Merge remote-tracking branch 'origin/master' into...

Merge remote-tracking branch 'origin/master' into 928-anonymous-logged-in-after-reopening-the-browser

CHANGELOG

@@ -13,7 +13,9 @@ minerva (14.0.0~beta.0) unstable; urgency=low
   * Small improvement: information about person who uploaded project is visible 
     in list of projects (#927)
   * Small improvement: user role introduced in edit user dialog (#924)
-  * Bug fix: work on FF Private Window mode could cause logout or raise an 
+  * Small improvement: tab with list of glyps is available when adding project
+    with glyphs (#925)
+  * Bug fix: work on FF Private Window mode could cause logout or raise an
     error on when opening new tab with minerva (#892)
   * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server 
     Error" (#889)
@@ -51,6 +53,8 @@ minerva (14.0.0~beta.0) unstable; urgency=low
   * Bug fix: after genome is removed list of genomes is refreshed (#922)
   * Bug fix: when session expired anonymous user could access admin panel with
     very limited access (#928)
+  * Bug fix: migrating from old minerva will grant WRITE_PROJECT privilege to
+    users who have manage comments or manage overlays privilege (#902)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 21 Aug 2019 21:00:00 +0200
 

frontend-js/src/main/js/gui/admin/AddProjectDialog.js

@@ -80,7 +80,6 @@ AddProjectDialog.prototype.createGui = function () {
     content: self.createOverviewImagesTabContent(),
     disabled: true
   });
-
 };
 
 /**
@@ -573,7 +572,7 @@ AddProjectDialog.prototype._createGlyphsTable = function () {
     var data = [];
     for (var i = 0; i < entries.length; i++) {
       var entry = entries[i];
-      if (entry.getType() === "GLYPHS") {
+      if (entry.getType() === "GLYPH") {
         var row = [];
         row[0] = entry.getFilename();
         data.push(row);
@@ -1366,7 +1365,7 @@ AddProjectDialog.prototype.setZipFileContent = function (file) {
             images++;
           } else if (entry.getType() === 'OVERLAY') {
             overlays++;
-          } else if (entry.getType() === 'GLYPHS') {
+          } else if (entry.getType() === 'GLYPH') {
             glyphs++;
           }
         }

frontend-js/src/main/js/gui/leftPanel/GuiUtils.js

@@ -1195,8 +1195,6 @@ GuiUtils.prototype.hideTab = function (abstractGuiElement, panel) {
 GuiUtils.prototype.disableTab = function (element, message) {
   var hideReason = $(".minerva-hide-reason", element);
   if (hideReason.length === 0) {
-    console.log("not hidden");
-
     $(element).children().css("visibility", "hidden");
     $("[class='minerva-help-button']", element).children().css("visibility", "visible");
     var hideReasonDiv = document.createElement("div");

persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190527__extract_center_line.sql

@@ -16,11 +16,32 @@ alter table reaction_table add column product integer;
 alter table reaction_table add column input_operator integer;
 alter table reaction_table add column output_operator integer;
 
-update reaction_table set reactant = (select id from reaction_node_table where node_type_db='REACTANT_NODE' and reaction_id=reaction_table.id order by id limit 1);
-update reaction_table set product = (select id from reaction_node_table where node_type_db='PRODUCT_NODE' and reaction_id=reaction_table.id order by id limit 1);
+--old version of computing first reactant, product, input and output operators (this version is ~100 slower than new one). This is an issue for big maps. For db with 30k reactions it toook 25minutes
+--
+--update reaction_table set reactant = (select id from reaction_node_table where node_type_db='REACTANT_NODE' and reaction_id=reaction_table.id order by id limit 1);
+--update reaction_table set product = (select id from reaction_node_table where node_type_db='PRODUCT_NODE' and reaction_id=reaction_table.id order by id limit 1);
+--update reaction_table set input_operator = (select id from reaction_node_table where node_type_db in ('AND_OPERATOR_NODE', 'ASSOCIATION_OPERATOR_NODE', 'NAND_OPERATOR_NODE', 'OR_OPERATOR_NODE', 'UNKNOWN_OPERATOR_NODE') and reaction_id=reaction_table.id order by id limit 1);
+--update reaction_table set output_operator = (select id from reaction_node_table where node_type_db in ('DISSOCIATION_OPERATOR_NODE', 'SPLIT_OPERATOR_NODE', 'TRUNCATION_OPERATOR_NODE') and reaction_id=reaction_table.id order by id limit 1);
 
-update reaction_table set input_operator = (select id from reaction_node_table where node_type_db in ('AND_OPERATOR_NODE', 'ASSOCIATION_OPERATOR_NODE', 'NAND_OPERATOR_NODE', 'OR_OPERATOR_NODE', 'UNKNOWN_OPERATOR_NODE') and reaction_id=reaction_table.id order by id limit 1);
-update reaction_table set output_operator = (select id from reaction_node_table where node_type_db in ('DISSOCIATION_OPERATOR_NODE', 'SPLIT_OPERATOR_NODE', 'TRUNCATION_OPERATOR_NODE') and reaction_id=reaction_table.id order by id limit 1);
+create table tmp_node (
+  node_id integer,
+  node_type_db varchar,
+  reaction_id integer,
+	CONSTRAINT tmp_fkey FOREIGN KEY (reaction_id)
+      REFERENCES reaction_table (id) MATCH SIMPLE
+      ON UPDATE NO ACTION ON DELETE NO ACTION
+);
+insert into tmp_node select min(id), node_type_db, reaction_id from reaction_node_table group by node_type_db, reaction_id;
+
+insert into tmp_node select min(id), 'INPUT_NODE', reaction_id from reaction_node_table where node_type_db in ('AND_OPERATOR_NODE', 'ASSOCIATION_OPERATOR_NODE', 'NAND_OPERATOR_NODE', 'OR_OPERATOR_NODE', 'UNKNOWN_OPERATOR_NODE') group by  reaction_id;
+insert into tmp_node select min(id), 'OUTPUT_NODE', reaction_id from reaction_node_table where node_type_db in ('DISSOCIATION_OPERATOR_NODE', 'SPLIT_OPERATOR_NODE', 'TRUNCATION_OPERATOR_NODE') group by  reaction_id;
+
+update reaction_table set reactant = tmp_node.node_id from tmp_node where tmp_node.reaction_id=reaction_table.id and tmp_node.node_type_db = 'REACTANT_NODE';
+update reaction_table set product = tmp_node.node_id from tmp_node where tmp_node.reaction_id=reaction_table.id and tmp_node.node_type_db = 'PRODUCT_NODE';
+update reaction_table set input_operator = tmp_node.node_id from tmp_node where tmp_node.reaction_id=reaction_table.id and tmp_node.node_type_db = 'INPUT_NODE';
+update reaction_table set output_operator = tmp_node.node_id from tmp_node where tmp_node.reaction_id=reaction_table.id and tmp_node.node_type_db = 'OUTPUT_NODE';
+
+drop table tmp_node;
 
 update reaction_table set start_point = (select one_before_last_point from reaction_node_table, polyline_data_table where reaction_node_table.id = reaction_table.reactant and polyline_data_table.id = line_id);
 update reaction_table set end_point = (select second_point from reaction_node_table, polyline_data_table where reaction_node_table.id = reaction_table.product and polyline_data_table.id = line_id);

persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190618__new_permission_model.sql

 --remove artifacts (privileges to non-existing projects)
-delete from privilege_table where (type = 'VIEW_PROJECT' or type ='EDIT_COMMENTS_PROJECT') and not id_object in (select id from project_table); 
+delete from privilege_table where (type = 'VIEW_PROJECT' or type ='EDIT_COMMENTS_PROJECT' or type='LAYOUT_MANAGEMENT') and not id_object in (select id from project_table);
 
 alter table privilege_table rename column id_object to object_id;
 delete from privilege_table where level = 0;
@@ -34,6 +34,12 @@ from (select user_id, object_id from privilege_table where type = 'VIEW_PROJECT'
 inner join (select id, object_id from privilege_table where type = 'READ_PROJECT') s2
 on s1.object_id = s2.object_id;
 
+insert into user_privilege_map_table (user_id, privilege_id)
+select s1.user_id, s2.id
+from (select user_id, object_id from privilege_table where type = 'EDIT_COMMENTS_PROJECT' or type = 'LAYOUT_MANAGEMENT') s1
+inner join (select id, object_id from privilege_table where type = 'WRITE_PROJECT') s2
+on s1.object_id = s2.object_id;
+
 insert into user_privilege_map_table (user_id, privilege_id)
 select s1.user_id, s2.id 
 from (select user_id, object_id from privilege_table where type = 'VIEW_PROJECT' and user_id in (select user_id from privilege_table where type = 'ADD_MAP')) s1