Open ivirshup opened 2 months ago
Hey, ran into what I think is a small bug in to_dict:
to_dict
import zarr from vitessce import ( VitessceWidget, VitessceConfig, Component as cm, CoordinationType as ct, AnnDataWrapper, ) TEST_ANNDATA_URI = "s3://tmp-census-zarr/v1/homo_sapiens/0041b9c3-6a49-4bf7-8514-9bc7190067a7.zarr" vc = VitessceConfig(schema_version="1.0.15") dataset = vc.add_dataset().add_object( AnnDataWrapper( adata_store=z.store, obs_embedding_paths=["obsm/X_umap"], obs_embedding_names=["UMAP"], obs_set_paths=["obs/cell_type"], obs_set_names=["cell_type"], obs_feature_matrix_path="X", # feature_filter_path="var/top_highly_variable" ) ) scatterplot = vc.add_view(cm.SCATTERPLOT, dataset=dataset, mapping="UMAP") layout = vc.layout(scatterplot) layout.to_dict()
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[12], line 26 23 scatterplot = vc.add_view(cm.SCATTERPLOT, dataset=dataset, mapping="UMAP") 24 layout = vc.layout(scatterplot) ---> 26 layout.to_dict() File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/config.py:1488, in VitessceConfig.to_dict(self, base_url) 1477 def to_dict(self, base_url=None): 1478 """ 1479 Convert the view config instance to a dict object. 1480 (...) 1484 :rtype: dict 1485 """ 1486 return { 1487 **self.config, -> 1488 "datasets": [d.to_dict(base_url) for d in self.config["datasets"]], 1489 "coordinationSpace": dict([ 1490 (c_type, dict([ 1491 (c_scope_name, c_scope.c_value) for c_scope_name, c_scope in c_scopes.items() 1492 ])) for c_type, c_scopes in self.config["coordinationSpace"].items() 1493 ]), 1494 # TODO: compute the x,y,w,h values if not explicitly defined 1495 "layout": [c.to_dict() for c in self.config["layout"]] 1496 } File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/config.py:1488, in <listcomp>(.0) 1477 def to_dict(self, base_url=None): 1478 """ 1479 Convert the view config instance to a dict object. 1480 (...) 1484 :rtype: dict 1485 """ 1486 return { 1487 **self.config, -> 1488 "datasets": [d.to_dict(base_url) for d in self.config["datasets"]], 1489 "coordinationSpace": dict([ 1490 (c_type, dict([ 1491 (c_scope_name, c_scope.c_value) for c_scope_name, c_scope in c_scopes.items() 1492 ])) for c_type, c_scopes in self.config["coordinationSpace"].items() 1493 ]), 1494 # TODO: compute the x,y,w,h values if not explicitly defined 1495 "layout": [c.to_dict() for c in self.config["layout"]] 1496 } File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/config.py:224, in VitessceConfigDataset.to_dict(self, base_url) 222 obj_file_defs = [] 223 for obj in self.objs: --> 224 obj_file_defs += obj.get_file_defs(base_url) 226 return { 227 **self.dataset, 228 "files": [f.to_dict() for f in self.dataset["files"]] + obj_file_defs, 229 } File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/wrappers.py:102, in AbstractWrapper.get_file_defs(self, base_url) 100 file_defs_with_base_url = [] 101 for file_def_creator in self.file_def_creators: --> 102 file_def = file_def_creator(base_url) 103 if file_def is not None: 104 file_defs_with_base_url.append(file_def) File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/wrappers.py:1183, in AnnDataWrapper.make_file_def_creator.<locals>.get_anndata_zarr(base_url) 1178 if self.is_h5ad: 1179 options["refSpecUrl"] = self.get_ref_url(base_url, dataset_uid, obj_i) 1181 obj_file_def = { 1182 "fileType": ft.ANNDATA_ZARR.value if not self.is_h5ad else ft.ANNDATA_H5AD.value, -> 1183 "url": self.get_zarr_url(base_url, dataset_uid, obj_i) if not self.is_h5ad else self.get_h5ad_url(base_url, dataset_uid, obj_i), 1184 "options": options 1185 } 1186 if self._request_init is not None: 1187 obj_file_def['requestInit'] = self._request_init File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/wrappers.py:1087, in AnnDataWrapper.get_zarr_url(self, base_url, dataset_uid, obj_i) 1085 return self._adata_url 1086 else: -> 1087 return self.get_local_dir_url(base_url, dataset_uid, obj_i, self._adata_path, self.local_dir_uid) File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/wrappers.py:133, in AbstractWrapper.get_local_dir_url(self, base_url, dataset_uid, obj_i, local_dir_path, local_dir_uid) 131 def get_local_dir_url(self, base_url, dataset_uid, obj_i, local_dir_path, local_dir_uid): 132 # Logic for files and directories is the same for this function. --> 133 return self.get_local_file_url(base_url, dataset_uid, obj_i, local_dir_path, local_dir_uid) File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/wrappers.py:129, in AbstractWrapper.get_local_file_url(self, base_url, dataset_uid, obj_i, local_file_path, local_file_uid) 127 if not self.is_remote and self.base_dir is not None: 128 return self._get_url_simple(base_url, file_path_to_url_path(local_file_path, prepend_slash=False)) --> 129 return self._get_url(base_url, dataset_uid, obj_i, local_file_uid) File ~/miniforge3/envs/cellxgene-census-dev-new/lib/python3.11/site-packages/vitessce/wrappers.py:200, in AbstractWrapper._get_url(self, base_url, dataset_uid, obj_i, *args) 199 def _get_url(self, base_url, dataset_uid, obj_i, *args): --> 200 return base_url + self._get_route_str(dataset_uid, obj_i, *args) TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
This is using Vitessce 3.3.3
Hey, ran into what I think is a small bug in
to_dict:This is using Vitessce 3.3.3