Merge branch 'dev'

@Alyx/Alyx.m

@@ -92,6 +92,7 @@
 
     function obj = set.BaseURL(obj, value)
       % Drop trailing slash and ensure protocol defined
+      if isempty(value); obj.BaseURL = ''; return; end % return on empty
       value = iff(value(1:4)~='http', ['https://' value], value);
       obj.BaseURL = iff(value(end)=='/', value(1:end-1), value);
     end
@@ -109,7 +110,7 @@
     % Checks for and uploads queued data to Alyx
     [data, statusCode] = flushQueue(obj)
     % Recovers the full filepath of a file on the repository, given the datasetURL
-    fullPath = getFile(obj, datasetURL)
+    [fullPath, exists] = getFile(obj, eid, type)
     % Query the database for a list of sessions
     [sessions, eids] = getSessions(obj, varargin)
     % Lists recorded subjects

@Alyx/getFile.m

@@ -1,36 +1,58 @@
-function fullPath = getFile(obj, datasetURL)
-%GETFILE Recovers the full filepath of a file on the repository, given the datasetURL
-%	This function is SUPER inefficient because it has to load all
-%	filerecords from the database, and then search for the specific
-%	filerecord whose parent dataset matches the one supplied as input.
+function [fullPath, exists] = getFile(obj, eid, type)
+%GETFILE Returns the full filepath for a given eid.
+%	Returns the full path of associated data files given a dataset or file
+%	record URL or eid (experiment ID). Also returns a logical array 
+% indicating whether files exist for each element in the `eid` array.
 %
-%   datasetURL: URL of a dataset on Alyx
+% Inputs:
+%   `eid`: a string or char array containing the full URL(s) or eid(s) of 
+%   dataset(s) / file record(s) on Alyx.
+%   `type`: a string indicating type of eid(s) ('dataset' (default) or 
+%   'file')
 %
-% See also ALYX, GETDATA
+% Outputs:
+%   `fullPath`: a cellstring containing the full data file path(s) for
+%   each element in the `eid` array
+%   `exists`: a logical array indicating whether files exist for each eid
+%   in the `eid` array
+%
+% See also ALYX, GETDATA, GETSESSIONS
 %
 % Part of Alyx
-% TODO: Create endpoint so this function is no longer inefficient?
 % 2017 PZH created
+% 2019 MW Rewrote
 
+if nargin < 3; type = 'dataset'; end
 
-% Get all file records
-filerecords = obj.getData('files');
-
-% Extract the datasets which are parent to the filerecords
-datasets = cellfun(@(fr) fr.dataset, filerecords, 'uni', 0);
-
-% Find whichever filerecord has input datasetURL as its parent
-idx = contains(datasets, datasetURL);
-
-if any(idx)
-  fr = filerecords{idx};
-  relPath = fr.relative_path; % Get relative path of file
-
-  repo = obj.getData('data-repository'); % Get absolute path of repository
-  fullPath = [repo{1}.path relPath]; % Recover the full path of the file on the repository
+% Convert array of strings to cell string
+if isstring(eid) && ~isscalar(eid)
+  eid = cellstr(eid);
 else
-  error('No filerecords with inputted datasetURL as its parent');
+  eid = ensureCell(eid);
 end
 
+% Validate URL (UUIDs have 36 characters)
+assert(all(cellfun(@(str)ischar(str) && length(str) >= 36, eid)), 'Invalid eid')
+eid = mapToCell(@(str)str(end-35:end), eid);
+
+% Get all file records
+switch lower(type)
+  case 'file'
+    filerecords = mapToCell(@(url)obj.getData(['files/', url]), eid);
+    repos = obj.getData('data-repository');
+    repos = containers.Map({repos.name}, {repos.data_url});
+    fullPath = mapToCell(@(s)[repos(s.data_repository) s.relative_path], filerecords);
+    exists = cellfun(@(s)s.exists, filerecords);
+    % Return as char if user expects one output
+    if numel(eid) == 1; fullPath = fullPath{1}; end
+  case 'dataset'
+    filerecords = catStructs(mapToCell(@(url)getOr(obj.getData(['datasets/', url]), 'file_records'), eid));
+    exists = [filerecords.exists];
+    fullPath = {filerecords.data_url};
+    % Remove records with empty url field
+    exists = exists(emptyElems(fullPath));
+    fullPath = rmEmpty(fullPath);
+  otherwise
+    error('Alyx:GetFile:InvalidType', 'Invalid eid type: must be ''dataset'' or ''file''')
 end
 

@Alyx/listSubjects.m

@@ -48,11 +48,8 @@
     subjects = [{'default'}, subjNames]';
   end
 else
-  % The master 'main' repository is the reference for the existence of
+  % The remote 'main' repositories are the reference for the existence of
   % experiments, as given by the folder structure
-  mainPath = dat.reposPath('main', 'master');
-
-  dirs = file.list(mainPath, 'dirs');
-  subjects = setdiff(dirs, {'@Recently-Snapshot', '@Recycle'}); %exclude the trash directories
+  subjects = dat.listSubjects;
 end
 end

@Alyx/newExp.m

@@ -102,8 +102,7 @@
 try 
   % Generate JSON path and save
   jsonParams = obj2json(expParams);
-  jsonPath = fullfile(fileparts(dat.expFilePath(expRef, 'parameters', 'master')),...
-      [expRef, '_parameters.json']);
+  jsonPath = dat.expFilePath(expRef, 'parameters', 'master', 'json');
   fid = fopen(jsonPath, 'w'); fprintf(fid, '%s', jsonParams); fclose(fid);
   % Register our JSON parameter set to Alyx
   files = [files; {jsonPath}];

README.md

@@ -1,4 +1,7 @@
 # Alyx-MATLAB
+![Custom badge](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Fgladius.serveo.net%2Fcoverage%2Falyx-matlab%2Fdev)
+![Custom badge](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Fgladius.serveo.net%2Fstatus%2Falyx-matlab%2Fdev)
+
 This repository contains a MATLAB class called Alyx, that facilitates RESTful POST and GET requests to an instance of the [Alyx database](http://alyx.readthedocs.io/en/latest/). 
 
 ## Getting started
@@ -153,4 +156,4 @@ For use with [Rigbox](https://github.com/cortex-lab/Rigbox), use the submodule t
 * [MD5 in MATLAB](https://uk.mathworks.com/matlabcentral/fileexchange/7919-md5-in-matlab) - For checksums (no longer used)
 
 ## Authors
-This code is maintained and developed by a number of people at [CortexLab](https://www.ucl.ac.uk/cortexlab).  See [contributors](https://github.com/cortex-lab/alyx-matlab/graphs/contributors) list for more info.
+This code is maintained and developed by a number of people at [CortexLab](https://www.ucl.ac.uk/cortexlab).  See [contributors](https://github.com/cortex-lab/alyx-matlab/graphs/contributors) list for more info.