Merge pull request #319 from guzman-raphael/package-ext

Fix merge issues and housekeeping items

Author: guzman-raphael

+dj/conn.m

@@ -51,13 +51,6 @@
         end
     end
 else
-    % optional environment variables specifying the connection.
-    env  = struct(...
-        'host', 'DJ_HOST', ...
-        'user', 'DJ_USER', ...
-        'pass', 'DJ_PASS', ...
-        'init', 'DJ_INIT');
-    
     % get host address
     if isempty(host)
         host = input('Enter datajoint host address> ','s');

.github/workflows/development.yaml

@@ -36,4 +36,4 @@ jobs:
           DOCKER_CLIENT_TIMEOUT: "120"
           COMPOSE_HTTP_TIMEOUT: "120"
         run: |
-          docker-compose -f LNX-docker-compose.yml up --build --exit-code-from app
+          docker-compose -f LNX-docker-compose.yaml up --build --exit-code-from app

.gitignore

@@ -3,7 +3,7 @@ mym/
 *.env
 notebook
 *getSchema.m
-docker-compose.yml
+docker-compose.yaml
 .vscode
 matlab.prf
 win.*

LNX-docker-compose.yml renamed to LNX-docker-compose.yaml

@@ -1,4 +1,4 @@
-# docker-compose -f LNX-docker-compose.yml --env-file LNX.env up --build --exit-code-from app
+# docker-compose -f LNX-docker-compose.yaml --env-file LNX.env up --build --exit-code-from app
 version: '2.2'
 x-net: &net
   networks:
@@ -79,11 +79,11 @@ services:
           try\
             websave([tempdir 'GHToolbox.mltbx'],\
                     ['https://github.com/datajoint/GHToolbox' \
-                    '/releases/download/' subsref(webread(['https://api.github.com/repos' \
+                     '/releases/download/' subsref(webread(['https://api.github.com/repos' \
                                                             '/datajoint/GHToolbox' \
                                                             '/releases/latest']),\
-                                                  substruct('.', 'tag_name')) \
-                    '/GHToolbox.mltbx']);\
+                                                   substruct('.', 'tag_name')) \
+                     '/GHToolbox.mltbx']);\
             matlab.addons.toolbox.installToolbox([tempdir 'GHToolbox.mltbx']);\
             fid = fopen('README.md', 'r');\
             docs = fread(fid, '*char')';\
@@ -92,18 +92,19 @@ services:
                         'Raphael Guzman',\
                         'raphael.h.guzman@gmail.com',\
                         ['Scientific workflow management framework built on top of a ' \
-                          'relational database.'],\
+                         'relational database.'],\
                         docs,\
-                        {'.vscode', '.git', '*.env', '.gitignore', '*.yml', 'tests', 'mym'\
-                          'docs-parts', '*.txt', '*.prf', '*.md'},\
+                        {'.vscode', '.git*', '*.env', '*.yaml', 'tests', 'mym', 'docs-parts',\
+                         '*.txt', '*.prf', '*.md', 'notebook'},\
                         @() strjoin(arrayfun(@(x) num2str(x),\
-                                              cell2mat(struct2cell(dj.version)),\
-                                              'uni', false),\
-                                    '.'),\
+                                             cell2mat(struct2cell(dj.version)),\
+                                             'uni', false),\
+                                     '.'),\
                         {'+dj', 'erd.m'});\
             matlab.addons.toolbox.installToolbox('DataJoint.mltbx');\
             cd(getenv('ORIG_DIR'));\
             addpath('tests');\
+            dir(fileparts(which('erd')));\
             res=run(Main);\
             disp(res);\
             if all([res.Passed])  exit, else exit(1), end;\

README.md

@@ -47,7 +47,7 @@ MATLAB_UID=1000
 MATLAB_GID=1000
 MYSQL_TAG=5.7
 ```
-* `cp local-docker-compose.yml docker-compose.yml`
+* `cp local-docker-compose.yaml docker-compose.yaml`
 * `docker-compose up` (Note configured `JUPYTER_PASSWORD`)
 * Select a means of running MATLAB e.g. Jupyter Notebook, GUI, or Terminal (see bottom)
 * Add `tests` directory to path e.g. in MATLAB, `addpath('tests')`

local-docker-compose.yml renamed to local-docker-compose.yaml

@@ -1,4 +1,4 @@
-# docker-compose -f local-docker-compose.yml --env-file LNX.env up --build
+# docker-compose -f local-docker-compose.yaml --env-file LNX.env up --build
 version: '2.4'
 x-net: &net
   networks:
@@ -105,8 +105,8 @@ services:
                        ['Scientific workflow management framework built on top of a ' \
                         'relational database.'],\
                        docs,\
-                       {'.vscode', '.git', '*.env', '.gitignore', '*.yml', 'tests', 'mym'\
-                        'docs-parts', '*.txt', '*.prf', '*.md'},\
+                       {'.vscode', '.git*', '*.env', '*.yaml', 'tests', 'mym', 'docs-parts',\
+                        '*.txt', '*.prf', '*.md', 'notebook'},\
                        @() strjoin(arrayfun(@(x) num2str(x),\
                                             cell2mat(struct2cell(dj.version)),\
                                             'uni', false),\
@@ -116,6 +116,7 @@ services:
           addpath('tests');\
           savepath;\
           cd(tempdir);\
+          dir(fileparts(which('erd')));\
           disp(dj.version);\
         "
         cd "$${ORIG_DIR}"

tests/TestConnection.m

@@ -39,5 +39,39 @@ function TestConnection_testPort(testCase)
                 testCase.CONN_INFO.password,'',true), ...
                 'MySQL:Error');
         end
+        function TestConnection_testTransactionRollback(testCase)
+            st = dbstack;
+            disp(['---------------' st(1).name '---------------']);
+            package = 'University';
+
+            c1 = dj.conn(...
+                testCase.CONN_INFO.host,... 
+                testCase.CONN_INFO.user,...
+                testCase.CONN_INFO.password,'',true);
+            dj.createSchema(package,[testCase.test_root '/test_schemas'], ...
+                [testCase.PREFIX '_university']);
+            schema = University.getSchema;
+            tmp = {
+                20   'Henry'   'Jupyter' '2020-11-25 12:34:56'
+                21   'Lacy'   'Mars' '2017-11-25 12:34:56'
+            };
+
+            insert(University.Student, tmp(1, :));
+
+            schema.conn.startTransaction
+            try
+                insert(University.Student, tmp(2, :));
+                assert(false, 'Customer:Error', 'Message')
+            catch ME
+                schema.conn.cancelTransaction
+                if ~strcmp(ME.identifier,'Customer:Error')
+                    rethrow(ME);
+                end
+            end
+
+            q = University.Student & 'student_id in (20,21)';
+            testCase.verifyEqual(q.count, 1);
+            testCase.verifyEqual(q.fetch1('student_id'), 20);
+        end
     end
 end

tests/TestTls.m

@@ -47,11 +47,6 @@ function TestTls_testRejectException(testCase)
                     'djssl', ...
                     '',true,false);
                 testCase.verifyTrue(false);
-            % catch
-            %     e = lasterror;
-            %     testCase.verifyEqual(e.identifier, 'MySQL:Error');
-            %     testCase.verifyTrue(contains(e.message,...
-            %         {'requires secure connection','Access denied'})); %MySQL8,MySQL5
             catch ME
                 testCase.verifyEqual(ME.identifier, 'MySQL:Error');
                 testCase.verifyTrue(contains(ME.message,'requires secure connection') || ...