WIP jupyterlab#4: Frontend compatibility for n-dimensional backend ch…

…anges

jupyterlab_hdf/baseHandler.py

@@ -81,10 +81,9 @@ def get(self, path):
         selected hyperslab of a dataset and return it as serialized JSON.
         """
         uri = '/' + self.get_query_argument('uri').lstrip('/')
-        select = self.get_query_argument('select', default='ALL')
+        select = self.get_query_argument('select', default=None)
         try:
             self.finish(json.dumps(self.manager.get(path, uri, select)))
-
         except HTTPError as err:
             self.set_status(err.code)
             response = err.response.body if err.response else str(err.code)

jupyterlab_hdf/data.py

@@ -15,7 +15,6 @@ class HdfDataManager(HdfBaseManager):
     """Implements HDF5 data handling
     """
     def _get(self, f, uri, select):
-        print("SELECT: " + str(select))
         return dsetChunk(f[uri], select)
 
 

jupyterlab_hdf/util.py

@@ -78,14 +78,9 @@ def _getHyperslabSlices(dsetshape, select):
     :returns: tuple of Python slices based on the SELECT query param
     """
 
-    # rank = len(dsetshape)
-    if select == 'ALL':
+    if select is None:
         # Default: return entire dataset
         return tuple(slice(0, extent) for extent in dsetshape)
-    # if rank == 1:
-    #     TODO: make brackets optional for 1d? Or not...
-    #     trimmed = select.
-    #     return slice()
 
     if not select.startswith('['):
         msg = "Bad Request: selection query missing start bracket"
@@ -98,6 +93,10 @@ def _getHyperslabSlices(dsetshape, select):
     select = select[1:-1]
 
     select_array = select.split(',')
+    if len(select_array) > len(dsetshape):
+        msg = "Bad Request: number of selected dimensions exceeds the rank of the dataset"
+        raise HTTPError(400, reason=msg)
+
     slices = []
     for dim, dim_slice in enumerate(select_array):
         extent = dsetshape[dim]

src/dataset.ts

@@ -251,8 +251,7 @@ export class HdfDatasetModelBase extends DataModel {
     const params = {
       fpath: this._fpath,
       uri: this._uri,
-      col: [colStart, colStop],
-      row: [rowStart, rowStop]
+      select: `[${rowStart}:${rowStop}, ${colStart}:${colStop}]`
     };
     hdfDataRequest(params, this._serverSettings).then(data => {
       this._blocks[rowBlock][colBlock] = data;

src/hdf.ts

@@ -73,19 +73,12 @@ export function hdfDataRequest(
   parameters: IContentsParameters,
   settings: ServerConnection.ISettings
 ): Promise<number[][]> {
-  // require the uri, row, and col query parameters
-  const { fpath, uri, row, col } = parameters;
-
-  // Remove
-  console.log("TEST QUERY: " + URLExt.objectToQueryString({ "test-slice": "[0:1, 3:4, 5:6, 0:-1]"}));
-  console.log("TEST QUERY: " + URLExt.objectToQueryString({ "test-lists": [[0, 1], [1, 2], [3, 4], [5, 6]]}));
-  // Remove
+  // require the uri query parameter, select is optional
+  const { fpath, uri, ...select } = parameters;
 
   const fullUrl =
     URLExt.join(settings.baseUrl, "hdf", "data", fpath).split("?")[0] +
-    URLExt.objectToQueryString({ uri, row, col });
-
-  console.log("fullUrl: " + fullUrl);
+    URLExt.objectToQueryString({ uri, ...select });
 
   return ServerConnection.makeRequest(fullUrl, {}, settings).then(response => {
     if (response.status !== 200) {
@@ -112,14 +105,11 @@ export interface IContentsParameters {
   uri: string;
 
   /**
-   * Row slice. Up to 3 integers, same syntax as for Python `slice` built-in.
-   */
-  row?: number[];
-
-  /**
-   * Column slice. Up to 3 integers, same syntax as for Python `slice` built-in.
+   * String representing an array of slices that determine a
+   * hyperslab selection of an HDF5 dataset. Syntax and semantics
+   * matches that of h5py's Dataset indexing.
    */
-  col?: number[];
+  select?: string;
 }
 
 /**

src/index.ts

@@ -208,13 +208,9 @@ function addBrowserCommands(
         fpath: args["fpath"] as string,
         uri: args["uri"] as string
       };
-      if (args["col"]) {
-        params.col = args["col"] as number[];
+      if (args["select"]) {
+        params.select = args["select"] as string;
       }
-      if (args["row"]) {
-        params.row = args["row"] as number[];
-      }
-
       return hdfContentsRequest(params, serverSettings);
     },
     label: "For an HDF5 file at `fpath`, fetch the contents at `uri`"