Mccalluc/consistent arrays

README.md

@@ -15,7 +15,7 @@ $ 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]
+                      [--to_json] [--conf_index I]
 
 Given HuBMAP Dataset JSON, generate a Vitessce viewconf, and load vitessce.io.
 
@@ -31,6 +31,9 @@ optional arguments:
   --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.
 ```
 
 ## Background

VERSION.txt

@@ -1 +1 @@
-0.0.6
+0.1.0

src/portal_visualization/builders/anndata_builders.py

@@ -9,7 +9,6 @@
 import zarr
 
 from .base_builders import ViewConfBuilder
-from ..utils import get_conf_cells
 
 
 class RNASeqAnnDataZarrViewConfBuilder(ViewConfBuilder):
@@ -18,14 +17,14 @@ class RNASeqAnnDataZarrViewConfBuilder(ViewConfBuilder):
     https://portal.hubmapconsortium.org/browse/dataset/e65175561b4b17da5352e3837aa0e497
     """
 
-    def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
-        super().__init__(entity, groups_token, assets_endpoint, **kwargs)
+    def __init__(self, entity, groups_token, assets_endpoint):
+        super().__init__(entity, groups_token, assets_endpoint)
         # Spatially resolved RNA-seq assays require some special handling,
         # and others do not.
         self._is_spatial = False
         self._scatterplot_w = 9
 
-    def get_conf_cells(self, marker=None):
+    def get_configs(self, marker=None):
         zarr_path = 'hubmap_ui/anndata-zarr/secondary_analysis.zarr'
         file_paths_found = [file["rel_path"] for file in self._entity["files"]]
         # Use .zgroup file as proxy for whether or not the zarr store is present.
@@ -77,7 +76,7 @@ def get_conf_cells(self, marker=None):
         ))
 
         vc = self._setup_anndata_view_config(vc, dataset, marker)
-        return get_conf_cells(vc)
+        return [vc]
 
     def _setup_anndata_view_config(self, vc, dataset, marker=None):
         scatterplot = vc.add_view(
@@ -118,8 +117,8 @@ class SpatialRNASeqAnnDataZarrViewConfBuilder(RNASeqAnnDataZarrViewConfBuilder):
     https://portal.hubmapconsortium.org/browse/dataset/2a590db3d7ab1e1512816b165d95cdcf
     """
 
-    def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
-        super().__init__(entity, groups_token, assets_endpoint, **kwargs)
+    def __init__(self, entity, groups_token, assets_endpoint):
+        super().__init__(entity, groups_token, assets_endpoint)
         # Spatially resolved RNA-seq assays require some special handling,
         # and others do not.
         self._is_spatial = True

src/portal_visualization/builders/base_builders.py

@@ -2,21 +2,40 @@
 from collections import namedtuple
 from abc import ABC, abstractmethod
 
+import nbformat
 
-ConfCells = namedtuple('ConfCells', ['conf', 'cells'])
+
+ConfigsCells = namedtuple('ConfigsCells', ['configs', 'cells'])
+
+
+def _get_cells_from_conf_list(confs):
+    cells = []
+    if len(confs) > 1:
+        cells.append(nbformat.v4.new_markdown_cell('Multiple visualizations are available.'))
+    for conf in confs:
+        cells.extend(_get_cells_from_conf(conf))
+    return cells
+
+
+def _get_cells_from_conf(conf):
+    imports, conf_expression = conf.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()'),
+    ]
 
 
 class NullViewConfBuilder():
-    def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
+    def __init__(self, entity, groups_token, assets_endpoint):
         # Just so it has the same signature as the other builders
         pass
 
-    def get_conf_cells(self, **kwargs):
-        return ConfCells(None, None)
+    def get_configs_cells(self, marker=None):
+        return ConfigsCells([], [])
 
 
 class ViewConfBuilder(ABC):
-    def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
+    def __init__(self, entity, groups_token, assets_endpoint):
         """Object for building the vitessce configuration.
         :param dict entity: Entity response from search index (from the entity API)
         :param str groups_token: Groups token for use in authenticating API
@@ -29,9 +48,15 @@ def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
         self._files = []
 
     @abstractmethod
-    def get_conf_cells(self, **kwargs):  # pragma: no cover
+    def get_configs(self):  # pragma: no cover
         raise NotImplementedError()
 
+    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)
+        return ConfigsCells(configs, cells)
+
     def _replace_url_in_file(self, file):
         """Replace url in incoming file object
         :param dict file: File dict which will have its rel_path replaced by url
@@ -118,5 +143,5 @@ def _get_file_paths(self):
 class _DocTestBuilder(ViewConfBuilder):  # pragma: no cover
     # The doctests on the methods in this file need a concrete class to instantiate:
     # We need a concrete definition for this method, even if it's never used.
-    def get_conf_cells(self, **kwargs):
-        pass
+    def get_configs(self):
+        raise NotImplementedError()

src/portal_visualization/builders/imaging_builders.py

@@ -8,7 +8,7 @@
     Component as cm,
 )
 
-from ..utils import get_matches, group_by_file_name, get_conf_cells
+from ..utils import get_matches, group_by_file_name
 from ..paths import IMAGE_PYRAMID_DIR, OFFSETS_DIR, SEQFISH_HYB_CYCLE_REGEX, SEQFISH_FILE_REGEX
 from .base_builders import ViewConfBuilder
 
@@ -23,7 +23,7 @@ def _get_img_and_offset_url(self, img_path, img_dir):
 
         >>> from pprint import pprint
         >>> class ConcreteBuilder(AbstractImagingViewConfBuilder):
-        ...     def get_conf_cells(self, **kwargs):
+        ...     def get_configs(self):
         ...         pass
         >>> builder = ConcreteBuilder(
         ...   entity={ "uuid": "uuid" },
@@ -56,15 +56,15 @@ def _setup_view_config_raster(self, vc, dataset, disable_3d=[]):
 
 
 class ImagePyramidViewConfBuilder(AbstractImagingViewConfBuilder):
-    def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
+    def __init__(self, entity, groups_token, assets_endpoint):
         """Wrapper class for creating a standard view configuration for image pyramids,
         i.e for high resolution viz-lifted imaging datasets like
         https://portal.hubmapconsortium.org/browse/dataset/dc289471333309925e46ceb9bafafaf4
         """
         self.image_pyramid_regex = IMAGE_PYRAMID_DIR
-        super().__init__(entity, groups_token, assets_endpoint, **kwargs)
+        super().__init__(entity, groups_token, assets_endpoint)
 
-    def get_conf_cells(self, **kwargs):
+    def get_configs(self):
         file_paths_found = self._get_file_paths()
         found_images = [
             path for path in get_matches(
@@ -93,7 +93,7 @@ def get_conf_cells(self, **kwargs):
         conf = vc.to_dict()
         # Don't want to render all layers
         del conf["datasets"][0]["files"][0]["options"]["renderLayers"]
-        return get_conf_cells(conf)
+        return [VitessceConfig.from_dict(conf)]
 
 
 class IMSViewConfBuilder(ImagePyramidViewConfBuilder):
@@ -102,8 +102,8 @@ class IMSViewConfBuilder(ImagePyramidViewConfBuilder):
     of all the channels separated out.
     """
 
-    def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
-        super().__init__(entity, groups_token, assets_endpoint, **kwargs)
+    def __init__(self, entity, groups_token, assets_endpoint):
+        super().__init__(entity, groups_token, assets_endpoint)
         # Do not show the separated mass-spec images.
         self.image_pyramid_regex = (
             re.escape(IMAGE_PYRAMID_DIR) + r"(?!/ometiffs/separate/)"
@@ -116,7 +116,7 @@ class SeqFISHViewConfBuilder(AbstractImagingViewConfBuilder):
     grouped together per position in a single Vitessce configuration.
     """
 
-    def get_conf_cells(self, **kwargs):
+    def get_configs(self):
         file_paths_found = [file["rel_path"] for file in self._entity["files"]]
         full_seqfish_regex = "/".join(
             [
@@ -159,13 +159,11 @@ def get_conf_cells(self, **kwargs):
             conf = vc.to_dict()
             # Don't want to render all layers
             del conf["datasets"][0]["files"][0]["options"]["renderLayers"]
-            confs.append(conf)
-        return get_conf_cells(confs)
+            confs.append(VitessceConfig.from_dict(conf))
+        return confs
 
     def _get_hybcycle(self, image_path):
         return re.search(SEQFISH_HYB_CYCLE_REGEX, image_path)[0]
 
     def _get_pos_name(self, image_path):
-        return re.search(SEQFISH_FILE_REGEX, image_path)[0].split(".")[
-            0
-        ]
+        return re.search(SEQFISH_FILE_REGEX, image_path)[0].split(".")[0]

src/portal_visualization/builders/scatterplot_builders.py

@@ -6,7 +6,6 @@
 )
 
 
-from ..utils import get_conf_cells
 from ..paths import SCRNA_SEQ_DIR, SCATAC_SEQ_DIR
 from .base_builders import ViewConfBuilder
 
@@ -18,7 +17,7 @@ class AbstractScatterplotViewConfBuilder(ViewConfBuilder):
     from h5ad-to-arrow.cwl.
     """
 
-    def get_conf_cells(self, **kwargs):
+    def get_configs(self):
         file_paths_expected = [file["rel_path"] for file in self._files]
         file_paths_found = self._get_file_paths()
         # We need to check that the files we expect actually exist.
@@ -33,7 +32,7 @@ def get_conf_cells(self, **kwargs):
         for file in self._files:
             dataset = dataset.add_file(**(self._replace_url_in_file(file)))
         vc = self._setup_scatterplot_view_config(vc, dataset)
-        return get_conf_cells(vc)
+        return [vc]
 
     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)
@@ -47,8 +46,8 @@ class RNASeqViewConfBuilder(AbstractScatterplotViewConfBuilder):
     from h5ad-to-arrow.cwl (August 2020 release).
     """
 
-    def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
-        super().__init__(entity, groups_token, assets_endpoint, **kwargs)
+    def __init__(self, entity, groups_token, assets_endpoint):
+        super().__init__(entity, groups_token, assets_endpoint)
         # All "file" Vitessce objects that do not have wrappers.
         self._files = [
             {
@@ -70,8 +69,8 @@ class ATACSeqViewConfBuilder(AbstractScatterplotViewConfBuilder):
     from h5ad-to-arrow.cwl.
     """
 
-    def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
-        super().__init__(entity, groups_token, assets_endpoint, **kwargs)
+    def __init__(self, entity, groups_token, assets_endpoint):
+        super().__init__(entity, groups_token, assets_endpoint)
         # All "file" Vitessce objects that do not have wrappers.
         self._files = [
             {