")}$(".dialog-box").find(".body").html(B);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function make_popupmenu(D,B){var A=$("").appendTo("body");$.each(B,function(G,F){$("").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(){var F=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.top+$(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)};
\ No newline at end of file
+var hidden_width=7;var border_tweak=9;var jq=jQuery;function ensure_dd_helper(){if(jq("#DD-helper").length==0){$("").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(F,B,C){var E=false;var D=null;resize=function(G){var H=G;if(G<0){G=0}jq(F).css("width",G);jq(C).css("left",H);jq(B).css("left",G+7);if(document.recalc){document.recalc()}};toggle=function(){if(E){jq(C).removeClass("hover");jq(C).animate({left:D},"fast");jq(F).css("left",-D).show().animate({left:0},"fast",function(){resize(D);jq(C).removeClass("hidden")});E=false}else{D=jq(C).position().left;jq(B).css("left",hidden_width);if(document.recalc){document.recalc()}jq(C).removeClass("hover");jq(F).animate({left:-D},"fast");jq(C).animate({left:-1},"fast",function(){jq(this).addClass("hidden")});E=true}};jq(C).hover(function(){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(G,H){jq("#DD-helper").show()},stop:function(G,H){jq("#DD-helper").hide();return false},drag:function(G,H){x=H.position.left;x=Math.min(400,Math.max(100,x));if(E){jq(F).css("left",0);jq(C).removeClass("hidden");E=false}resize(x);H.position.left=x;H.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show();var A=function(G){if((E&&G=="show")||(!E&&G=="hide")){toggle()}};return{force_panel:A}}function make_right_panel(A,E,H){var J=false;var G=false;var C=null;var D=function(K){jq(A).css("width",K);jq(E).css("right",K+9);jq(H).css("right",K).css("left","");if(document.recalc){document.recalc()}};var I=function(){if(J){jq(H).removeClass("hover");jq(H).animate({right:C},"fast");jq(A).css("right",-C).show().animate({right:0},"fast",function(){D(C);jq(H).removeClass("hidden")});J=false}else{C=jq(document).width()-jq(H).position().left-border_tweak;jq(E).css("right",hidden_width+1);if(document.recalc){document.recalc()}jq(H).removeClass("hover");jq(A).animate({right:-C},"fast");jq(H).animate({right:-1},"fast",function(){jq(this).addClass("hidden")});J=true}G=false};var B=function(K){var L=jq(E).width()-(J?C:0);if(L")}$(".dialog-box").find(".body").html(B);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function make_popupmenu(D,B){var A=$("").appendTo("body");$.each(B,function(G,F){$("").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(){var F=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.top+$(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)};
\ No newline at end of file
diff --git a/static/scripts/packed/galaxy.ui.scrollPanel.js b/static/scripts/packed/galaxy.ui.scrollPanel.js
index b16bbeeca48..fd0e8056d1d 100644
--- a/static/scripts/packed/galaxy.ui.scrollPanel.js
+++ b/static/scripts/packed/galaxy.ui.scrollPanel.js
@@ -1 +1 @@
-$.ui.plugin.add("draggable","scrollPanel",{drag:function(G,H){var J=$(this).data("draggable");clearTimeout(J.timeout);var B=H.options,D=J.element,A=B.panel,C=A.position(),I=A.width(),E=A.height();viewport=A.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),element_w=D.width(),element_h=D.height(),moved=false,close=5,nudge=23,p_min_x=-(I-viewport_w),p_min_y=-(E-viewport_h),p_max_x=0,p_max_y=0,min_vis_x=-C.left,max_vis_x=min_vis_x+viewport_w,min_vis_y=-C.top,max_vis_y=min_vis_y+viewport_h,mouse_x=H.position.left+J.offset.click.left;mouse_y=H.position.top+J.offset.click.top;if((C.left
-
+ %else:
+
+ %endif
+
+ ${group.name}
+
+
+
+
+
+
+
+
+
+
+
+ <%
+ render_quick_find = len( groups_members_roles ) > 50
+ ctr = 0
+ %>
+ %if render_quick_find:
+ <%
+ anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
+ anchor_loc = 0
+ anchored = False
+ curr_anchor = 'A'
+ %>
+
+%endif
diff --git a/templates/admin/dataset_security/deleted_roles.mako b/templates/admin/dataset_security/deleted_roles.mako
new file mode 100644
index 00000000000..64153e05e50
--- /dev/null
+++ b/templates/admin/dataset_security/deleted_roles.mako
@@ -0,0 +1,112 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a row
+<%def name="render_row( role, groups, users, ctr, anchored, curr_anchor )">
+ %if ctr % 2 == 1:
+
+ %else:
+
+ %endif
+
+ ${role.description}
+
+
+
+
+
+
+
+
+
+
+
+ <%
+ render_quick_find = len( roles_groups_users ) > 50
+ ctr = 0
+ %>
+ %if render_quick_find:
+ <%
+ anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
+ anchor_loc = 0
+ anchored = False
+ curr_anchor = 'A'
+ %>
+
+%endif
diff --git a/templates/admin/dataset_security/group.mako b/templates/admin/dataset_security/group.mako
new file mode 100644
index 00000000000..64c809e0ee0
--- /dev/null
+++ b/templates/admin/dataset_security/group.mako
@@ -0,0 +1,57 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a role
+<%def name="render_role( group, role )">
+
+ %if role and not role.type == trans.app.model.Role.types.PRIVATE:
+ ${role.description}
+
+
+ %elif role:
+ ${role.description}
+ %endif
+
+
+
+## Render a user
+<%def name="render_user( group, user )">
+
+ ${user.email}
+
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if len( users ) > 0 or len( roles ) > 0:
+
+
+%endif
diff --git a/templates/admin/dataset_security/group_create.mako b/templates/admin/dataset_security/group_create.mako
new file mode 100644
index 00000000000..69e82acc749
--- /dev/null
+++ b/templates/admin/dataset_security/group_create.mako
@@ -0,0 +1,115 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a user row
+<%def name="render_user_row( user, ctr )">
+ %if ctr % 2 == 1:
+
+ %else:
+
+ %endif
+ ${user.email}
+
+
+
+## Render a role row
+<%def name="render_role_row( role, ctr, anchored, curr_anchor )">
+ %if ctr % 2 == 1:
+
+ %else:
+
+ %endif
+
+ %if not anchored:
+
+ ${role.name}: ${role.description}
+ %else:
+ ${role.name}: ${role.description}
+ %endif
+
+
+
+
+
+ %else:
+
+ %endif
+
+ %if check:
+ ${user.email}
+ %else:
+ ${user.email}
+ %endif
+ %if not anchored:
+
+
+ %endif
+
+
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if len( users ) == 0:
+ There are no Galaxy users
+ %else:
+
+ %endif
+
+ %if check:
+ ${role.name}
+ %else:
+ ${role.name}
+ %endif
+
+ ${role.description}
+
+ ${role.type}
+ %if not anchored:
+
+
+ %endif
+
+
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if len( roles ) == 0:
+ There are no Galaxy roles
+ %else:
+
+ %endif
+
+ ${group.name}
+
+
+
+
+
+
+
+
+
+
+
+ <%
+ render_quick_find = len( groups_members_roles ) > 50
+ ctr = 0
+ %>
+ %if render_quick_find:
+ <%
+ anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
+ anchor_loc = 0
+ anchored = False
+ curr_anchor = 'A'
+ %>
+
+%endif
diff --git a/templates/admin/dataset_security/role.mako b/templates/admin/dataset_security/role.mako
new file mode 100644
index 00000000000..2b90190fc17
--- /dev/null
+++ b/templates/admin/dataset_security/role.mako
@@ -0,0 +1,117 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+
+
+
+<%def name="render_select( name, options )">
+
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
+%if len( library_dataset_actions ) > 0: +
+
+%endif
diff --git a/templates/admin/dataset_security/role_create.mako b/templates/admin/dataset_security/role_create.mako
new file mode 100644
index 00000000000..34c940a9d2a
--- /dev/null
+++ b/templates/admin/dataset_security/role_create.mako
@@ -0,0 +1,118 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a user row
+<%def name="render_user_row( user, ctr )">
+ %if ctr % 2 == 1:
+
+ %else:
+
+ %endif
+ ${user.email}
+
+
+
+## Render a group row
+<%def name="render_group_row( group, ctr, anchored, curr_anchor )">
+ %if ctr % 2 == 1:
+
+ %else:
+
+ %endif
+
+ %if not anchored:
+
+ ${group.name}
+ %else:
+ ${group.name}
+ %endif
+
+
+
+
+
+ %else:
+
+ %endif
+
+ ${role.name}
+
+
+
+ ${role.description}
+ ${role.type}
+
+
+
+
+
+
+
+
+ <%
+ render_quick_find = len( roles ) > 50
+ ctr = 0
+ %>
+ %if render_quick_find:
+ <%
+ anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
+ anchor_loc = 0
+ anchored = False
+ curr_anchor = 'A'
+ %>
+
+%endif
diff --git a/templates/admin/dataset_security/user.mako b/templates/admin/dataset_security/user.mako
new file mode 100644
index 00000000000..5db4cf72afa
--- /dev/null
+++ b/templates/admin/dataset_security/user.mako
@@ -0,0 +1,57 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a role
+<%def name="render_role( user, role )">
+
+ %if role and not role.type == trans.app.model.Role.types.PRIVATE:
+ ${role.description}
+
+
+ %elif role:
+ ${role.description}
+ %endif
+
+
+
+## Render a group
+<%def name="render_group( user, group )">
+
+ ${group.name}
+
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if len( groups ) > 0 or len( roles ) > 0:
+
+
+%endif
diff --git a/templates/admin/dataset_security/user_groups_edit.mako b/templates/admin/dataset_security/user_groups_edit.mako
new file mode 100644
index 00000000000..d380dc44a9d
--- /dev/null
+++ b/templates/admin/dataset_security/user_groups_edit.mako
@@ -0,0 +1,100 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a row
+<%def name="render_row( group, ctr, anchored, curr_anchor, check )">
+ %if ctr % 2 == 1:
+
+ %else:
+
+ %endif
+
+ %if check:
+ ${group.name}
+ %else:
+ ${group.name}
+ %endif
+ %if not anchored:
+
+
+ %endif
+
+
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if len( groups ) == 0:
+ There are no Galaxy groups
+ %else:
+
+ %endif
+
+ %if check:
+ ${role.name}
+ %else:
+ ${role.name}
+ %endif
+ %if not anchored:
+
+
+ %endif
+
+
+
+
+
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+%if len( roles ) == 0:
+ There are no Galaxy roles
+ %else:
+
+ %endif
+
+ ${user.email}
+
+
+
+
+
+
+
+
+
+
+ <%
+ render_quick_find = len( users_groups_roles ) > 50
+ ctr = 0
+ %>
+ %if render_quick_find:
+ <%
+ anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
+ anchor_loc = 0
+ anchored = False
+ curr_anchor = 'A'
+ %>
+
+%endif
diff --git a/templates/admin/index.mako b/templates/admin/index.mako
new file mode 100644
index 00000000000..544f480974d
--- /dev/null
+++ b/templates/admin/index.mako
@@ -0,0 +1,114 @@
+<%inherit file="/base_panels.mako"/>
+
+<%def name="init()">
+<%
+ self.has_left_panel=True
+ self.has_right_panel=False
+ self.active_view="admin"
+%>
+
+
+<%def name="stylesheets()">
+
+ ${parent.stylesheets()}
+
+ ## TODO: Clean up these styles and move into panel_layout.css (they are
+ ## used here and in the editor).
+
+
+
+
+<%def name="left_panel()">
+
+
+ %if subfolder:
+
@@ -41,7 +41,7 @@
if hist == trans.get_history():
cur_history_text = " (current history)"
%>
-
- Unsequenced Genomes of the World | June 2008
+ Unsequenced Genomes of the World | October 2008
- Przewalski's Horse (Equus przewalskii) | Escondido, California + Costa's hummingbird (Calypte costae) | Kings Canyon NP, California
diff --git a/templates/admin/center.mako b/templates/admin/center.mako
new file mode 100644
index 00000000000..6ff53306b35
--- /dev/null
+++ b/templates/admin/center.mako
@@ -0,0 +1,125 @@
+<%inherit file="/base.mako"/>
+
+<%def name="title()">Galaxy Administration
+
+
- Przewalski's Horse (Equus przewalskii) | Escondido, California + Costa's hummingbird (Calypte costae) | Kings Canyon NP, California
Administration
+ +Choose a task from the menu on the left.
++ Security - Data security in Galaxy is a new feature, so familiarize yourself with the details, which can be found + here or in our data security page. The data security + process incorporates users, groups and roles, and enables the application of certain restrictions on datasets. The default process + is to not apply any security restrictions to datasets, and data becomes more restricted with each new "permission restriction" applied + to it. With no restrictions, users should not see any difference in the way Galaxy has always worked. The general definitions of + these entities are: +
-
+
- + Users - registered Galaxy users that have created a Galaxy account. Users can be members of a group and can + be associated with 1 or more roles. If a user is not authenticated during a Galaxy session, they will not have access to any + of the security features, and datasets they create during that session will have no security restrictions applied to them + (i.e., they will be considered "public"). + + +
- + Groups - a set of 0 or more users which are considered members of the group. Groups can be associated with 0 + or more roles, simplifying the process of applying "permission restrictions" to the data between a select group of users. + + +
-
+ Roles - associate users and groups with specific permissions on datasets. For example, users in groups A and B
+ can be associated with role C which gives them the "access" permission on datasets D, E and F. Roles have a type which is currently
+ one of the following:
+
-
+
- + private - every user is associated automatically with their own private role, and administrators cannot + manage them. + +
- + user - this is currently not used, but eventually any registered user will be able to create a new role + and this will be it's type. + +
- + sharing - a role created automatically during a Galaxy session that enables a user to share data with + another user. This can generally be considered a temporary role, but this role type is evolving. + +
- admin - a role created by a Galaxy administrator. +
+
+ -
+ Permissions - for any dataset, applying one of the following role "permission restrictions" will restrict the
+ use of the dataset.
+
-
+
-
+ access - users associated with the role can import this dataset into their history for analysis.
+
+ If no roles with the 'access' permission restriction are associated with a dataset, the dataset is "public" and may + be shared with anyone. Public library datasets will be accessible to all users (as well as anyone not logged in + during a Galaxy session) from the list of libraries displayed when the "Access Libraries stored locally" tool is used. +
++ Associating a dataset with a role that includes the "access" permission restriction narrows the set of users that can + access it. For example, if 'Role A' includes the "access" permission restriction and 'Role A' is associated with the dataset, + only those users and groups who are associated with 'Role A' may access the dataset. +
++ If multiple roles that include the "access" permission restriction are associated with a dataset, access to the + dataset is derived from the intersection of the users associated with the roles. For example, if 'Role A' and 'Role B' are + associated with a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset. +
++ In order for a user to make a dataset private to just themselves, they should associate the dataset with their private role + (the role identical to their Galaxy user name / email address). Associating additional roles that include the 'access' + permission restriction is not advised since the behavior will probably not be as expected. Role permission restrictions + are always logically "ANDed" together, so only the user will be able to access the dataset since they are the only member of + their "private role". To make a dataset private to themselves and one or more other users, the user should create a new role + (note: this functionality is still under development for non administrator users) and associate the dataset with that role, + not their "private role". +
++ Private data (data associated with roles that include the "access" permission restriction) must be made public in order + to be used with external sources, such as the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" + tool. Being "made public" means removing the association of all roles that include the "access" permission restriction from + the dataset. +
+
+ - edit metadata - users associated with the role can edit this dataset's metadata in the dataset library. +
- + manage permissions - users associated with the role can manage the roles associated with this dataset. If no + roles that include the 'manage permissions' are associated with the dataset, only administrators can modify it's permission + restrictions. + +
+ -
+ access - users associated with the role can import this dataset into their history for analysis.
+
The menu on the left provides the following features
+-
+
- + Manage users - provides a view of the registered users and all groups and non-private roles associated + with each user. + + +
- + Manage groups - provides a view of all groups along with the members of the group and the roles associated with + each group (both private and non-private roles). Non-private roles include a link to a page that allows you to manage the users + and groups that are associated with the role. The page also includes a view of the library datasets that are associated with the + role and the various "permission restrictions" applied to each dataset. + + +
- + Manage non-private roles - provides a view of all non-private roles along with the role type, and the users and groups that + are associated with the role. + + +
- + Manage libraries - Dataset libraries enable a Galaxy administrator to upload datasets into a library. Only + administrators can create dataset libraries and maintain their contents ( datasets ) and the security applied to them. From + the Galaxy analysis view, the "Access Libraries stored locally" tool in the "Get Data" tool + section allows users to access the datasets in a library ( if the user is not restricted from accessing the datasets by the + security rules applied to them ) by "uploading" them into their histories. This "uploading" process will not make a copy of + the dataset, however, but will be a sort of pointer to the dataset on disk. This approach allows for multiple users to have + access to a single ( possibly very large ) dataset on disk. + +
-
+ %for user in members:
+
- ${user.email} + %endfor +
-
+ %for role in roles:
+
- ${role.description} + %endfor +
Deleted Groups
+ +%if msg: + ${render_msg( msg, messagetype )} +%endif + +%if len( groups_members_roles ) == 0: + There are no deleted Galaxy groups +%else: +| + Jump to letter: + %for a in anchors: + | ${a} + %endfor + | +||
| Name | +Members | +Roles | +
-
+ %for group in groups:
+
- ${group.name} + %endfor +
-
+ %for user in users:
+
- ${user.email} + %endfor +
Deleted Roles
+ +%if msg: + ${render_msg( msg, messagetype )} +%endif + +%if len( roles_groups_users ) == 0: + There are no deleted Galaxy roles +%else: +| + Jump to letter: + %for a in anchors: + | ${a} + %endfor + | +||
| Name | +Associated Groups | +Associated Users | +
| Users associated with ${group.name} | +Roles associated with ${group.name} | +
+
|
+
+
|
+
Create Group
+ +%if msg: + ${render_msg( msg, messagetype )} +%endif + + diff --git a/templates/admin/dataset_security/group_members_edit.mako b/templates/admin/dataset_security/group_members_edit.mako new file mode 100644 index 00000000000..c10cbc1e9ee --- /dev/null +++ b/templates/admin/dataset_security/group_members_edit.mako @@ -0,0 +1,101 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +## Render a row +<%def name="render_row( user, ctr, anchored, curr_anchor, check )"> + %if ctr % 2 == 1: +
+
diff --git a/templates/admin/dataset_security/group_roles_edit.mako b/templates/admin/dataset_security/group_roles_edit.mako
new file mode 100644
index 00000000000..c574715d1c3
--- /dev/null
+++ b/templates/admin/dataset_security/group_roles_edit.mako
@@ -0,0 +1,110 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a row
+<%def name="render_row( role, ctr, anchored, curr_anchor, check )">
+ %if ctr % 2 == 1:
+ Change group name
+
+
+
+-
+ %for user in members:
+
- ${user.email} + %endfor +
-
+ %for role in roles:
+
- + %if not role.type == trans.app.model.Role.types.PRIVATE: + ${role.description} + %else: + ${role.description} + %endif + + %endfor +
Groups
+ + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +%if len( groups_members_roles ) == 0: + There are no Galaxy groups +%else: +| + Jump to letter: + %for a in anchors: + | ${a} + %endfor + | +||
| Name | +Associated Users | +Associated Roles | +
+
+Role '${role.name}'
+
+
+
++
+%if len( library_dataset_actions ) > 0: +
Library datasets associated with role '${role.name}'
+
+
|
+
})
+ ${library.name}
+ 
+ ${folder_path}
+ Create Role
+ +%if msg: + ${render_msg( msg, messagetype )} +%endif + + diff --git a/templates/admin/dataset_security/role_rename.mako b/templates/admin/dataset_security/role_rename.mako new file mode 100644 index 00000000000..d70844d6f55 --- /dev/null +++ b/templates/admin/dataset_security/role_rename.mako @@ -0,0 +1,41 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +
+
diff --git a/templates/admin/dataset_security/roles.mako b/templates/admin/dataset_security/roles.mako
new file mode 100644
index 00000000000..1f7d9df74b0
--- /dev/null
+++ b/templates/admin/dataset_security/roles.mako
@@ -0,0 +1,129 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a row
+<%def name="render_row( role, ctr, anchored, curr_anchor )">
+ %if ctr % 2 == 1:
+ Change role name and description
+
+
+
+-
+ %for ura in role.users:
+
- + ${ura.user.email} + + + + %endfor +
-
+ %for gra in role.groups:
+
- + ${gra.group.name} + + + + %endfor +
Roles
+ + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +%if len( roles ) == 0: + There are no Galaxy roles +%else: +| + Jump to letter: + %for a in anchors: + | ${a} + %endfor + | +||||
| Name | +Description | +Type | +Associated Users | +Associated Groups | +
| Groups of which ${user.email} is a member | +Roles associated with ${user.email} | +
+
|
+
+
|
+
+ Reset password
+ Change associated groups
+ Change associated roles
+ %if allow_user_deletion:
+ Mark user deleted
+ %endif
+
+ -
+ %for group in groups:
+
- ${group.name} + %endfor +
-
+ %for role in roles:
+
- ${role.description} + %endfor +
Users
+ +-
+
- Create a new user + %if allow_user_deletion: +
- Manage deleted users + %endif +
| + Jump to letter: + %for a in anchors: + | ${a} + %endfor + | +||
| Associated Groups | +Associated Roles | +|
+
+ Administration
+
+
+
+
+<%def name="center_panel()">
+
+
+
+
diff --git a/templates/admin/library/add_dataset_from_history.mako b/templates/admin/library/add_dataset_from_history.mako
new file mode 100644
index 00000000000..e8fd815bba5
--- /dev/null
+++ b/templates/admin/library/add_dataset_from_history.mako
@@ -0,0 +1,22 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Add Dataset to Library from History
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
+
+
+
+
+ Security
+
+
+
+
+
+
+ Data
+
+
+
+
+
+
+
+
+ Server
+
+
+
+
diff --git a/templates/admin/library/browser.mako b/templates/admin/library/browser.mako
new file mode 100644
index 00000000000..06646e0720a
--- /dev/null
+++ b/templates/admin/library/browser.mako
@@ -0,0 +1,226 @@
+<%inherit file="/base.mako"/>
+<%namespace file="common.mako" import="render_dataset" />
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Import from Library
+<%def name="stylesheets()">
+
+
+
+
+<%
+def name_sorted( l ):
+ return sorted( l, lambda a, b: cmp( a.name.lower(), b.name.lower() ) )
+%>
+
+
+
+<%def name="render_folder( parent, parent_pad, deleted, created_lfda_ids )">
+ <%
+ ##if not trans.app.security_agent.check_folder_contents( trans.user, parent ):
+ ## return ""
+ pad = parent_pad + 20
+ if parent_pad == 0:
+ expander = "/static/images/silk/resultset_bottom.png"
+ folder = "/static/images/silk/folder_page.png"
+ subfolder = False
+ else:
+ expander = "/static/images/silk/resultset_next.png"
+ folder = "/static/images/silk/folder.png"
+ subfolder = True
+
+ if created_lfda_ids and not isinstance ( created_lfda_ids, list ):
+ created_lfda_id_list = created_lfda_ids.split( ',' )
+ if created_lfda_id_list:
+ created_lfda_ids = [ int( lfda_id ) for lfda_id in created_lfda_id_list ]
+ %>
+ Active datasets in your current history (${history.name})
+
+
+
+
+ })
})
+ ${parent.name}
+ %if parent.description:
+ - ${parent.description}
+ %endif
+
+
+ %if not deleted:
+
+ %endif
+ -
+ %else:
+
- ${render_dataset( dataset, selected, deleted )} + %endfor +
- + Create a new library + +
- + Manage deleted libraries + + %endif +
-
+ %endif
+ %if deleted:
+ <%
+ parent_folders = parent.folders
+ parent_datasets = parent.datasets
+ %>
+ %else:
+ <%
+ parent_folders = parent.active_folders
+ parent_datasets = parent.active_datasets
+ %>
+ %endif
+ %for folder in name_sorted( parent_folders ):
+ ${render_folder( folder, pad, deleted, created_lfda_ids )}
+ %endfor
+ %for dataset in name_sorted( parent_datasets ):
+ <%
+ if created_lfda_ids and dataset.id in created_lfda_ids:
+ selected = True
+ else:
+ selected = False
+ %>
+
+ %if deleted: + Deleted + %endif + Libraries +
+ +-
+ %if not deleted:
+
+
+ ## Header row for library items (name, state, action buttons)
+
+
+ ## Body for library items, extra info and actions, data "peek"
+
+ %else:
+
+ %endif
+
+ ${user.email}
+
+
+ %if not anchored:
+
+
+ %endif
+
+
+
+
+
+ <%
+ render_quick_find = len( users ) > 50
+ ctr = 0
+ %>
+ %if render_quick_find:
+ <%
+ anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
+ anchor_loc = 0
+ anchored = False
+ curr_anchor = 'A'
+ %>
+
+%endif
diff --git a/templates/admin/user/reset_password.mako b/templates/admin/user/reset_password.mako
new file mode 100644
index 00000000000..62d45cb0a12
--- /dev/null
+++ b/templates/admin/user/reset_password.mako
@@ -0,0 +1,35 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+
-
-
diff --git a/templates/base.mako b/templates/base.mako
index e4f0d881a35..64437d13af9 100644
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -1,16 +1,16 @@
-
-${self.title()}
-
-${self.stylesheets()}
-${self.javascripts()}
-
+
+ ${self.title()}
+
+ ${self.stylesheets()}
+ ${self.javascripts()}
+
-
- ${next.body()}
-
+
+ ${next.body()}
+
## Default title
@@ -28,4 +28,4 @@ ${self.javascripts()}
##
-
\ No newline at end of file
+
diff --git a/templates/base_panels.mako b/templates/base_panels.mako
index 29a2dee470e..08516467652 100644
--- a/templates/base_panels.mako
+++ b/templates/base_panels.mako
@@ -1,6 +1,18 @@
## This needs to be on the first line, otherwise IE6 goes into quirks mode
+<%
+ self.has_left_panel=True
+ self.has_right_panel=True
+ self.message_box_visible=False
+ self.message_box_class=""
+ self.active_view=None
+%>
+
+<%def name="init()">
+ ## Override
+
+
## Default title
<%def name="title()">Galaxy
@@ -8,14 +20,30 @@
<%def name="stylesheets()">
+
## Default javascripts
<%def name="javascripts()">
-
+
## Default late-load javascripts
@@ -27,45 +55,69 @@
-
+
## Masthead
<%def name="masthead()">
-
+
+
+
+## Messagebox
+<%def name="message_box_content()">
## Document
+
+ ${self.init()}
+
- ${self.title()}
- ${self.javascripts()}
- ${self.stylesheets()}
+ ${self.title()}
+ ${self.javascripts()}
+ ${self.stylesheets()}
- ## Background displays first
-
- ## Layer iframes over backgrounds
-
+
+ %endif
+ ## Recurse for child datasets
+ %if len( data.visible_children ) > 0:
+
+
diff --git a/templates/admin/library/dataset.mako b/templates/admin/library/dataset.mako
new file mode 100644
index 00000000000..68c620f8e42
--- /dev/null
+++ b/templates/admin/library/dataset.mako
@@ -0,0 +1,105 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/dataset/security_common.mako" import="render_permission_form" />
+
+
+<%def name="title()">Edit Dataset Attributes
+
+<%def name="datatype( dataset, datatypes )">
+
+
+
+<%
+ roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all()
+%>
+
+%if isinstance( dataset, list ):
+ <%
+ name_str = '%d selected datasets' % len( dataset )
+ %>
+ ${render_permission_form( dataset[0].dataset, name_str, h.url_for( action='dataset' ), 'id', ",".join( [ str(d.id) for d in dataset ] ), roles )}
+%else:
+ ${render_permission_form( dataset.dataset, dataset.name, h.url_for( action='dataset' ), 'id', dataset.id, roles )}
+%endif
+
+%if not isinstance( dataset, list ):
+ ${data.blurb}
+
+ %if data.has_data:
+ %for display_app in data.datatype.get_display_types():
+ <% display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %>
+ %if len( display_links ) > 0:
+ ${data.datatype.get_display_label(display_app)}
+ %for display_name, display_link in display_links:
+ ${display_name}
+ %endfor
+ %endif
+ %endfor
+ %endif
+
+ %if data.peek != "no peek":
+ ${data.display_peek()}
+ There are ${len( data.visible_children )} secondary datasets.
+ %for idx, child in enumerate( data.visible_children ):
+ ${ render_dataset( child, selected, deleted ) }
+ %endfor
+
+ %endif
+
+
+
+ Edit Attributes
+
+
+
+
+
+
+
+%endif
diff --git a/templates/admin/library/new_dataset.mako b/templates/admin/library/new_dataset.mako
new file mode 100644
index 00000000000..3888d629aee
--- /dev/null
+++ b/templates/admin/library/new_dataset.mako
@@ -0,0 +1,110 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<% import os %>
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+Change data type
+
+
+
+
+
diff --git a/templates/admin/library/new_folder.mako b/templates/admin/library/new_folder.mako
new file mode 100644
index 00000000000..8ce7207e96a
--- /dev/null
+++ b/templates/admin/library/new_folder.mako
@@ -0,0 +1,41 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+Create a new library dataset
+
+
+
+
+
diff --git a/templates/admin/library/new_library.mako b/templates/admin/library/new_library.mako
new file mode 100644
index 00000000000..c514d2965b3
--- /dev/null
+++ b/templates/admin/library/new_library.mako
@@ -0,0 +1,35 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+Create a new folder
+
+
+
+
+
diff --git a/templates/admin/library/rename_folder.mako b/templates/admin/library/rename_folder.mako
new file mode 100644
index 00000000000..8638edf60a1
--- /dev/null
+++ b/templates/admin/library/rename_folder.mako
@@ -0,0 +1,41 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+Create a new library
+
+
+
+
+
diff --git a/templates/admin/library/rename_library.mako b/templates/admin/library/rename_library.mako
new file mode 100644
index 00000000000..9114248a942
--- /dev/null
+++ b/templates/admin/library/rename_library.mako
@@ -0,0 +1,48 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+Edit folder name and description
+
+
+
+
+
diff --git a/templates/admin/memdump.mako b/templates/admin/memdump.mako
index e99c5585c19..edbf154e5a5 100644
--- a/templates/admin/memdump.mako
+++ b/templates/admin/memdump.mako
@@ -1,4 +1,5 @@
<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
<%def name="title()">Memory Profiling
<%
@@ -44,7 +45,7 @@
%if msg:
-
+ ${render_msg( msg, messagetype )}
%endif
%if heap is None:
diff --git a/templates/admin/reload_tool.mako b/templates/admin/reload_tool.mako
new file mode 100644
index 00000000000..292a4a2d811
--- /dev/null
+++ b/templates/admin/reload_tool.mako
@@ -0,0 +1,30 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+Change library name and description
+
+
+
+
+
diff --git a/templates/admin/user/create.mako b/templates/admin/user/create.mako
new file mode 100644
index 00000000000..ef076e75096
--- /dev/null
+++ b/templates/admin/user/create.mako
@@ -0,0 +1,43 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+ ${render_msg( msg, messagetype )}
+%endif
+
+Reload Tool
+
+
+
+
+
diff --git a/templates/admin/user/deleted_users.mako b/templates/admin/user/deleted_users.mako
new file mode 100644
index 00000000000..0847cf25a63
--- /dev/null
+++ b/templates/admin/user/deleted_users.mako
@@ -0,0 +1,91 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a row
+<%def name="render_row( user, ctr, anchored, curr_anchor )">
+ %if ctr % 2 == 1:
+ Create account
+
+
+
+Deleted Users
+ +%if msg: + ${render_msg( msg, messagetype )} +%endif + +%if len( users ) == 0: + There are no deleted Galaxy users +%else: +| + Jump to letter: + %for a in anchors: + | ${a} + %endfor + | +||
+
diff --git a/templates/admin_main.mako b/templates/admin_main.mako
deleted file mode 100644
index f9c26121124..00000000000
--- a/templates/admin_main.mako
+++ /dev/null
@@ -1,33 +0,0 @@
-<%inherit file="/base.mako"/>
-<%def name="title()">Galaxy Administration
-
-Reset user password
+
+
+
+
- Galaxy Administration- %if msg: -${msg} - %endif - |
-
| - - | -
- ${self.masthead()}
-
-
- ${self.left_panel()}
-
-
-
- ${self.center_panel()}
-
-
-
- ${self.right_panel()}
-
+ ## Background displays first
+
+ ## Layer iframes over backgrounds
+
+ ${self.masthead()}
+
+
+ %if self.has_left_panel:
+
+ ${self.left_panel()}
+
+
+
+
+ %endif
+
+ ${self.center_panel()}
+
+ %if self.has_right_panel:
+
+
+ ${self.right_panel()}
+
+ %endif
## Allow other body level elements
- ${next.body()}
+ ${next.body()}
## Scripts can be loaded later since they progressively add features to
## the panels, but do not change layout
diff --git a/templates/dataset/copy_view.mako b/templates/dataset/copy_view.mako
index 97c932bac32..ba4f265ce43 100644
--- a/templates/dataset/copy_view.mako
+++ b/templates/dataset/copy_view.mako
@@ -25,7 +25,7 @@
if data.id in source_dataset_ids:
checked = " checked"
%>
- ${data.hid}: ${data.name}
+ ${data.hid}: ${data.name}
%endfor
${i + 1}${cur_history_text}: ${hist.name}
+ ${i + 1}${cur_history_text}: ${hist.name}
%endfor
%if trans.get_user():
<%
@@ -50,12 +50,12 @@
checked = " checked"
%>
-
New history named:
+ New history named:
%endif
-
+
diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index 39936d24f4c..c29b77677b0 100644
--- a/templates/dataset/edit_attributes.mako
+++ b/templates/dataset/edit_attributes.mako
@@ -1,146 +1,195 @@
<%inherit file="/base.mako"/>
-<%def name="title()">History Item Attributes
+<%def name="title()">Edit Dataset Attributes
<%def name="datatype( dataset, datatypes )">
-
+
-
-
+
+%endif
-
- Edit Attributes
-
-
+
-
@@ -27,4 +28,90 @@
-
\ No newline at end of file
+
+%else:
+
+
+%endif
diff --git a/templates/library/browser.mako b/templates/library/browser.mako
new file mode 100644
index 00000000000..ba1d313b07d
--- /dev/null
+++ b/templates/library/browser.mako
@@ -0,0 +1,171 @@
+<%inherit file="/base.mako"/>
+<%namespace file="common.mako" import="render_dataset" />
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Import from Library
+<%def name="stylesheets()">
+
+
+
+
+<%
+def name_sorted( l ):
+ return sorted( l, lambda a, b: cmp( a.name.lower(), b.name.lower() ) )
+%>
+
+
+
+
+
+
+
+<%def name="render_folder( parent, parent_pad )">
+ <%
+ if not trans.app.security_agent.check_folder_contents( trans.user, parent ):
+ return ""
+ pad = parent_pad + 20
+ if parent_pad == 0:
+ expander = "/static/images/silk/resultset_bottom.png"
+ folder = "/static/images/silk/folder_page.png"
+ subfolder = False
+ else:
+ expander = "/static/images/silk/resultset_next.png"
+ folder = "/static/images/silk/folder.png"
+ subfolder = True
+ %>
+
+
+ %if subfolder:
+
Change data type
-
-
+%endif
diff --git a/templates/dataset/security_common.mako b/templates/dataset/security_common.mako
new file mode 100644
index 00000000000..517836f18d4
--- /dev/null
+++ b/templates/dataset/security_common.mako
@@ -0,0 +1,87 @@
+<%def name="render_select( current_actions, action_key, action, all_roles )">
+ <%
+ in_roles = []
+ for a in current_actions:
+ if a.action == action.action:
+ in_roles.append( a.role )
+ out_roles = filter( lambda x: x not in in_roles, all_roles )
+ %>
+ ${action.description}
+
+
+
+
+<%def name="render_permission_form( obj, obj_name, form_url, id_name, id, all_roles )">
+ <%
+ if isinstance( obj, trans.app.model.User ):
+ current_actions = obj.default_permissions
+ obj_str = 'user %s' % obj_name
+ elif isinstance( obj, trans.app.model.History ):
+ current_actions = obj.default_permissions
+ obj_str = 'history %s' % obj_name
+ elif isinstance( obj, trans.app.model.Dataset ):
+ current_actions = obj.actions
+ obj_str = obj_name
+ else:
+ current_actions = obj.dataset.actions
+ obj_str = 'unknown object %s' %obj_name
+ %>
+
+
+ Roles associated:
+
+ +
+ +
+ +
+ Roles not associated:
+
+ +
+ +
+ +
+
+
+
diff --git a/templates/form.mako b/templates/form.mako
index c003de02585..9fe2a413884 100644
--- a/templates/form.mako
+++ b/templates/form.mako
@@ -10,6 +10,10 @@ $(function(){
+%if header:
+ ${header}
+%endif
+
Manage permissions and role associations for ${obj_str}
+
+
+
+ ${form.title}
@@ -21,9 +25,11 @@ $(function(){
cls += " form-row-error"
%>
Change default permissions for the current history
%endif
Show deleted datasets in history
Delete current history
diff --git a/templates/history/permissions.mako b/templates/history/permissions.mako
new file mode 100644
index 00000000000..a189523440d
--- /dev/null
+++ b/templates/history/permissions.mako
@@ -0,0 +1,7 @@
+<%inherit file="/base.mako"/>
+<%def name="title()">Change Default Permissions on New Datasets in This History
+<%namespace file="/dataset/security_common.mako" import="render_permission_form" />
+
+%if trans.user:
+ ${render_permission_form( trans.history, trans.history.name, h.url_for(), 'id', None, trans.user.all_roles() )}
+%endif
diff --git a/templates/history/share.mako b/templates/history/share.mako
index 5e64e66756a..8728587cb45 100644
--- a/templates/history/share.mako
+++ b/templates/history/share.mako
@@ -1,6 +1,7 @@
<%inherit file="/base.mako"/>
<%def name="title()">Share histories
+%if not can_change and not cannot_change:
+ %if input.use_label:
+ %endif
diff --git a/templates/history/options.mako b/templates/history/options.mako
index dfe3ffd9d09..14b3e981455 100644
--- a/templates/history/options.mako
+++ b/templates/history/options.mako
@@ -18,6 +18,7 @@
%endif
Construct workflow from the current history
Share current history
+ Share Histories
+
+ ${parent.name}
+ %if parent.description:
+ - ${parent.description}
+ %endif
+
+ -
+ %else:
+
- ${render_dataset( dataset )} + %endif + %endfor +
-
+ %endif
+ %for folder in name_sorted( parent.active_folders ):
+ ${render_folder( folder, pad )}
+ %endfor
+ %for dataset in name_sorted( parent.active_datasets ):
+ %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=dataset.dataset ):
+
Libraries
+ +%if msg: + ${render_msg( msg, messagetype )} +%endif + +%if not libraries: + No libraries contain datasets that you are allowed to access +%else: + <% can_access = False %> +
+
+ ## Header row for library items (name, state, action buttons)
+
+
+ ## Body for library items, extra info and actions, data "peek"
+
+ diff --git a/templates/no_access.mako b/templates/no_access.mako new file mode 100644 index 00000000000..031cafbaf5f --- /dev/null +++ b/templates/no_access.mako @@ -0,0 +1,15 @@ +<%inherit file="/base.mako"/> + +<%def name="javascripts()"> + ${parent.javascripts()} + + + + diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako index 139bf19dfb1..f09229dbd1c 100644 --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -6,7 +6,11 @@ else: data_state = data.state %> -
+
+ %endif
+ ## Recurse for child datasets
+ %if len( data.visible_children ) > 0:
+
+
diff --git a/templates/message.mako b/templates/message.mako
index 551b60c4735..3e6783245e5 100644
--- a/templates/message.mako
+++ b/templates/message.mako
@@ -1,32 +1,44 @@
<%inherit file="/base.mako"/>
<%def name="javascripts()">
-${parent.javascripts()}
-
+ if ( parent.handle_minwidth_hint )
+ {
+ parent.handle_minwidth_hint( -1 );
+ }
+
+
+## Render a message
+<%def name="render_msg( msg, messagetype='done' )">
+
+ ${data.blurb}
+
+ %if data.has_data:
+ %for display_app in data.datatype.get_display_types():
+ <% display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %>
+ %if len( display_links ) > 0:
+ ${data.datatype.get_display_label(display_app)}
+ %for display_name, display_link in display_links:
+ ${display_name}
+ %endfor
+ %endif
+ %endfor
+ %endif
+
+ %if data.peek != "no peek":
+ ${data.display_peek()}
+ There are ${len( data.visible_children )} secondary datasets.
+ %for idx, child in enumerate( data.visible_children ):
+ ${render_dataset( child )}
+ %endfor
+
+ %endif
+ + diff --git a/templates/no_access.mako b/templates/no_access.mako new file mode 100644 index 00000000000..031cafbaf5f --- /dev/null +++ b/templates/no_access.mako @@ -0,0 +1,15 @@ +<%inherit file="/base.mako"/> + +<%def name="javascripts()"> + ${parent.javascripts()} + + + + diff --git a/templates/root/history_common.mako b/templates/root/history_common.mako index 139bf19dfb1..f09229dbd1c 100644 --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -6,7 +6,11 @@ else: data_state = data.state %> -
+ %if not trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ):
+
+ %else:
+
+ %endif
%if data.deleted:
@@ -36,7 +40,9 @@
## Body for history items, extra info and actions, data "peek"
- %if data_state == "queued":
+ %if not trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ):
+
@@ -13,8 +28,12 @@
## If a specific tool id was specified, load it in the middle frame
<%
- if tool_id is not None:
+ if trans.app.config.require_login and not trans.user:
+ center_url = h.url_for( controller='user', action='login' )
+ elif tool_id is not None:
center_url = h.url_for( 'tool_runner', tool_id=tool_id, from_noframe=True )
+ elif workflow_id is not None:
+ center_url = h.url_for( controller='workflow', action='run', id=workflow_id )
elif m_c is not None:
center_url = h.url_for( controller=m_c, action=m_a )
else:
@@ -29,12 +48,12 @@
-
\ No newline at end of file
+
diff --git a/templates/root/masthead.mako b/templates/root/masthead.mako
index 58d8f1776db..270d9f59d3c 100644
--- a/templates/root/masthead.mako
+++ b/templates/root/masthead.mako
@@ -9,32 +9,65 @@
-
+
+
diff --git a/templates/root/tool_menu.mako b/templates/root/tool_menu.mako
index c2d77210905..a135b6ff1f8 100644
--- a/templates/root/tool_menu.mako
+++ b/templates/root/tool_menu.mako
@@ -90,7 +90,7 @@
You do not have permission to view this dataset.
+ %elif data_state == "queued":
Job is waiting to run
%elif data_state == "running":
Job is currently running
diff --git a/templates/root/index.mako b/templates/root/index.mako
index f573571162b..69c3ab49ff8 100644
--- a/templates/root/index.mako
+++ b/templates/root/index.mako
@@ -1,11 +1,26 @@
<%inherit file="/base_panels.mako"/>
+<%def name="init()">
+<%
+ self.has_left_panel=True
+ self.has_right_panel=True
+ self.active_view="analysis"
+%>
+%if trans.app.config.require_login and not trans.user:
+
+%endif
+
+
<%def name="left_panel()">
Tools
}) |
Galaxy${brand} |
- - Info: report bugs - | wiki - | screencasts - | blog + %if not app.config.require_login or ( app.config.require_login and trans.user): + View: + analysis + | workflow + %if admin_user == "true": + | admin + %endif + + + + %endif + + Info: report bugs + | wiki + | screencasts + + %if app.config.use_remote_user: Logged in as ${t.user.email} %else: %if t.user: - Logged in as ${t.user.email}: manage - | logout + Logged in as ${t.user.email}: manage + %if app.config.require_login: + | logout + %else: + | logout + %endif %else: - Account: create - | login + Account: + %if app.config.allow_user_creation: + create | + %endif + login %endif %endif + |
%if t.user:
%for m in t.user.stored_workflow_menu_entries:
@@ -110,4 +110,4 @@
-
\ No newline at end of file
+
diff --git a/templates/user/index.mako b/templates/user/index.mako
index 2b11262cece..04303c9b0a4 100644
--- a/templates/user/index.mako
+++ b/templates/user/index.mako
@@ -8,6 +8,7 @@
Login
Create new account
-%endif
\ No newline at end of file
+%endif
diff --git a/templates/user/permissions.mako b/templates/user/permissions.mako
new file mode 100644
index 00000000000..45b44795f38
--- /dev/null
+++ b/templates/user/permissions.mako
@@ -0,0 +1,7 @@
+<%inherit file="/base.mako"/>
+<%def name="title()">Change Default Permissions on New Histories
+<%namespace file="/dataset/security_common.mako" import="render_permission_form" />
+
+%if trans.user:
+ ${render_permission_form( trans.user, trans.user.email, h.url_for(), 'id', None, trans.user.all_roles() )}
+%endif
diff --git a/templates/workflow/editor.mako b/templates/workflow/editor.mako
index 18d7b862fed..3b3cf7ee055 100644
--- a/templates/workflow/editor.mako
+++ b/templates/workflow/editor.mako
@@ -1,6 +1,18 @@
<%inherit file="/base_panels.mako"/>
-<%def name="title()">Galaxy Workflow Editor
+<%def name="init()">
+<%
+ self.active_view="workflow"
+ self.message_box_visible=True
+ self.message_box_class="warning"
+%>
+
+
+<%def name="message_box_content()">
+ Workflow support is currently in beta testing.
+ Workflows may not work with all tools, may fail unexpectedly, and may
+ not be compatible with future updates to Galaxy.
+
<%def name="late_javascripts()">
@@ -229,7 +241,7 @@
}
var close_editor = function() {
- <% next_url = h.url_for( controller='root', m_c='workflow' ) %>
+ <% next_url = h.url_for( controller='workflow', action='index' ) %>
if ( workflow && workflow.has_changes ) {
do_close = function() {
window.onbeforeunload = undefined;
@@ -301,11 +313,12 @@
<%def name="stylesheets()">
- ${parent.stylesheets()}
-
- ## Also include "base.css" for styling tool menu and forms (details)
+ ## Include "base.css" for styling tool menu and forms (details)
+ ## But make sure styles for the layout take precedence
+ ${parent.stylesheets()}
+
- Change your password
- Update your email address +
- Change default permissions for new histories
- Logout