Merge pull request #37 from dereklu888/nf-external-links

Add external links to files (if available) and display in context menu

.gitignore

@@ -13,3 +13,4 @@ dist/
 venvs/
 fixtures/
 .idea
+.hypothesis

datalad_deprecated/ls_webui.py

@@ -26,6 +26,9 @@
 from datalad_deprecated.utils import safe_print
 from datalad.utils import with_pathsep
 from datalad.utils import Path
+import datalad.api as dl
+
+import datalad_deprecated.metadata.extractors.datalad_core as dc
 
 from datalad_deprecated.metadata.consts import (
     OLDMETADATA_DIR,
@@ -199,7 +202,8 @@ def fs_traverse(path, repo, parent=None,
                 render=True,
                 recurse_datasets=False,
                 recurse_directories=False,
-                json=None, basepath=None):
+                json=None, basepath=None,
+                file_metadata=None):
     """Traverse path through its nodes and returns a dictionary of relevant
     attributes attached to each node
 
@@ -216,6 +220,9 @@ def fs_traverse(path, repo, parent=None,
     render: bool
        To render from within function or not. Set to false if results to be
        manipulated before final render
+    file_metadata: dict
+       Extracted metadata of all files in the dataset being traversed in.
+       This will be used to attach external urls to files if they have them.
 
     Returns
     -------
@@ -298,6 +305,8 @@ def fs_traverse(path, repo, parent=None,
                         subdir = fs_extract(nodepath,
                                             repo,
                                             basepath=basepath or path)
+                if file_metadata and nodepath in file_metadata:
+                    subdir['external_urls'] = file_metadata[nodepath]
                 # append child metadata to list
                 children.extend([subdir])
 
@@ -352,6 +361,15 @@ def ds_traverse(rootds, parent=None, json=None,
     fsparent = fs_extract(parent.path, parent.repo, basepath=rootds.path) \
         if parent else None
 
+    # from my understanding, this constructs a file metadata map that maps file path to external urls found 
+    # (the map is passed to fs_traverse)
+    metadata_raw = dl.extract_metadata(types=["datalad_core"], dataset=rootds)
+    metadata_map = {}
+
+    for file_metadata in metadata_raw:
+        if file_metadata['type'] == 'file' and 'datalad_core' in file_metadata['metadata'] and 'url' in file_metadata['metadata']['datalad_core']:
+            metadata_map[file_metadata['path']] = file_metadata['metadata']['datalad_core']['url']
+
     # (recursively) traverse file tree of current dataset
     fs = fs_traverse(
         rootds.path, rootds.repo,
@@ -361,7 +379,8 @@ def ds_traverse(rootds, parent=None, json=None,
         # XXX note that here I kinda flipped the notions!
         recurse_datasets=recurse_datasets,
         recurse_directories=recurse_directories,
-        json=json
+        json=json,
+        file_metadata=metadata_map
     )
 
     # BUT if we are recurse_datasets but not recurse_directories

datalad_deprecated/resources/website/assets/js/main.js

@@ -583,6 +583,24 @@ function directory(jQuery, md5) {
         menu +=  '<li class="context-option external"><a href="' + data.url + '">Open External Link</a></li>';
       }
 
+      // add in external urls for any files that have them
+      if (data.external_urls) {
+        if (data.external_urls.length == 1) {
+            menu +=  '<li class="context-option external"><a href="' + data.external_urls[0] + '">' + 'Open External URL' + '</a></li>';
+        }
+        // if there are multiple external urls, list at most 5 (currently just gets the first 5)
+        else if (data.external_urls.length > 1) {
+            menu +=  '<li class="context-option separator">External URLs</li>';
+            for (var i = 0; i < Math.min(5, data.external_urls.length); i++) {
+              var link = document.createElement("a");
+              link.href = data.external_urls[i];
+              link.protocol = "https";
+              menu +=  '<li class="context-option service"><a href="' + data.external_urls[i] + '">' + link.hostname + '</a></li>';
+            }
+        }
+
+      }
+
       if (data.type === 'dir' || data.type === 'git' || data.type === 'annex') {
         var folderUrl = traverse.next
         if (folderUrl.indexOf("?dir=") > -1){

datalad_deprecated/tests/test_auto.py

@@ -265,7 +265,7 @@ def generate_nii(f):
 
     def verify_nii(f, mode="r"):
         ni = nib.load(f)
-        assert_array_equal(ni.get_data(), d)
+        assert_array_equal(ni.get_fdata(), d)
 
     _test_proxying_open(generate_nii, verify_nii)