Merge pull request #674 from aodn/hotfix_2.6.8

Hotfix 2.6.8

AutomaticQC/imosTiltVelocitySetQC.m

@@ -176,8 +176,8 @@
 
 if isempty(firstTiltThreshold) && auto
     % couldn't find this instrument so quit the test
-    disp(['Warning: imosTiltVelositySetQC could not be performed on ' sample_data.toolbox_input_file ...
-        ' instrument = "' instrument '" => Fill imosTiltVelositySetQC.txt with relevant make/model information if you wish to run this test on this dataset.']);
+    disp(['Warning: imosTiltVelocitySetQC could not be performed on ' sample_data.toolbox_input_file ...
+        ' instrument = "' instrument '" => Fill imosTiltVelocitySetQC.txt with relevant make/model information if you wish to run this test on this dataset.']);
     return;
 end
 
@@ -188,7 +188,7 @@
   names = {'firstTiltThreshold [deg]', 'firstFlagThreshold [imosQCFlag]', 'secondTiltThreshold [deg]', 'secondFlagThreshold [imosQCFlag]'};
   values = {firstTiltThreshold, firstFlagThreshold, secondTiltThreshold, secondFlagThreshold};
   funcs = {isdeg, isvalidQC, isdeg, isvalidQC};
-  results = uiNumericalBox(names,values,funcs,'title','imosTiltVelositySetQC - Threshold Limits','panelTitle',matchedName);
+  results = uiNumericalBox(names,values,funcs,'title','imosTiltVelocitySetQC - Threshold Limits','panelTitle',matchedName);
   [firstTiltThreshold,firstFlagThreshold,secondTiltThreshold,secondFlagThreshold] = results{:};
 end
 

AutomaticQC/imosTimeSeriesSpikeQC.m

@@ -47,18 +47,23 @@
 
 if (is_profile || time_missing), return, end
 
-has_burst_duration = false;
-has_burst_interval = false;
-try
-    has_burst_duration = sample_data.meta.instrument_burst_duration;
-    has_burst_interval = sample_data.meta.instrument_burst_interval;
-catch
-    try
-        has_burst_duration = sample_data.instrument_burst_duration;
-        has_burst_interval = sample_data.meta.instrument_burst_interval;
-    end
+
+if isfield(sample_data.meta,'instrument_burst_duration')
+    burst_duration = sample_data.meta.instrument_burst_duration;
+    valid_burst_duration = ~isempty(burst_duration) && ~isnan(burst_duration) && burst_duration>0;
+elseif isfield(sample_data,'instrument_burst_duration')
+    burst_duration = sample_data.meta.instrument_burst_duration;
+    valid_burst_duration = ~isempty(burst_duration) && ~isnan(burst_duration) && burst_duration>0;
 end
-has_burst = has_burst_duration || has_burst_interval;
+if isfield(sample_data.meta,'instrument_burst_interval')
+    burst_interval = sample_data.meta.instrument_burst_interval;
+    valid_burst_interval = ~isempty(burst_interval) && ~isnan(burst_interval) && burst_interval>0;
+elseif isfield(sample_data,'instrument_burst_interval')
+    burst_interval = sample_data.meta.instrument_burst_interval;
+    valid_burst_interval = ~isempty(burst_interval) && ~isnan(burst_interval) && burst_interval>0;
+end
+
+has_burst = (valid_burst_duration) || (valid_burst_interval);
 
 if has_burst
     opts_file = ['AutomaticQC' filesep 'imosTimeSeriesSpikeQCBurst.txt'];

Parser/netcdfParse.m

@@ -182,9 +182,9 @@
   sample_data.meta.instrument_make            = '';
   sample_data.meta.instrument_model           = '';
   sample_data.meta.instrument_serial_no       = '';
-  sample_data.meta.instrument_sample_interval = NaN;
-  sample_data.meta.instrument_burst_duration  = NaN;
-  sample_data.meta.instrument_burst_interval  = NaN;
+  sample_data.meta.instrument_sample_interval = '';
+  sample_data.meta.instrument_burst_duration  = '';
+  sample_data.meta.instrument_burst_interval  = '';
   sample_data.meta.featureType                = '';
 
   %special names mappings

Util/CellUtils/inCellPartialMatchString.m

@@ -0,0 +1,93 @@
+function [is_complete, indexes] = inCellPartialMatchString(xcell,ycell,first_match_only)
+% function [indexes,is_complete] = inCellPartialMatchString(xcell, ycell,first_match_only)
+%
+% Check if each string entry in ycell is within any string entry in xcell.
+%
+% If all the content of a ycell{n} string
+% is found within the string of xcell{m}
+% the m index is stored.
+%
+% For simple partial string matching, use the contains function
+%
+% See examples for usage.
+%
+% Inputs:
+%
+% xcell - a cell with items as strings.
+% ycell - a string or another cell with items as strings.
+% first_match_only - a boolean to skip subsequent matches of ycell in xcell.
+%                  - Default: false
+%
+% Output:
+%
+% is_complete - a boolean to indicate that all ycell items
+%               were matched.
+% indexes - a cell of indexes where matches occur in xcell.
+%
+%
+% Example:
+% % complete match
+% xnames = {'a','ab','abc','123'};
+% ynames = {'a','3'};
+% [is_complete, indexes] = inCellPartialMatchString(xnames,ynames);
+% assert(is_complete)
+% assert(isequal({1,2,3,4},indexes))
+% [is_complete, indexes] = inCellPartialMatchString(xnames,ynames,true);
+% assert(is_complete)
+% assert(isequal({1,4},indexes))
+%
+% % incomplete match
+% xnames = {'a','b','c','123'};
+% ynames = {'x','y','z','3'};
+% [is_complete, indexes] = inCellPartialMatchString(xnames,ynames);
+% assert(~is_complete)
+% assert(isequal({4},indexes))
+%
+% % no match
+% xnames = {'x','y','z'};
+% ynames = {'a','b','c'};
+% [is_complete, indexes] = inCellPartialMatchString(xnames,ynames);
+% assert(~is_complete)
+% assert(isequal({},indexes))
+
+%
+% author: [email protected]
+%
+narginchk(2, 3)
+if nargin<3
+    first_match_only = false;
+end
+
+if ~iscell(ycell)
+    ycell = {ycell};
+end
+
+indexes = cell(1,numel(ycell)*numel(xcell));
+ydetection = zeros(1,numel(ycell));
+
+c = 0;
+for k = 1:numel(ycell)
+    if ~ischar(ycell{k})
+        error('The second argument index `ycell{%d}` is not a string', k);
+    end
+    for kk = 1:length(xcell)
+        if ~ischar(xcell{kk})
+            error('The first argument index `xcell{%d}` is not a string', k);
+        end
+        if contains(xcell{kk},ycell{k})
+            c = c + 1;
+            indexes{c} = kk;
+            ydetection(k) = true;
+            if first_match_only
+                break
+            end
+        end
+    end
+end
+
+indexes = indexes(1:c);
+if isempty(indexes)
+    indexes = {};
+end
+is_complete = all(ydetection);
+end

build.py

@@ -66,8 +66,7 @@ def find_matlab_rootpath(arch_str):
 
 def run(command: str):
     """Run a command at shell/cmdline."""
-    proc = sp.run(command, stdout=sp.PIPE, stderr=sp.PIPE, shell=True, check=True)
-    return proc.stdout.decode("utf-8").strip(), proc.stderr.decode("utf-8").strip()
+    return sp.run(command, shell=True, check=True)
 
 
 def create_java_call_sig_compile(root_path: str) -> str:
@@ -287,14 +286,15 @@ def write_version(afile: str, version: str) -> None:
     print(repo_info)
 
     print(f"Calling {java_call}..")
-    stdout, stderr = run(java_call)
-    if stderr:
+    ok = run(java_call)
+    if not ok:
         raise Exception(f"{jcall} failed")
 
     print(f"Calling {mcc_call}...")
     for mcall in mcc_call:
-        stdout, stderr = run(mcall)
-        if stderr:
+        print(f"Executing {mcall}")
+        ok = run(mcall)
+        if not ok:
             raise Exception(f"{mcall} failed")
 
     print(f"The toolbox architecture is {ARCH_NAMES[arch]}.")

imosToolbox.m

@@ -37,7 +37,7 @@ function imosToolbox(auto, varargin)
 %
 
 % Set current toolbox version
-toolboxVersion = ['2.6.7 - ' computer];
+toolboxVersion = ['2.6.8 - ' computer];
 
 if nargin == 0, auto = 'manual'; end
 
@@ -49,16 +49,25 @@ function imosToolbox(auto, varargin)
 path = '';
 if ~isdeployed
     [path, ~, ~] = fileparts(which('imosToolbox.m'));
-
     % set Matlab path for this session (add all recursive directories to Matlab
     % path)
-    searchPath = textscan(genpath(path), '%s', 'Delimiter', pathsep);
-    searchPath = searchPath{1};
-    iPathToRemove = ~cellfun(@isempty, strfind(searchPath, [filesep '.']));
-    searchPath(iPathToRemove) = [];
-    searchPath = cellfun(@(x)([x pathsep]), searchPath, 'UniformOutput', false);
-    searchPath = [searchPath{:}];
-    addpath(searchPath);
+    addpath(fullfile(path,'Util/Path'));
+    addpath(fullfile(path,'Util/CellUtils'));
+    addpath(fullfile(path,'Util/Schema'));
+
+    [~,subfolders] = FilesInFolder(path);
+    ignored_subfolders = {'.git','.mypy_cache','imos-toolbox/snapshot','imos-toolbox/data','imos-toolbox/dist'};
+    [~,ignore_indexes] = inCellPartialMatchString(subfolders,ignored_subfolders);
+    valid_subfolders = popFromCell(subfolders,subfolders([ignore_indexes{:}]));
+
+    rmpath(fullfile(path,'Util/Path'));
+    rmpath(fullfile(path,'Util/CellUtils'));
+    rmpath(fullfile(path,'Util/Schema'));
+
+    cell_of_folders_strings = cellfun(@genpath,valid_subfolders,'UniformOutput',false);
+    all_folders_as_string= cat(2,cell_of_folders_strings{:});
+    addpath(path);
+    addpath(all_folders_as_string);
 end
 if isempty(path), path = pwd; end