_library_import_dir = /var/opt/galaxy/import/users
# path to sendmail
 sendmail_path = /usr/sbin/sendmail

    

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[galaxy-dev] [hg] galaxy 2453: Fixes and functional tests for uploading direc...