Merge pull request #1160 from sbesson/10805_matlab_bug

Matlab fixes

components/tools/OmeroM/src/annotations/getDatasetCommentAnnotations.m

@@ -5,6 +5,10 @@
 %    annotations linked to the datasets specified by the input identifiers
 %    and owned by the session user.
 %
+%    cas = getDatasetCommentAnnotations(session, datasets) returns all
+%    comment annotations linked to the input datasets and owned by the
+%    session user.
+%
 %    cas = getDatasetCommentAnnotations(session,  ids, 'include', include)
 %    only returns comment annotations with the input namespace.
 %
@@ -14,6 +18,7 @@
 %    Examples:
 %
 %        cas = getDatasetCommentAnnotations(session, ids)
+%        cas = getDatasetCommentAnnotations(session, datasets)
 %        cas = getDatasetCommentAnnotations(session, ids, 'include', include)
 %        cas = getDatasetCommentAnnotations(session, ids, 'exclude', exclude)
 %

components/tools/OmeroM/src/annotations/getDatasetFileAnnotations.m

@@ -5,6 +5,10 @@
 %    annotations linked to the datasets specified by the input identifiers
 %    and owned by the session user.
 %
+%    fas = getDatasetFileAnnotations(session, datasets) returns all file
+%    annotations linked to the input datasets and owned by the session
+%    user.
+%
 %    fas = getDatasetFileAnnotations(session,  ids, 'include', include) only
 %    returns file annotations with the input namespace.
 %
@@ -14,6 +18,7 @@
 %    Examples:
 %
 %        fas = getDatasetFileAnnotations(session, ids)
+%        fas = getDatasetFileAnnotations(session, datasets)
 %        fas = getDatasetFileAnnotations(session, ids, 'include', include)
 %        fas = getDatasetFileAnnotations(session, ids, 'exclude', exclude)
 %

components/tools/OmeroM/src/annotations/getDatasetTagAnnotations.m

@@ -5,6 +5,10 @@
 %    annotations linked to the datasets specified by the input identifiers
 %    ids and owned by the session user.
 %
+%    tas = getDatasetTagAnnotations(session, datasets) returns all tag
+%    annotations linked to the input datasets and owned by the session
+%    user.
+%
 %    tas = getDatasetTagAnnotations(session,  ids, 'include', include) only
 %    returns tag annotations with the input namespace.
 %
@@ -14,8 +18,9 @@
 %    Examples:
 %
 %        tas = getDatasetTagAnnotations(session, ids)
-%        fas = getDatasetTagAnnotations(session, ids, 'include', include)
-%        fas = getDatasetTagAnnotations(session, ids, 'exclude', exclude)
+%        tas = getDatasetTagAnnotations(session, datasets)
+%        tas = getDatasetTagAnnotations(session, ids, 'include', include)
+%        tas = getDatasetTagAnnotations(session, ids, 'exclude', exclude)
 %
 % See also: GETOBJECTANNOTATIONS, GETDATASETCOMMENTANNOTATIONS,
 % GETDATASETFILEANNOTATIONS, GETDATASETXMLANNOTATIONS

components/tools/OmeroM/src/annotations/getDatasetXmlAnnotations.m

@@ -1,21 +1,26 @@
 function xas = getDatasetXmlAnnotations(session, ids, varargin)
 % GETDATASETXMLANNOTATIONS Retrieve xml annotations linked to datasets
 %
-%    fas = getDatasetXmlAnnotations(session, ids) returns all xml
+%    xas = getDatasetXmlAnnotations(session, ids) returns all xml
 %    annotations linked to the datasets specified by the input identifiers
 %    and owned by the session user.
 %
-%    fas = getDatasetXmlAnnotations(session,  ids, 'include', include) only
+%    xas = getDatasetXmlAnnotations(session, datasets) returns all xml
+%    annotations linked to the input datasets and owned by the session
+%    user.
+%
+%    xas = getDatasetXmlAnnotations(session,  ids, 'include', include) only
 %    returns xml annotations with the input namespace.
 %
-%    fas = getDatasetXmlAnnotations(session,  ids, 'exclude', exclude)
+%    xas = getDatasetXmlAnnotations(session,  ids, 'exclude', exclude)
 %    excludes xml annotations with the input namespace.
 %
 %    Examples:
 %
-%        fas = getDatasetXmlAnnotations(session, ids)
-%        fas = getDatasetXmlAnnotations(session, ids, 'include', include)
-%        fas = getDatasetXmlAnnotations(session, ids, 'exclude', exclude)
+%        xas = getDatasetXmlAnnotations(session, ids)
+%        xas = getDatasetXmlAnnotations(session, datasets)
+%        xas = getDatasetXmlAnnotations(session, ids, 'include', include)
+%        xas = getDatasetXmlAnnotations(session, ids, 'exclude', exclude)
 %
 % See also: GETOBJECTANNOTATIONS, GETDATASETCOMMENTANNOTATIONS,
 % GETDATASETTAGANNOTATIONS, GETDATASETFILEANNOTATIONS

components/tools/OmeroM/src/annotations/getImageCommentAnnotations.m

@@ -5,6 +5,9 @@
 %    annotations linked to the image specified by the input identifiers ids
 %    and owned by the session user.
 %
+%    cas = getImageCommentAnnotations(session, images) returns all comment
+%    annotations linked to the input images and owned by the session user.
+%
 %    cas = getImageCommentAnnotations(session,  ids, 'include', include)
 %    only returns comment annotations with the input namespace.
 %
@@ -14,6 +17,7 @@
 %    Examples:
 %
 %        cas = getImageCommentAnnotations(session, ids)
+%        cas = getImageCommentAnnotations(session, images)
 %        cas = getImageCommentAnnotations(session, ids, 'include', include)
 %        cas = getImageCommentAnnotations(session, ids, 'exclude', exclude)
 %

components/tools/OmeroM/src/annotations/getImageFileAnnotations.m

@@ -5,6 +5,9 @@
 %    annotations linked to the image specified by the input identifiers ids
 %    and owned by the session user.
 %
+%    fas = getImageFileAnnotations(session, images) returns all file
+%    annotations linked to the input images and owned by the session user.
+%
 %    fas = getImageFileAnnotations(session,  ids, 'include', include) only
 %    returns file annotations with the input namespace.
 %
@@ -14,6 +17,7 @@
 %    Examples:
 %
 %        fas = getImageFileAnnotations(session, ids)
+%        fas = getImageFileAnnotations(session, images)
 %        fas = getImageFileAnnotations(session, ids, 'include', include)
 %        fas = getImageFileAnnotations(session, ids, 'exclude', exclude)
 %

components/tools/OmeroM/src/annotations/getImageTagAnnotations.m

@@ -5,6 +5,9 @@
 %    linked to the image specified by the input identifiers ids and owned 
 %    by the session user.
 %
+%    tas = getImageTagAnnotations(session, images) returns all tag
+%    annotations linked to the input images and owned by the session user.
+%
 %    tas = getImageTagAnnotations(session,  ids, 'include', include) only
 %    returns tag annotations with the input namespace.
 %
@@ -14,8 +17,9 @@
 %    Examples:
 %
 %        tas = getImageTagAnnotations(session, ids)
-%        fas = getImageTagAnnotations(session, ids, 'include', include)
-%        fas = getImageTagAnnotations(session, ids, 'exclude', exclude)
+%        tas = getImageTagAnnotations(session, images)
+%        tas = getImageTagAnnotations(session, ids, 'include', include)
+%        tas = getImageTagAnnotations(session, ids, 'exclude', exclude)
 %
 % See also: GETOBJECTANNOTATIONS, GETIMAGECOMMENTANNOTATIONS,
 % GETIMAGEFILEANNOTATIONS, GETIMAGEXMLANNOTATIONS

components/tools/OmeroM/src/annotations/getImageXmlAnnotations.m

@@ -1,21 +1,25 @@
 function xas = getImageXmlAnnotations(session, ids, varargin)
 % GETIMAGEXMLANNOTATIONS Retrieve xml annotations linked to images
 %
-%    fas = getImageXmlAnnotations(session, ids) returns all xml
+%    xas = getImageXmlAnnotations(session, ids) returns all xml
 %    annotations linked to the image specified by the input identifiers ids
 %    and owned by the session user.
 %
-%    fas = getImageXmlAnnotations(session,  ids, 'include', include) only
+%    xas = getImageXmlAnnotations(session, images) returns all xml
+%    annotations linked to the input images and owned by the session user.
+%
+%    xas = getImageXmlAnnotations(session,  ids, 'include', include) only
 %    returns xml annotations with the input namespace.
 %
-%    fas = getImageXmlAnnotations(session,  ids, 'exclude', exclude)
+%    xas = getImageXmlAnnotations(session,  ids, 'exclude', exclude)
 %    excludes xml annotations with the input namespace.
 %
 %    Examples:
 %
-%        fas = getImageXmlAnnotations(session, ids)
-%        fas = getImageXmlAnnotations(session, ids, 'include', include)
-%        fas = getImageXmlAnnotations(session, ids, 'exclude', exclude)
+%        xas = getImageXmlAnnotations(session, ids)
+%        xas = getImageXmlAnnotations(session, images)
+%        xas = getImageXmlAnnotations(session, ids, 'include', include)
+%        xas = getImageXmlAnnotations(session, ids, 'exclude', exclude)
 %
 % See also: GETOBJECTANNOTATIONS, GETIMAGECOMMENTANNOTATIONS,
 % GETIMAGETAGANNOTATIONS, GETIMAGEFILEANNOTATIONS

components/tools/OmeroM/src/annotations/getObjectAnnotations.m

@@ -1,23 +1,30 @@
 function annotations = getObjectAnnotations(session, annotationType, parentType, ids, varargin)
 % GETOBJECTANNOTATIONS Retrieve annotations of a given type associated with an object
 %
-%    files = getObjectAnnotations(session, annotationType, parentType, ids)
+%    anns = getObjectAnnotations(session, annotationType, parentType, ids)
 %    returns all annotations of type annotationType linked to the object of
 %    type parentType and identifiers ids owned by the session user.
 %
-%    files = getObjectAnnotations(session, annotationType, parentType, ids,
+%    anns = getObjectAnnotations(session, annotationType, parentType,
+%    parents) returns all annotations of type annotationType linked to the
+%    input parent objects of type parentType owned by the session user.
+%
+%    anns = getObjectAnnotations(session, annotationType, parentType, ids,
 %    'include', include) only returns annotations with the input namespace.
 %
-%    files = getObjectAnnotations(session, annotationType, parentType, ids,
+%    anns = getObjectAnnotations(session, annotationType, parentType, ids,
 %    'exclude', exclude) excludes annotations with the input namespace.
 %
 %    Examples:
 %
-%        anns = getObjectAnnotations(session, annotationType, parentType, ids)
-%        anns = getObjectAnnotations(session, annotationType, parentType, ids,...
-%        'include', include)
-%        anns = getObjectAnnotations(session, annotationType, parentType, ids,...
-%        'exclude', exclude)
+%        anns = getObjectAnnotations(session, annotationType, parentType,
+%        ids)
+%        anns = getObjectAnnotations(session, annotationType, parentType,
+%        parents)
+%        anns = getObjectAnnotations(session, annotationType, parentType,
+%        ids, 'include', include)
+%        anns = getObjectAnnotations(session, annotationType, parentType,
+%        ids, 'exclude', exclude)
 %
 % See also: GETIMAGEFILEANNOTATIONS, GETIMAGETAGANNOTATIONS,
 % GETIMAGECOMMENTANNOTATIONS
@@ -54,6 +61,9 @@
 metadataService = session.getMetadataService();
 
 % Convert input into java.util.ArrayList;
+if ~isnumeric(ids),
+    ids = arrayfun(@(x) x.getId().getValue(), ids);
+end
 ids = toJavaList(ids, 'java.lang.Long');
 include = toJavaList(ip.Results.include, 'java.lang.String');
 exclude = toJavaList(ip.Results.exclude, 'java.lang.String');

components/tools/OmeroM/src/annotations/getPlateCommentAnnotations.m

@@ -5,6 +5,10 @@
 %    annotations linked to the plates specified by the input identifiers ids
 %    and owned by the session user.
 %
+%    cas = getPlateCommentAnnotations(session, plates) returns all comment
+%    annotations linked to the input plates and owned by the session
+%    user.
+%
 %    cas = getPlateCommentAnnotations(session,  ids, 'include', include)
 %    only returns comment annotations with the input namespace.
 %
@@ -14,6 +18,7 @@
 %    Examples:
 %
 %        cas = getPlateCommentAnnotations(session, ids)
+%        cas = getPlateCommentAnnotations(session, plates)
 %        cas = getPlateCommentAnnotations(session, ids, 'include', include)
 %        cas = getPlateCommentAnnotations(session, ids, 'exclude', exclude)
 %

components/tools/OmeroM/src/annotations/getPlateFileAnnotations.m

@@ -5,6 +5,9 @@
 %    annotations linked to the plates specified by the input identifiers
 %    and owned by the session user.
 %
+%    fas = getPlateFileAnnotations(session, plates) returns all file
+%    annotations linked to the input plates and owned by the session user.
+%
 %    fas = getPlateFileAnnotations(session,  ids, 'include', include) only
 %    returns file annotations with the input namespace.
 %
@@ -14,6 +17,7 @@
 %    Examples:
 %
 %        fas = getPlateFileAnnotations(session, ids)
+%        fas = getPlateFileAnnotations(session, plates)
 %        fas = getPlateFileAnnotations(session, ids, 'include', include)
 %        fas = getPlateFileAnnotations(session, ids, 'exclude', exclude)
 %

components/tools/OmeroM/src/annotations/getPlateTagAnnotations.m

@@ -5,6 +5,9 @@
 %    linked to the plates specified by the input identifiers ids and owned 
 %    by the session user.
 %
+%    tas = getPlateTagAnnotations(session, plates) returns all tag
+%    annotations linked to the input plates and owned by the session user.
+%
 %    tas = getPlateTagAnnotations(session,  ids, 'include', include) only
 %    returns tag annotations with the input namespace.
 %
@@ -14,8 +17,9 @@
 %    Examples:
 %
 %        tas = getPlateTagAnnotations(session, ids)
-%        fas = getPlateTagAnnotations(session, ids, 'include', include)
-%        fas = getPlateTagAnnotations(session, ids, 'exclude', exclude)
+%        tas = getPlateTagAnnotations(session, plates)
+%        tas = getPlateTagAnnotations(session, ids, 'include', include)
+%        tas = getPlateTagAnnotations(session, ids, 'exclude', exclude)
 %
 % See also: GETOBJECTANNOTATIONS, GETPLATECOMMENTANNOTATIONS,
 % GETPLATEFILEANNOTATIONS, GETPLATEXMLANNOTATIONS

components/tools/OmeroM/src/annotations/getPlateXmlAnnotations.m

@@ -1,21 +1,25 @@
 function xas = getPlateXmlAnnotations(session, ids, varargin)
 % GETPLATEXMLANNOTATIONS Retrieve xml annotations linked to plates
 %
-%    fas = getPlateXmlAnnotations(session, ids) returns all xml
+%    xas = getPlateXmlAnnotations(session, ids) returns all xml
 %    annotations linked to the plates specified by the input identifiers
 %    and owned by the session user.
 %
-%    fas = getPlateXmlAnnotations(session,  ids, 'include', include) only
+%    xas = getPlateXmlAnnotations(session, plates) returns all xml
+%    annotations linked to the input plates and owned by the session user.
+%
+%    xas = getPlateXmlAnnotations(session,  ids, 'include', include) only
 %    returns xml annotations with the input namespace.
 %
-%    fas = getPlateXmlAnnotations(session,  ids, 'exclude', exclude)
+%    xas = getPlateXmlAnnotations(session,  ids, 'exclude', exclude)
 %    excludes xml annotations with the input namespace.
 %
 %    Examples:
 %
-%        fas = getPlateXmlAnnotations(session, ids)
-%        fas = getPlateXmlAnnotations(session, ids, 'include', include)
-%        fas = getPlateXmlAnnotations(session, ids, 'exclude', exclude)
+%        xas = getPlateXmlAnnotations(session, ids)
+%        xas = getPlateXmlAnnotations(session, plates)
+%        xas = getPlateXmlAnnotations(session, ids, 'include', include)
+%        xas = getPlateXmlAnnotations(session, ids, 'exclude', exclude)
 %
 % See also: GETOBJECTANNOTATIONS, GETPLATECOMMENTANNOTATIONS,
 % GETPLATETAGANNOTATIONS, GETPLATEFILEANNOTATIONS

components/tools/OmeroM/src/annotations/getProjectCommentAnnotations.m

@@ -5,6 +5,10 @@
 %    annotations linked to the projects specified by the input identifiers
 %    and owned by the session user.
 %
+%    cas = getProjectCommentAnnotations(session, projects) returns all
+%    comment annotations linked to the input projects and owned by the
+%    session user.
+%
 %    cas = getProjectCommentAnnotations(session,  ids, 'include', include)
 %    only returns comment annotations with the input namespace.
 %
@@ -14,6 +18,7 @@
 %    Examples:
 %
 %        cas = getProjectCommentAnnotations(session, ids)
+%        cas = getProjectCommentAnnotations(session, projects)
 %        cas = getProjectCommentAnnotations(session, ids, 'include', include)
 %        cas = getProjectCommentAnnotations(session, ids, 'exclude', exclude)
 %

components/tools/OmeroM/src/annotations/getProjectFileAnnotations.m

@@ -5,6 +5,10 @@
 %    annotations linked to the projects specified by the input identifiers
 %    and owned by the session user.
 %
+%    fas = getProjectFileAnnotations(session, projects) returns all file
+%    annotations linked to the input projects and owned by the session
+%    user.
+%
 %    fas = getProjectFileAnnotations(session,  ids, 'include', include) only
 %    returns file annotations with the input namespace.
 %
@@ -14,6 +18,7 @@
 %    Examples:
 %
 %        fas = getProjectFileAnnotations(session, ids)
+%        fas = getProjectFileAnnotations(session, projects)
 %        fas = getProjectFileAnnotations(session, ids, 'include', include)
 %        fas = getProjectFileAnnotations(session, ids, 'exclude', exclude)
 %

components/tools/OmeroM/src/annotations/getProjectTagAnnotations.m

@@ -5,6 +5,10 @@
 %    annotations linked to the projects specified by the input identifiers
 %    ids and owned by the session user.
 %
+%    tas = getProjectTagAnnotations(session, projects) returns all tag
+%    annotations linked to the input projects and owned by the session
+%    user.
+%
 %    tas = getProjectTagAnnotations(session,  ids, 'include', include) only
 %    returns tag annotations with the input namespace.
 %
@@ -14,8 +18,9 @@
 %    Examples:
 %
 %        tas = getProjectTagAnnotations(session, ids)
-%        fas = getProjectTagAnnotations(session, ids, 'include', include)
-%        fas = getProjectTagAnnotations(session, ids, 'exclude', exclude)
+%        tas = getProjectTagAnnotations(session, projects)
+%        tas = getProjectTagAnnotations(session, ids, 'include', include)
+%        tas = getProjectTagAnnotations(session, ids, 'exclude', exclude)
 %
 % See also: GETOBJECTANNOTATIONS, GETPROJECTCOMMENTANNOTATIONS,
 % GETPROJECTFILEANNOTATIONS, GETPROJECTXMLANNOTATIONS