Add functionality for installing extensions

+matnwb/+extension/dispExtensionInfo.m

@@ -0,0 +1,15 @@
+function dispExtensionInfo(extensionName)
+    arguments
+        extensionName (1,1) string
+    end
+
+    T = matnwb.extension.listExtensions();
+    isMatch = T.name == extensionName;
+    extensionList = join( compose("  %s", [T.name]), newline );
+    assert( ...
+        any(isMatch), ...
+        'NWB:DisplayExtensionMetadata:ExtensionNotFound', ...
+        'Extension "%s" was not found in the extension catalog:\n%s', extensionName, extensionList)
+    metadata = table2struct(T(isMatch, :));
+    disp(metadata)
+end

+matnwb/+extension/installAll.m

@@ -0,0 +1,6 @@
+function installAll()
+    T = matnwb.extension.listExtensions();
+    for i = 1:height(T)
+        matnwb.extension.installExtension( T.name(i) )
+    end
+end

+matnwb/+extension/installExtension.m

@@ -0,0 +1,126 @@
+function installExtension(extensionName)
+    arguments
+        extensionName (1,1) string
+    end
+
+    repoTargetFolder = fullfile(userpath, "NWB-Extension-Source");
+    if ~isfolder(repoTargetFolder); mkdir(repoTargetFolder); end
+
+    T = matnwb.extension.listExtensions();
+    isMatch = T.name == extensionName;
+
+    extensionList = join( compose("  %s", [T.name]), newline );
+    assert( ...
+        any(isMatch), ...
+        'NWB:InstallExtension:ExtensionNotFound', ...
+        'Extension "%s" was not found in the extension catalog:\n', extensionList)
+
+    defaultBranchNames = ["main", "master"];
+
+    wasDownloaded = false;
+    for i = 1:2
+        try
+            repositoryUrl = T{isMatch, 'src'};
+            if endsWith(repositoryUrl, '/')
+                repositoryUrl = extractBefore(repositoryUrl, strlength(repositoryUrl));
+            end
+            if contains(repositoryUrl, 'github.com')
+                downloadUrl = sprintf( '%s/archive/refs/heads/%s.zip', repositoryUrl, defaultBranchNames(i) );
+
+            elseif contains(repositoryUrl, 'gitlab.com')
+                repoPathSegments = strsplit(repositoryUrl, '/');
+                repoName = repoPathSegments{end};
+                downloadUrl = sprintf( '%s/-/archive/%s/%s-%s.zip', ...
+                    repositoryUrl, defaultBranchNames(i), repoName, defaultBranchNames(i));
+            else
+                error('NWB:InstallExtension:UnknownRepository', ...
+                    'Extension "%s" is located in an unsupported repository / source location. Please create an issue on matnwb''s github page', extensionName)
+            end
+            repoTargetFolder = downloadZippedRepo(downloadUrl, repoTargetFolder, true, true);
+            wasDownloaded = true;
+            break
+        catch ME
+            if strcmp(ME.identifier, 'MATLAB:webservices:HTTP404StatusCodeError')
+                continue
+            else
+                rethrow(ME)
+            end
+        end
+    end
+    if ~wasDownloaded
+        error('NWB:InstallExtension:DownloadFailed', ...
+            'Failed to download spec for extension "%s"', extensionName)
+    end
+    L = dir(fullfile(repoTargetFolder, 'spec', '*namespace.yaml'));
+    assert(...
+        ~isempty(L), ...
+        'NWB:InstallExtension:NamespaceNotFound', ...
+        'No namespace file was found for extension "%s"', extension.Identifier ...
+        )
+    assert(...
+        numel(L)==1, ...
+        'NWB:InstallExtension:MultipleNamespacesFound', ...
+        'More than one namespace file was found for extension "%s"', extension.Identifier ...
+        )
+    generateExtension( fullfile(L.folder, L.name) );
+end
+
+function repoFolder = downloadZippedRepo(githubUrl, targetFolder, updateFlag, throwErrorIfFails)
+%downloadZippedRepo Download zipped repo
+
+    if nargin < 3; updateFlag = false; end
+    if nargin < 4; throwErrorIfFails = false; end
+
+    if isa(updateFlag, 'char') && strcmp(updateFlag, 'update')
+        updateFlag = true;
+    end
+
+    % Create a temporary path for storing the downloaded file.
+    [~, ~, fileType] = fileparts(githubUrl);
+    tempFilepath = [tempname, fileType];
+
+    % Download the file containing the addon toolbox
+    try
+        tempFilepath = websave(tempFilepath, githubUrl);
+        fileCleanupObj = onCleanup( @(fname) delete(tempFilepath) );
+    catch ME
+        if throwErrorIfFails
+            rethrow(ME)
+        end
+    end
+
+    unzippedFiles = unzip(tempFilepath, tempdir);
+    unzippedFolder = unzippedFiles{1};
+    if endsWith(unzippedFolder, filesep)
+        unzippedFolder = unzippedFolder(1:end-1);
+    end
+
+    [~, repoFolderName] = fileparts(unzippedFolder);
+    targetFolder = fullfile(targetFolder, repoFolderName);
+
+    if updateFlag && isfolder(targetFolder)
+
+        % Delete current version
+        if isfolder(targetFolder)
+            if contains(path, fullfile(targetFolder, filesep))
+                pathList = strsplit(path, pathsep);
+                pathList_ = pathList(startsWith(pathList, fullfile(targetFolder, filesep)));
+                rmpath(strjoin(pathList_, pathsep))
+            end
+            try
+                rmdir(targetFolder, 's')
+            catch
+                warning('Could not remove old installation... Please report')
+            end
+        end
+    else
+        % pass
+    end
+
+    movefile(unzippedFolder, targetFolder);
+
+    % Delete the temp zip file
+    clear fileCleanupObj
+
+    repoFolder = targetFolder;
+end

+matnwb/+extension/listExtensions.m

@@ -0,0 +1,53 @@
+function extensionTable = listExtensions(options)
+    arguments
+        options.Refresh (1,1) logical = false
+    end
+
+    persistent extensionRecords
+
+    if isempty(extensionRecords) || options.Refresh
+        catalogUrl = "https://raw.githubusercontent.com/nwb-extensions/nwb-extensions.github.io/refs/heads/main/data/records.json";
+        extensionRecords = jsondecode(webread(catalogUrl));
+        extensionRecords = consolidateStruct(extensionRecords);
+
+        extensionRecords = struct2table(extensionRecords);
+
+        fieldsKeep = ["name", "version", "last_updated", "src", "license", "maintainers", "readme"];
+        extensionRecords = extensionRecords(:, fieldsKeep);
+
+        for name = fieldsKeep
+            if ischar(extensionRecords.(name){1})
+                extensionRecords.(name) = string(extensionRecords.(name));
+            end
+        end
+    end
+    extensionTable = extensionRecords;
+end
+
+function structArray = consolidateStruct(S)
+    % Get all field names of S
+    mainFields = fieldnames(S);
+
+    % Initialize an empty struct array
+    structArray = struct();
+
+    % Iterate over each field of S
+    for i = 1:numel(mainFields)
+        subStruct = S.(mainFields{i}); % Extract sub-struct
+
+        % Add all fields of the sub-struct to the struct array
+        fields = fieldnames(subStruct);
+        for j = 1:numel(fields)
+            structArray(i).(fields{j}) = subStruct.(fields{j});
+        end
+    end
+
+    % Ensure consistency by filling missing fields with []
+    allFields = unique([fieldnames(structArray)]);
+    for i = 1:numel(structArray)
+        missingFields = setdiff(allFields, fieldnames(structArray(i)));
+        for j = 1:numel(missingFields)
+            structArray(i).(missingFields{j}) = [];
+        end
+    end
+end

.gitignore

@@ -7,3 +7,14 @@ workspace/
 *.swp
 .DS_Store
 +tests/env.mat
+
+# Ignore everything in the +types/ folder
++types/*
+
+# Explicitly include these subdirectories
+!+types/+core/
+!+types/+hdmf_common/
+!+types/+hdmf_experimental/
+!+types/+untyped/
+!+types/+util/
+

nwbInstallExtension.m

@@ -0,0 +1,79 @@
+function nwbInstallExtension(extensionName)
+% nwbInstallExtension - Installs a specified NWB extension.
+%
+%   nwbInstallExtension(extensionName) installs a Neurodata Without Borders 
+%   (NWB) extension to extend the functionality of the core NWB schemas. 
+%   extensionName is a scalar string or a string array, containing the name
+%   of one or more extensions from the Neurodata Extesions Catalog
+%
+% Usage:
+%   nwbInstallExtension(extensionName)
+%
+% Valid Extension Names:
+%  - "ndx-miniscope"
+%  - "ndx-simulation-output"
+%  - "ndx-ecog"
+%  - "ndx-fret"
+%  - "ndx-icephys-meta"
+%  - "ndx-events"
+%  - "ndx-nirs"
+%  - "ndx-hierarchical-behavioral-data"
+%  - "ndx-sound"
+%  - "ndx-extract"
+%  - "ndx-photometry"
+%  - "ndx-acquisition-module"
+%  - "ndx-odor-metadata"
+%  - "ndx-whisk"
+%  - "ndx-ecg"
+%  - "ndx-franklab-novela"
+%  - "ndx-photostim"
+%  - "ndx-multichannel-volume"
+%  - "ndx-depth-moseq"
+%  - "ndx-probeinterface"
+%  - "ndx-dbs"
+%  - "ndx-hed"
+%  - "ndx-ophys-devices"
+%
+% Example:
+%   % Install the "ndx-miniscope" extension
+%   nwbInstallExtension("ndx-miniscope")
+%
+% See also:
+%   matnwb.extension.listExtensions, matnwb.extension.installExtension
+
+    arguments
+        extensionName (1,:) string {mustBeMember(extensionName, [...
+            "ndx-miniscope", ...
+            "ndx-simulation-output", ...
+            "ndx-ecog", ...
+            "ndx-fret", ...
+            "ndx-icephys-meta", ...
+            "ndx-events", ...
+            "ndx-nirs", ...
+            "ndx-hierarchical-behavioral-data", ...
+            "ndx-sound", ...
+            "ndx-extract", ...
+            "ndx-photometry", ...
+            "ndx-acquisition-module", ...
+            "ndx-odor-metadata", ...
+            "ndx-whisk", ...
+            "ndx-ecg", ...
+            "ndx-franklab-novela", ...
+            "ndx-photostim", ...
+            "ndx-multichannel-volume", ...
+            "ndx-depth-moseq", ...
+            "ndx-probeinterface", ...
+            "ndx-dbs", ...
+            "ndx-hed", ...
+            "ndx-ophys-devices" ...
+            ] ...
+        )} = []
+    end
+    if isempty(extensionName)
+        T = matnwb.extension.listExtensions();
+        extensionList = join( compose("  %s", [T.name]), newline );
+        error("Please specify the name of an extension. Available extensions:\n\n%s\n", extensionList)
+    else
+        matnwb.extension.installExtension(extensionName)
+    end
+end

resources/function_templates/nwbInstallExtension.txt

@@ -0,0 +1,35 @@
+function nwbInstallExtension(extensionName)
+% nwbInstallExtension - Installs a specified NWB extension.
+%
+%   nwbInstallExtension(extensionName) installs a Neurodata Without Borders 
+%   (NWB) extension to extend the functionality of the core NWB schemas. 
+%   extensionName is a scalar string or a string array, containing the name
+%   of one or more extensions from the Neurodata Extesions Catalog
+%
+% Usage:
+%   nwbInstallExtension(extensionName)
+%
+% Valid Extension Names:
+{{extensionNamesDoc}}
+%
+% Example:
+%   % Install the "ndx-miniscope" extension
+%   nwbInstallExtension("ndx-miniscope")
+%
+% See also:
+%   matnwb.extension.listExtensions, matnwb.extension.installExtension
+
+    arguments
+        extensionName (1,:) string {mustBeMember(extensionName, [...
+{{extensionNames}} ...
+            ] ...
+        )} = []
+    end
+    if isempty(extensionName)
+        T = matnwb.extension.listExtensions();
+        extensionList = join( compose("  %s", [T.name]), newline );
+        error("Please specify the name of an extension. Available extensions:\n\n%s\n", extensionList)
+    else
+        matnwb.extension.installExtension(extensionName)
+    end
+end

tools/maintenance/matnwb_createNwbInstallExtension.m

@@ -0,0 +1,28 @@
+function matnwb_createNwbInstallExtension()
+% matnwb_createNwbInstallExtension - Create nwbInstallExtension from template
+%
+%   This function can be run to update the list of available extension
+%   names in the function's arguments block based on the neurodata
+%   extensions catalog
+
+    matnwbRootDir = misc.getMatnwbDir();
+    fcnTemplate = fileread(fullfile(matnwbRootDir, ...
+        'resources', 'function_templates', 'nwbInstallExtension.txt'));
+
+    extensionTable = matnwb.extension.listExtensions();
+    extensionNames = extensionTable.name;
+
+    indentStr = repmat(' ', 1, 12);
+    extensionNamesStr = compose("%s""%s""", indentStr, extensionNames);
+    extensionNamesStr = strjoin(extensionNamesStr, ", ..." + newline);
+    fcnStr = replace(fcnTemplate, "{{extensionNames}}", extensionNamesStr);
+
+    extensionNamesStr = compose("%%  - ""%s""", extensionNames);
+    extensionNamesStr = strjoin(extensionNamesStr, newline);
+    fcnStr = replace(fcnStr, "{{extensionNamesDoc}}", extensionNamesStr);
+
+
+    fid = fopen(fullfile(matnwbRootDir, 'nwbInstallExtension.m'), "wt");
+    fwrite(fid, fcnStr);
+    fclose(fid);
+end