Mccalluc/consistent names

README.md

@@ -15,9 +15,10 @@ $ pip install .
 $ src/vis-preview.py --help
 usage: vis-preview.py [-h] (--url URL | --json JSON) [--types_url URL]
                       [--assets_url URL] [--token TOKEN] [--marker MARKER]
-                      [--to_json] [--conf_index I]
+                      [--to_json] [--config_index I]
 
-Given HuBMAP Dataset JSON, generate a Vitessce viewconf, and load vitessce.io.
+Given HuBMAP Dataset JSON, generate a Vitessce view config, and load
+vitessce.io.
 
 optional arguments:
   -h, --help        show this help message and exit
@@ -30,10 +31,10 @@ optional arguments:
   --token TOKEN     Globus groups token; Only needed if data is not public
   --marker MARKER   Marker to highlight in visualization; Only used in some
                     visualizations.
-  --to_json         Output viewconf, rather than open in browser.
-  --conf_index I    Old untiled imagery produces multiple viewconfs, one for
-                    each tile. This allows you display a viewconf other than
-                    the first.
+  --to_json         Output view config, rather than open in browser.
+  --config_index I  Old untiled imagery produces multiple view configs, one
+                    for each tile. This allows you display a view config other
+                    than the first.
 ```
 
 ## Background

src/portal_visualization/builders/anndata_builders.py

@@ -31,7 +31,7 @@ def get_configs(self, marker=None):
         if f'{zarr_path}/.zgroup' not in file_paths_found:
             message = f'RNA-seq assay with uuid {self._uuid} has no .zarr store at {zarr_path}'
             raise FileNotFoundError(message)
-        vc = VitessceConfig(name=self._uuid)
+        config = VitessceConfig(name=self._uuid)
         adata_url = self._build_assets_url(zarr_path, use_token=False)
         # Some of the keys (like marker_genes_for_heatmap) here are from our pipeline
         # https://github.com/hubmapconsortium/portal-containers/blob/master/containers/anndata-to-ui
@@ -55,7 +55,7 @@ def get_configs(self, marker=None):
                 cell_set_obs_names.append("Predicted ASCT Cell Type")
         z = zarr.open(adata_url, mode='r', storage_options={'client_kwargs': request_init})
         gene_alias = 'var/hugo_symbol' if 'var' in z and 'hugo_symbol' in z['var'] else None
-        dataset = vc.add_dataset(name=self._uuid).add_object(AnnDataWrapper(
+        dataset = config.add_dataset(name=self._uuid).add_object(AnnDataWrapper(
             adata_url=adata_url,
             mappings_obsm=["X_umap"],
             mappings_obsm_names=["UMAP"],
@@ -75,37 +75,37 @@ def get_configs(self, marker=None):
             gene_alias=gene_alias
         ))
 
-        vc = self._setup_anndata_view_config(vc, dataset, marker)
-        return [vc]
+        config = self._setup_anndata_view_config(config, dataset, marker)
+        return [config]
 
-    def _setup_anndata_view_config(self, vc, dataset, marker=None):
-        scatterplot = vc.add_view(
+    def _setup_anndata_view_config(self, config, dataset, marker=None):
+        scatterplot = config.add_view(
             cm.SCATTERPLOT, dataset=dataset, mapping="UMAP", x=0, y=0, w=self._scatterplot_w, h=6)
-        cell_sets = vc.add_view(
+        cell_sets = config.add_view(
             cm.CELL_SETS, dataset=dataset, x=9, y=0, w=3, h=3)
-        gene_list = vc.add_view(
+        gene_list = config.add_view(
             cm.GENES, dataset=dataset, x=9, y=4, w=3, h=3)
-        cell_sets_expr = vc.add_view(
+        cell_sets_expr = config.add_view(
             cm.CELL_SET_EXPRESSION, dataset=dataset, x=7, y=6, w=5, h=4)
-        heatmap = vc.add_view(
+        heatmap = config.add_view(
             cm.HEATMAP, dataset=dataset, x=0, y=6, w=7, h=4)
         # Adding heatmap to coordination doesn't do anything,
         # but it also doesn't hurt anything.
         # Vitessce feature request to add it:
         # https://github.com/vitessce/vitessce/issues/1298
 
-        self._add_spatial_view(dataset, vc)
+        self._add_spatial_view(dataset, config)
 
         if marker:
-            vc.link_views(
+            config.link_views(
                 [cell_sets, gene_list, scatterplot, cell_sets_expr, heatmap],
                 [CoordinationType.GENE_SELECTION, CoordinationType.CELL_COLOR_ENCODING],
                 [[marker], "geneSelection"]
             )
 
-        return vc
+        return config
 
-    def _add_spatial_view(self, dataset, vc):
+    def _add_spatial_view(self, dataset, config):
         # This class does not have a spatial_view...
         # but the subclass does, and overrides this method.
         pass
@@ -124,9 +124,9 @@ def __init__(self, entity, groups_token, assets_endpoint):
         self._is_spatial = True
         self._scatterplot_w = 4
 
-    def _add_spatial_view(self, dataset, vc):
-        spatial = vc.add_view(cm.SPATIAL, dataset=dataset, x=4, y=0, w=5, h=6)
-        [cells_layer] = vc.add_coordination('spatialCellsLayer')
+    def _add_spatial_view(self, dataset, config):
+        spatial = config.add_view(cm.SPATIAL, dataset=dataset, x=4, y=0, w=5, h=6)
+        [cells_layer] = config.add_coordination('spatialCellsLayer')
         cells_layer.set_value(
             {
                 "visible": True,

src/portal_visualization/builders/base_builders.py

@@ -8,20 +8,20 @@
 ConfigsCells = namedtuple('ConfigsCells', ['configs', 'cells'])
 
 
-def _get_cells_from_conf_list(confs):
+def _get_cells_from_config_list(configs):
     cells = []
-    if len(confs) > 1:
+    if len(configs) > 1:
         cells.append(nbformat.v4.new_markdown_cell('Multiple visualizations are available.'))
-    for conf in confs:
-        cells.extend(_get_cells_from_conf(conf))
+    for config in configs:
+        cells.extend(_get_cells_from_config(config))
     return cells
 
 
-def _get_cells_from_conf(conf):
-    imports, conf_expression = conf.to_python()
+def _get_cells_from_config(config):
+    imports, config_expression = config.to_python()
     return [
         nbformat.v4.new_code_cell(f'from vitessce import {", ".join(imports)}'),
-        nbformat.v4.new_code_cell(f'conf = {conf_expression}\nconf.widget()'),
+        nbformat.v4.new_code_cell(f'config = {config_expression}\nconfig.widget()'),
     ]
 
 
@@ -54,7 +54,7 @@ def get_configs(self):  # pragma: no cover
     def get_configs_cells(self, marker=None):
         kwargs = {'marker': marker} if marker is not None else {}
         configs = self.get_configs(**kwargs)
-        cells = _get_cells_from_conf_list(configs)
+        cells = _get_cells_from_config_list(configs)
         return ConfigsCells(configs, cells)
 
     def _replace_url_in_file(self, file):
@@ -100,7 +100,7 @@ def _build_assets_url(self, rel_path, use_token=True):
         return f"{base_url}?{token_param}" if use_token else base_url
 
     def _get_request_init(self):
-        """Get request headers for requestInit parameter in Vitessce conf.
+        """Get request headers for requestInit parameter in Vitessce config.
         This is needed for non-public zarr stores because the client forms URLs for zarr chunks,
         not the above _build_assets_url function.
 

src/portal_visualization/builders/imaging_builders.py

@@ -46,13 +46,13 @@ def _get_img_and_offset_url(self, img_path, img_dir):
             ),
         )
 
-    def _setup_view_config_raster(self, vc, dataset, disable_3d=[]):
-        vc.add_view(cm.SPATIAL, dataset=dataset, x=3, y=0, w=9, h=12)
-        vc.add_view(cm.DESCRIPTION, dataset=dataset, x=0, y=8, w=3, h=4)
-        vc.add_view(cm.LAYER_CONTROLLER, dataset=dataset, x=0, y=0, w=3, h=8).set_props(
+    def _setup_view_config_raster(self, config, dataset, disable_3d=[]):
+        config.add_view(cm.SPATIAL, dataset=dataset, x=3, y=0, w=9, h=12)
+        config.add_view(cm.DESCRIPTION, dataset=dataset, x=0, y=8, w=3, h=4)
+        config.add_view(cm.LAYER_CONTROLLER, dataset=dataset, x=0, y=0, w=3, h=8).set_props(
             disable3d=disable_3d, disableChannelsIfRgbDetected=True
         )
-        return vc
+        return config
 
 
 class ImagePyramidViewConfBuilder(AbstractImagingViewConfBuilder):
@@ -76,8 +76,8 @@ def get_configs(self):
             message = f"Image pyramid assay with uuid {self._uuid} has no matching files"
             raise FileNotFoundError(message)
 
-        vc = VitessceConfig(name="HuBMAP Data Portal")
-        dataset = vc.add_dataset(name="Visualization Files")
+        config = VitessceConfig(name="HuBMAP Data Portal")
+        dataset = config.add_dataset(name="Visualization Files")
         images = []
         for img_path in found_images:
             img_url, offsets_url = self._get_img_and_offset_url(
@@ -89,11 +89,11 @@ def get_configs(self):
                 )
             )
         dataset = dataset.add_object(MultiImageWrapper(images))
-        vc = self._setup_view_config_raster(vc, dataset)
-        conf = vc.to_dict()
+        config = self._setup_view_config_raster(config, dataset)
+        config_as_dict = config.to_dict()
         # Don't want to render all layers
-        del conf["datasets"][0]["files"][0]["options"]["renderLayers"]
-        return [VitessceConfig.from_dict(conf)]
+        del config_as_dict["datasets"][0]["files"][0]["options"]["renderLayers"]
+        return [VitessceConfig.from_dict(config_as_dict)]
 
 
 class IMSViewConfBuilder(ImagePyramidViewConfBuilder):
@@ -131,13 +131,13 @@ def get_configs(self):
             raise FileNotFoundError(message)
         # Get all files grouped by PosN names.
         images_by_pos = group_by_file_name(found_images)
-        confs = []
-        # Build up a conf for each Pos.
+        configs = []
+        # Build up a config for each Pos.
         for images in images_by_pos:
             image_wrappers = []
             pos_name = self._get_pos_name(images[0])
-            vc = VitessceConfig(name=pos_name)
-            dataset = vc.add_dataset(name=pos_name)
+            config = VitessceConfig(name=pos_name)
+            dataset = config.add_dataset(name=pos_name)
             sorted_images = sorted(images, key=self._get_hybcycle)
             for img_path in sorted_images:
                 img_url, offsets_url = self._get_img_and_offset_url(
@@ -151,16 +151,16 @@ def get_configs(self):
                     )
                 )
             dataset = dataset.add_object(MultiImageWrapper(image_wrappers))
-            vc = self._setup_view_config_raster(
-                vc,
+            config = self._setup_view_config_raster(
+                config,
                 dataset,
                 disable_3d=[self._get_hybcycle(img_path) for img_path in sorted_images]
             )
-            conf = vc.to_dict()
+            config_as_dict = config.to_dict()
             # Don't want to render all layers
-            del conf["datasets"][0]["files"][0]["options"]["renderLayers"]
-            confs.append(VitessceConfig.from_dict(conf))
-        return confs
+            del config_as_dict["datasets"][0]["files"][0]["options"]["renderLayers"]
+            configs.append(VitessceConfig.from_dict(config_as_dict))
+        return configs
 
     def _get_hybcycle(self, image_path):
         return re.search(SEQFISH_HYB_CYCLE_REGEX, image_path)[0]

src/portal_visualization/builders/scatterplot_builders.py

@@ -26,18 +26,18 @@ def get_configs(self):
             message = f'Files for uuid "{self._uuid}" not found as expected: ' \
                 f'Expected: {file_paths_expected}; Found: {file_paths_found}'
             raise FileNotFoundError(message)
-        vc = VitessceConfig(name="HuBMAP Data Portal")
-        dataset = vc.add_dataset(name="Visualization Files")
+        config = VitessceConfig(name="HuBMAP Data Portal")
+        dataset = config.add_dataset(name="Visualization Files")
         # The sublcass initializes _files in its __init__ method
         for file in self._files:
             dataset = dataset.add_file(**(self._replace_url_in_file(file)))
-        vc = self._setup_scatterplot_view_config(vc, dataset)
-        return [vc]
+        config = self._setup_scatterplot_view_config(config, dataset)
+        return [config]
 
-    def _setup_scatterplot_view_config(self, vc, dataset):
-        vc.add_view(cm.SCATTERPLOT, dataset=dataset, mapping="UMAP", x=0, y=0, w=9, h=12)
-        vc.add_view(cm.CELL_SETS, dataset=dataset, x=9, y=0, w=3, h=12)
-        return vc
+    def _setup_scatterplot_view_config(self, config, dataset):
+        config.add_view(cm.SCATTERPLOT, dataset=dataset, mapping="UMAP", x=0, y=0, w=9, h=12)
+        config.add_view(cm.CELL_SETS, dataset=dataset, x=9, y=0, w=3, h=12)
+        return config
 
 
 class RNASeqViewConfBuilder(AbstractScatterplotViewConfBuilder):