Pull request to merge changes (#3)

* Added a function, extract_tree, to
extract the full tree of ONC location codes.  Once loaded, the locations
can be navigated with tab completion

* Added a check to see if any files returned.
If not, returns an error message

* Fixed a bug where "getTree" was improperly parsed
by util.param

* Fixed a bug where .mat files were
not properly downloaded

onc/+onc/DataProductFile.m

@@ -100,7 +100,9 @@
                     else
                         this.fileSize = strlength(response.Body.Data);
                     end
-                    saveResult = util.save_as_file(response, outPath, filename, overwrite);
+                    %save_as_file doesn't work properly! Use urlwrite instead
+                    [~, saveResult] = urlwrite(uri.EncodedURI,fullfile(outPath, filename));
+                    %saveResult = util.save_as_file(response, outPath, filename, overwrite);
                     this.downloadingTime = round(duration, 3);
 
                     % log status

onc/+onc/OncDiscovery.m

@@ -110,7 +110,19 @@
             % - method:  ([char])  Method to request, one of {'get', 'getTree'}
             %
             % Returns: ([struct]) List of elements found
-            [method] = util.param(varargin, 'method', 'get');
+
+            %BUG: if varargin = {'method','getTree'}, not actually using getTree...
+            %[method] = util.param(varargin, 'method', 'get'); 
+            if nargin>3
+                if strcmpi(varargin{1},'method') & strcmpi(varargin{2},'getTree')
+                    [method] = util.param(varargin, 'method', 'getTree'); 
+                else 
+                    [method] = util.param(varargin, 'method', 'get'); 
+                end
+            else
+                [method] = util.param(varargin, 'method', 'get'); 
+            end
+
             url = this.serviceUrl(service);
 
             filters = util.sanitize_filters(filters);

onc/+util/extract_tree.m

@@ -0,0 +1,136 @@
+function tree = extract_tree(this)
+%Code to extract the Search Tree, and all of the "location codes"
+%Can run with no input and get the entire tree, or give it a starting point
+%further down the tree.  The codes for these can be found in Search Tree
+%Maintenance. These codes can then be used for input to onc.getDevices by
+%providing the locationCodes 
+%
+% Ex. 1 : All ONC locations
+% tree = extract_tree
+% Ex. 2: Just the Salish Sea
+% tree = extract_tree('SAL')
+%
+% Example usage once extracted:
+% >> my_token = '17x081dx-x36x-48c1-x930-01b2d1697x83';  % Found in your ONC profile
+% >> onc = Onc(my_token);
+% Then, type: 
+% >> onc.tree
+% Then click the "tab" key to see all options, and select one. Continue to
+% add periods and select tab-completion until you've narrowed down your
+% desired site.  
+% >> onc.tree.Pacific.Salish_Sea.Baynes_Sound.Baynes_Sound_Mooring.L2mbss.aa_info
+
+
+%if nargin == 0
+    filters = {'locationCode', 'ONC'};
+%else
+%    filters = {'locationCode', varargin{1}};
+%end
+
+%filters = {'locationCode', %'ARCT','dateFrom','2019-07-27T00:00:00.000Z','dateTo','2019-08-27T00:00:00.000Z'}; % Not compatible with getTree
+result = this.getLocationHierarchy(filters);
+%onc.print(result);
+%To get this to work, I had to edit the code in OncDiscovery L118 to
+%actually use the "getTree" method... was not properly working, and was
+%continuing to use the "get" method  
+
+%GOAL: Create a tab/auto-complete dictionary for reference ti easily scan through the
+%search tree directory and get site and device codes
+
+field{1,1} = result.locationName; %Arctic
+%tree.(field{1,1}) = field{1,1};
+
+%Info for the top Level
+struct_set_info{1} = 'locationCode';
+struct_set_info{2} = result.locationCode;
+struct_set_info{3} = 'locationName';
+struct_set_info{4} = result.locationName;
+struct_set_info{5} = 'hasDeviceData';
+struct_set_info{6} = result.hasDeviceData;
+struct_set_info{7} = 'description';
+struct_set_info{8} = result.description;
+struct_set{1} = 'aa_info';
+struct_set{2} = struct(struct_set_info{:});
+%Children of the top Level:
+for ii=1:size(result.children,1) 
+    treeLocationName = strjoin(strsplit(result.children(ii).locationName,' '),'');
+    treeLocationName = strjoin(strsplit(treeLocationName,'-'),'');
+    %result.children(ii).locationName = strjoin(strsplit(result.children(ii).locationName,' '),'');
+    %result.children(ii).locationName = strjoin(strsplit(result.children(ii).locationName,'-'),'');
+    struct_set{2*(ii+1) - 1} = treeLocationName;
+    struct_set{2*(ii+1)} = '';
+end
+tree = struct(struct_set{:});
+
+
+%Enter a recursive loop to construct the tree:
+tree = probe_children(result.children, tree);
+
+
+end
+
+
+function tree = probe_children(input, tree)
+%This is a recursive loop to get details about each child
+
+    for ii=1:size(input,1)
+
+        %Clear variables:
+        clear struct_set struct_set_info
+
+        %Info for the top Level
+        struct_set_info{1} = 'locationCode';
+        struct_set_info{2} = input(ii).locationCode;
+        struct_set_info{3} = 'locationName';
+        struct_set_info{4} = input(ii).locationName;
+        struct_set_info{5} = 'hasDeviceData';
+        struct_set_info{6} = input(ii).hasDeviceData;
+        struct_set_info{7} = 'description';
+        struct_set_info{8} = input(ii).description;
+        struct_set{1} = 'aa_info';
+        struct_set{2} = struct(struct_set_info{:});
+        %Children of the top Level:
+        for jj=1:size(input(ii).children,1)
+            %location_name = input(ii).children(jj).locationName;
+            treeLocationName = strjoin(strsplit(input(ii).children(jj).locationName,' '),'_');
+            treeLocationName = strjoin(strsplit(treeLocationName,'-'),'_');
+            treeLocationName = strjoin(strsplit(treeLocationName,'('),'_');
+            treeLocationName = strjoin(strsplit(treeLocationName,')'),'_');
+            treeLocationName = strjoin(strsplit(treeLocationName,'.'),'_');
+            treeLocationName = strjoin(strsplit(treeLocationName,''''),'_');
+            treeLocationName = strjoin(strsplit(treeLocationName,'/'),'_');
+
+            %Split and check to see if the first character is a number
+            split_parts = strsplit(treeLocationName,'_');
+            if isempty(split_parts{1})
+                for kk=1:length(split_parts)-1
+                	split_parts{kk} = split_parts{kk+1};
+                end
+                split_parts = split_parts(1:end-1);
+
+            elseif ~isnan(str2double(split_parts{1}(1)))  
+                if length(split_parts)>1
+                    temp = split_parts{1};
+                    split_parts{1} = split_parts{2};
+                    split_parts{2} = temp;
+                else
+                    split_parts{1} = ['L',split_parts{1}]; 
+                end
+            end
+            treeLocationName = strjoin(split_parts,'_');
+
+            struct_set{2*(jj+1) - 1} = treeLocationName;
+            struct_set{2*(jj+1)} = '';
+        end
+        fieldnames = fields(tree);
+        tree.(fieldnames{ii+1}) = struct(struct_set{:});
+
+        tree.(fieldnames{ii+1}) = probe_children(input(ii).children, tree.(fieldnames{ii+1}));
+        %input(ii).children = probe_children(input(ii).children);
+
+
+
+    end
+
+end
+

onc/+util/filter_by_extension.m

@@ -15,12 +15,19 @@
 
     % determine the row structure
     isStructRow = false;
-    if ~isempty(results.files)
-        if isa(results.files(1), 'struct')
-            isStructRow = true;
+
+    if isfield(results,'files')
+        if ~isempty(results.files)
+            if isa(results.files(1), 'struct')
+                isStructRow = true;
+            end
         end
+
+    else
+        error('%s: %s (error ID %d)',results.errors.errorMessage, results.errors.parameter, results.errors.errorCode);
     end
-
+
+
     % preallocate an array of flags
     flags = zeros([n, 1], 'logical');
 

onc/Onc.m

@@ -8,6 +8,7 @@
     % showInfo - Print verbose comments for debugging
     % outPath  - Output path for downloaded files
     % timeout  - Number of seconds before a request to the API is canceled
+    % tree     - ONC data search tree
     %
     % ONC Methods:
     % 
@@ -53,6 +54,7 @@
         showInfo = false    % Print verbose comments for debugging
         outPath  = 'output' % Output path for downloaded files
         timeout  = 60       % Number of seconds before a request to the API is canceled
+        tree     = []       % ONC Data Search Tree
     end
 
     properties (SetAccess = private)
@@ -102,6 +104,32 @@
             if not(this.production)
                 this.baseUrl = 'https://qa.oceannetworks.ca/';
             end
+
+            %If a search tree file exists, load it.  If not, generate and save one
+            [source_path,~,~] = fileparts(which('Onc.m'));
+            tree_path = fullfile(source_path,'onc_tree.mat');
+            if ~exist(tree_path,'file')
+                fprintf('\n Loading ONC search tree.  Accessible with onc.tree \n');
+                tree = util.extract_tree(this);
+                save(tree_path, 'tree')
+            elseif exist(tree_path,'file')
+                %Check if it's more than a week old. If so, update it:
+                dir_files = dir(source_path);
+                filenames = {dir_files(:).name};
+                [~,idx] = ismember('onc_tree.mat',filenames);
+                treeFileDate = dir_files(idx).datenum;
+                if now - treeFileDate > 7
+                    fprintf('\n Updating ONC search tree.  Accessible with onc.tree \n');
+                    tree = util.extract_tree(this);
+                    save(tree_path, 'tree')
+                end
+            end
+            temp = load(tree_path);
+            this.tree = temp.tree;
+            %These codes can then be used for input to onc.getDevices by
+            %providing the locationCodes
+
+
         end
 
         function print(~, data)
@@ -130,6 +158,7 @@ function print(~, data)
             dt.Format = 'yyyy-MM-dd''T''HH:mm:ss.SSS''Z''';
             text = sprintf('%s', char(dt));
         end
+
     end
 
     methods (Access = private)