Add dj.config + support methods and remove dj.set

+dj/+config/load.m

@@ -0,0 +1,10 @@
+function load(fname)
+    switch nargin
+        case 0
+            dj.internal.Settings.load();
+        case 1
+            dj.internal.Settings.load(fname);
+        otherwise
+        error('Exceeded 1 input limit.');
+    end
+end

+dj/+config/restore.m

@@ -0,0 +1,3 @@
+function out = restore()
+    out = dj.internal.Settings.restore();
+end

+dj/+config/save.m

@@ -0,0 +1,10 @@
+function save(fname)
+    switch nargin
+        case 0
+            dj.internal.Settings.save();
+        case 1
+            dj.internal.Settings.save(fname);
+        otherwise
+        error('Exceeded 1 input limit.');
+    end
+end

+dj/+config/saveGlobal.m

@@ -0,0 +1,3 @@
+function saveGlobal()
+    dj.internal.Settings.saveGlobal();
+end 

+dj/+config/saveLocal.m

@@ -0,0 +1,3 @@
+function saveLocal()
+    dj.internal.Settings.saveLocal();
+end

+dj/+internal/AutoPopulate.m

@@ -111,12 +111,12 @@
             %
             % See also dj.internal.AutoPopulate/parpopulate
 
-            if ~dj.set('populateAncestors')
+            if ~dj.config('queryPopulate_ancestors')
                 rels = {self};
             else
                 % get all ancestors to be populated before self
                 assert(nargout==0, ...
-                    'parpopulate cannot return output when populateAncestors is true')
+                    'parpopulate cannot return output when queryPopulate_ancestors is true')
                 rels = cellfun(@feval, self.ancestors, 'uni', false);
                 rels = rels(cellfun(@(x) isa(x,'dj.internal.AutoPopulate'), rels));
             end
@@ -171,7 +171,7 @@ function parpopulate(self, varargin)
             %
             % See also dj.internal.AutoPopulate/populate
 
-            if ~dj.set('populateAncestors')
+            if ~dj.config('queryPopulate_ancestors')
                 rels = {self};
             else
                 % get all ancestors to be populated before self
@@ -375,7 +375,7 @@ function cleanup(self, key)
                                 success = false;
                             end
                         end
-                        if ~success && dj.set('verbose')
+                        if ~success && strcmpi(dj.config('loglevel'), 'DEBUG')
                             fprintf('** %s: skipping already reserved\n', self.className)
                             disp(key)
                         end
@@ -433,8 +433,8 @@ function createJobTable(self)
         function populateSanityChecks(self)
             % Performs sanity checks that are common to populate,
             % parpopulate and batch_populate.
-            % To disable the sanity check: dj.set('populateCheck',false)
-            if dj.set('populateCheck')
+            % To disable the sanity check: dj.config('queryPopulate_check',false)
+            if dj.config('queryPopulate_check')
                 source = self.getKeySource;
                 abovePopRel = setdiff(self.primaryKey(1:min(end,length(source.primaryKey))), source.primaryKey);
                 if ~all(ismember(source.primaryKey, self.primaryKey))

+dj/+internal/GeneralRelvar.m

@@ -83,7 +83,7 @@ function disp(self)
                     attrList{i} = hdr.names{i};
                 end
             end
-            maxRows = dj.set('maxPreviewRows');
+            maxRows = dj.config('displayLimit');
             preview = self.fetch(attrList{:}, sprintf('LIMIT %d', maxRows+1));
             if ~isempty(preview)
                 hasMore = length(preview) > maxRows;

+dj/+internal/Settings.m

@@ -0,0 +1,153 @@
+classdef Settings < matlab.mixin.Copyable
+    properties (Constant)
+        LOCALFILE = './dj_local_conf.json'
+        GLOBALFILE = '~/.datajoint_config.json'
+        DEFAULTS = struct( ...
+            'databaseHost', 'localhost', ...
+            'databasePassword', [], ...
+            'databaseUser', [], ...
+            'databasePort', 3306, ...
+            'databaseUse_tls', [], ...
+            'databaseReconnect_transaction', false, ...
+            'connectionInit_function', [], ...
+            'loglevel', 'INFO', ...
+            'safemode', true, ...
+            'displayLimit', 12, ... how many rows to display when previewing a relation
+            'displayDiagram_hierarchy_radius', [2 1], ...    levels up and down the hierachy to display in `erd schema.Table`
+            'displayDiagram_font_size', 12, ...  font size to use in ERD labels
+            'queryPopulate_check', true, ...
+            'queryPopulate_ancestors', false, ...
+            'queryBigint_to_double', false, ...
+            'queryIgnore_extra_insert_fields', false ...  when false, throws an error in `insert(self, tuple)` when tuple has extra fields.
+        )
+    end
+    properties
+        result
+    end
+    methods(Static)
+        function out = Settings(name, value)
+            current_state = stateAccess;
+            out.result = current_state;
+            if nargin == 1 || nargin == 2
+                assert(ischar(name), 'DataJoint:Config:InvalidType', ...
+                    'Setting name must be a string');
+                token = regexp(['.', name], '(\W)(\w+)', 'tokens');
+                token = vertcat(token{:}).';
+                token(1,:) = strrep(strrep(token(1,:), '{', '{}'), '(', '()');
+                value_vector = str2double(token(2,:));
+                index = ~isnan(value_vector);
+                token(2, index) = num2cell(num2cell(value_vector(index)));
+                subscript = substruct(token{:});
+                if nargout
+                    try
+                        out.result = subsref(current_state, subscript);
+                    catch ME
+                        switch ME.identifier
+                            case 'MATLAB:nonExistentField'
+                                error('DataJoint:Config:InvalidKey', ...
+                                    'Setting `%s` does not exist', name);
+                            otherwise
+                                rethrow(ME);
+                        end
+                    end                    
+                else
+                    out.result = [];
+                end
+            end
+            if nargin == 2
+                new_state = subsasgn(current_state, subscript, value);
+                stateAccess('set', new_state);
+            end
+        end
+        function out = restore()
+            out = stateAccess('restore');
+        end
+        function save(fname)
+            c = dj.internal.Settings;
+            dj.lib.saveJSONfile(c.result, fname);
+        end
+        function load(fname)
+            if ~nargin
+                fname = dj.internal.Settings.LOCALFILE;
+            end
+            raw = fileread(fname);
+            new_state = fixProps(jsondecode(raw), raw);
+            stateAccess('load', new_state);
+        end
+        function saveLocal()
+            dj.internal.Settings.save(dj.internal.Settings.LOCALFILE);
+        end
+        function saveGlobal()
+            dj.internal.Settings.save(dj.internal.Settings.GLOBALFILE);
+        end
+    end
+end
+function data = fixProps(data, raw)
+    newFields = fieldnames(data);
+    for i=1:length(newFields) 
+        for j=1:length(data.(newFields{i}))
+            if isstruct(data.(newFields{i})(j))
+                if exist('res','var')
+                    res(end + 1) = fixProps(data.(newFields{i})(j), raw);
+                else
+                    res = fixProps(data.(newFields{i})(j), raw);
+                end
+                if j == length(data.(newFields{i}))
+                    data.(newFields{i}) = res;
+                    clear res;
+                end
+            end            
+        end
+        newFields{i} = regexprep(regexp(raw, ...
+            regexprep(newFields{i},'_','.'), 'match', 'once'), ...
+            '\.[a-zA-Z0-9]','${upper($0(2))}');
+    end
+    data = cell2struct(struct2cell(data), newFields);
+end
+function out = stateAccess(operation, new)
+    function envVarUpdate()
+        % optional environment variables specifying the connection.
+        if getenv('DJ_HOST')
+            STATE.databaseHost = getenv('DJ_HOST');
+        end
+        if getenv('DJ_USER')
+            STATE.databaseUser = getenv('DJ_USER');
+        end
+        if getenv('DJ_PASS')
+            STATE.databasePassword = getenv('DJ_PASS');
+        end
+        if getenv('DJ_INIT')
+            STATE.connectionInit_function = getenv('DJ_INIT');
+        end
+    end
+    switch nargin
+        case 0
+            operation = '';
+        case 1
+        case 2
+        otherwise
+        error('Exceeded 2 input limit.')
+    end
+    persistent STATE
+    if (isempty(STATE) && ~strcmpi(operation, 'load')) || strcmpi(operation, 'restore')
+        % default settings
+        STATE = orderfields(dj.internal.Settings.DEFAULTS);
+        if exist(dj.internal.Settings.LOCALFILE, 'file') == 2
+            dj.internal.Settings.load(dj.internal.Settings.LOCALFILE);
+        elseif exist(dj.internal.Settings.GLOBALFILE, 'file') == 2
+            dj.internal.Settings.load(dj.internal.Settings.GLOBALFILE);
+        end
+        envVarUpdate();
+    end
+    % return STATE prior to change
+    out = STATE;
+    if any(strcmpi(operation, {'set', 'load'}))
+        % merge with existing STATE
+        STATE = rmfield(STATE, intersect(fieldnames(STATE), fieldnames(new)));
+        names = [fieldnames(STATE); fieldnames(new)];
+        STATE = orderfields(cell2struct([struct2cell(STATE); struct2cell(new)], names, 1));
+        if strcmpi(operation, 'load')
+            envVarUpdate();
+        end
+    end
+end

+dj/+internal/Table.m

@@ -191,11 +191,11 @@ function erd(self, up, down)
 
             self.create
             if nargin<=2
-                down = dj.set('tableErdRadius');
+                down = dj.config('displayDiagram_hierarchy_radius');
                 down = down(2);
             end
             if nargin<=1
-                up = dj.set('tableErdRadius');
+                up = dj.config('displayDiagram_hierarchy_radius');
                 up = up(1);
             end
 
@@ -465,7 +465,7 @@ function syncDef(self)
             if isempty(path)
                 fprintf('File %s.m is not found\n', self.className);
             else
-                if ~dj.set('suppressPrompt') ...
+                if dj.config('safemode') ...
                         && ~strcmpi('yes', dj.internal.ask(sprintf('Update the table definition and class definition in %s?',path)))
                     disp 'No? Table definition left untouched.'
                 else
@@ -549,7 +549,7 @@ function drop(self)
                 end
 
                 % if any table has data, give option to cancel
-                doPrompt = doPrompt && ~dj.set('suppressPrompt');  % suppress prompt
+                doPrompt = doPrompt && dj.config('safemode');  % suppress prompt
                 if doPrompt && ~strcmpi('yes', dj.internal.ask('Proceed to drop?'))
                     disp 'User cancelled table drop'
                 else

+dj/+lib/saveJSONfile.m

@@ -0,0 +1,83 @@
+function saveJSONfile(data, jsonFileName)
+% Modified from FileExchange entry:
+% https://www.mathworks.com/matlabcentral/fileexchange/...
+%   50965-structure-to-json?focused=3876199&tab=function
+% saves the values in the structure 'data' to a file in JSON indented format.
+%
+% Example:
+%     data.name = 'chair';
+%     data.color = 'pink';
+%     data.metrics.height = 0.3;
+%     data.metrics.width = 1.3;
+%     saveJSONfile(data, 'out.json');
+%
+% Output 'out.json':
+% {
+% 	"name" : "chair",
+% 	"color" : "pink",
+% 	"metrics" : {
+% 		"height" : 0.3,
+% 		"width" : 1.3
+% 		}
+% 	}
+%
+    fid = fopen(jsonFileName,'w');
+    writeElement(fid, data,'');
+    fprintf(fid,'\n');
+    fclose(fid);
+end
+function writeElement(fid, data,tabs)
+    namesOfFields = fieldnames(data);
+    tabs = sprintf('%s\t',tabs);
+    fprintf(fid,'{\n%s',tabs);
+    key = true;
+    for i = 1:length(namesOfFields) - 1
+        currentField = namesOfFields{i};
+        currentElementValue = data.(currentField);
+        writeSingleElement(fid, currentField,currentElementValue,tabs, key);
+        fprintf(fid,',\n%s',tabs);
+    end
+    currentField = namesOfFields{end};
+    currentElementValue = data.(currentField);
+    writeSingleElement(fid, currentField,currentElementValue,tabs, key);
+    fprintf(fid,'\n%s}',tabs(1:end-1));
+end
+function writeSingleElement(fid, currentField,currentElementValue,tabs, key)
+    % if this is an array and not a string then iterate on every
+    % element, if this is a single element write it
+    currentField = regexprep(currentField,'[a-z0-9][A-Z]','${$0(1)}.${lower($0(2))}');
+    if key
+        fprintf(fid,'"%s" : ' , currentField);
+    end
+    if length(currentElementValue) > 1 && ~ischar(currentElementValue)
+        fprintf(fid,'[\n%s\t',tabs);
+        for m = 1:length(currentElementValue)-1
+            if isstruct(currentElementValue(m))
+                writeElement(fid, currentElementValue(m),tabs);
+            else
+                writeSingleElement(fid, '',currentElementValue(m),tabs, false)
+            end
+            fprintf(fid,',\n%s\t',tabs);
+        end
+        if isstruct(currentElementValue(end))
+            writeElement(fid, currentElementValue(end),tabs);
+        else
+            writeSingleElement(fid, '',currentElementValue(end),tabs, false)
+        end
+        fprintf(fid,'\n%s]',tabs);
+    elseif isstruct(currentElementValue)
+        writeElement(fid, currentElementValue,tabs);
+    elseif isempty(currentElementValue)
+        fprintf(fid,'null');
+    elseif isnumeric(currentElementValue)
+        fprintf(fid,'%g' ,currentElementValue);
+    elseif islogical(currentElementValue)
+        if currentElementValue
+            fprintf(fid,'true');
+        else
+            fprintf(fid,'false');
+        end 
+    else %ischar or something else ...
+        fprintf(fid,'"%s"',currentElementValue);
+    end
+end

+dj/Connection.m

@@ -150,7 +150,7 @@ function reload(self)
             ret = ~isempty(self.connId) && 0==mym(self.connId, 'status');
 
             if ~ret && self.inTransaction
-                if dj.set('reconnectTimedoutTransaction')
+                if dj.config('databaseReconnect_transaction')
                     warning 'Reconnected after server disconnected during a transaction'
                 else
                     error 'Server disconnected during a transaction'
@@ -170,7 +170,7 @@ function reload(self)
                 end
             end
             v = varargin;
-            if dj.set('bigint_to_double')
+            if dj.config('queryBigint_to_double')
                 v{end+1} = 'bigint_to_double';
             end
             if nargout>0

+dj/ERD.m

@@ -144,7 +144,7 @@ function draw(self)
             for i=1:self.graph.numnodes
                 if tiers(i)<7  % ignore jobs, logs, etc.
                     isPart = tiers(i)==6;
-                    fs = dj.set('erdFontSize')*(1 - 0.3*isPart);
+                    fs = dj.config('displayDiagram_font_size')*(1 - 0.3*isPart);
                     fc = isPart*0.3*[1 1 1];
                     name = self.conn.tableToClass(self.graph.Nodes.Name{i});
                     text(h.XData(i)+0.1, h.YData(i), name, ...