mirror of
https://github.com/chanzuckerberg/cellxgene.git
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prepare - work around anndata bug (#1260)
* work around anndata bug 344 * fix accidental cut and paste error * Use modified make_index_unique function Temporarily copy code from https://github.com/theislab/anndata/pull/345 until the issue is resolved and released. * Add notes and test for make_index_unique * Lint fix * Format python Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
This commit is contained in:
Bruce Martin
co-authored by
Matt Weiden
Matt Weiden
parent
db7a485796
commit
d99b84ba09
+5
-10
@@ -138,7 +138,7 @@ def dataset_args(func):
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"-t",
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default=DEFAULT_CONFIG.single_dataset__title,
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metavar="<text>",
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help="Title to display. If omitted will use file name."
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help="Title to display. If omitted will use file name.",
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)
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@click.option(
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"--about",
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@@ -300,7 +300,7 @@ def launch(
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experimental_annotations_ontology_obo,
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experimental_enable_reembedding,
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config_file,
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dump_default_config
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dump_default_config,
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):
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"""Launch the cellxgene data viewer.
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This web app lets you explore single-cell expression data.
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@@ -342,29 +342,22 @@ def launch(
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server__port=port,
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server__scripts=scripts,
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server__open_browser=open_browser,
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single_dataset__datapath=datapath,
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single_dataset__title=title,
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single_dataset__about=about,
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single_dataset__obs_names=obs_names,
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single_dataset__var_names=var_names,
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multi_dataset__dataroot=dataroot,
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user_annotations__enable=not disable_annotations,
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user_annotations__local_file_csv__file=annotations_file,
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user_annotations__local_file_csv__directory=annotations_dir,
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user_annotations__ontology__enable=experimental_annotations_ontology,
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user_annotations__ontology__obo_location=experimental_annotations_ontology_obo,
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presentation__max_categories=max_category_items,
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embeddings__names=embedding,
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embeddings__enable_reembedding=experimental_enable_reembedding,
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diffexp__enable=not disable_diffexp,
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diffexp__lfc_cutoff=diffexp_lfc_cutoff,
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adaptor__anndata_adaptor__backed=backed,
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)
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@@ -386,6 +379,7 @@ def launch(
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# create the server
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from server.app.app import Server
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server = Server(matrix_data_cache_manager, user_annotations, app_config)
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if not app_config.server__verbose:
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@@ -411,7 +405,8 @@ def launch(
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debug=app_config.server__debug,
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port=app_config.server__port,
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threaded=not app_config.server__debug,
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use_debugger=False)
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use_debugger=False,
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)
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except OSError as e:
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if e.errno == errno.EADDRINUSE:
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raise click.ClickException("Port is in use, please specify an open port using the --port flag.") from e
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+60
-10
@@ -1,6 +1,7 @@
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from os.path import expanduser, isdir, isfile, sep, splitext
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import click
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import pandas as pd
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from numpy import ndarray, unique
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from scipy.sparse.csc import csc_matrix
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@@ -23,12 +24,7 @@ from server.common.utils import sort_options
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show_default=True,
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)
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@click.option(
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"--recipe",
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"-r",
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default="none",
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type=click.Choice(["none", "seurat", "zheng17"]),
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help="Preprocessing to run.",
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show_default=True,
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"--recipe", "-r", default="none", type=click.Choice(["none", "seurat", "zheng17"]), show_default=True,
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)
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@click.option("--output", "-o", default="", help="Save a new file to filename.", metavar="<filename>")
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@click.option("--plotting", "-p", default=False, is_flag=True, help="Generate plots.", show_default=True)
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@@ -44,10 +40,16 @@ from server.common.utils import sort_options
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"(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details).",
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)
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@click.option(
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"--make-obs-names-unique", default=True, is_flag=True, help="Ensure obs index is unique.", show_default=True
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"--make-obs-names-unique/--no-make-obs-names-unique",
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default=True,
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help="Ensure obs index is unique.",
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show_default=True,
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)
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@click.option(
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"--make-var-names-unique", default=True, is_flag=True, help="Ensure var index is unique.", show_default=True
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"--make-var-names-unique/--no-make-var-names-unique",
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default=True,
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help="Ensure var index is unique.",
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show_default=True,
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)
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@click.help_option("--help", "-h", help="Show this message and exit.")
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def prepare(
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@@ -129,9 +131,9 @@ def prepare(
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raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
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adata.var_names = adata.var[set_var_names]
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if make_obs_names_unique:
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adata.obs_names_make_unique()
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adata.obs.index = make_index_unique(adata.obs.index)
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if make_var_names_unique:
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adata.var_names_make_unique()
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adata.var.index = make_index_unique(adata.var.index)
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if not adata._obs.index.is_unique:
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click.echo("Warning: obs index is not unique")
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if not adata._var.index.is_unique:
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@@ -221,3 +223,51 @@ def prepare(
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adata.write(output)
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click.echo("[cellxgene] Success!")
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# TODO (mweiden): remove this once this issue is resolved https://github.com/theislab/anndata/issues/344
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# Note: tentative solution here https://github.com/theislab/anndata/pull/345
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def make_index_unique(index: pd.Index, join: str = "-"):
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"""
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Makes the index unique by appending a number string to each duplicate index element: '1', '2', etc.
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If a tentative name created by the algorithm already exists in the index, it tries the next integer in the sequence.
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The first occurrence of a non-unique value is ignored.
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Parameters
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----------
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join
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The connecting string between name and integer.
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Examples
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--------
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>>> from anndata import AnnData
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>>> adata1 = AnnData(np.ones((3, 2)), dict(obs_names=['a', 'b', 'c']))
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>>> adata2 = AnnData(np.zeros((3, 2)), dict(obs_names=['d', 'b', 'b']))
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>>> adata = adata1.concatenate(adata2)
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>>> adata.obs_names
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Index(['a', 'b', 'c', 'd', 'b', 'b'], dtype='object')
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>>> adata.obs_names_make_unique()
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>>> adata.obs_names
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Index(['a', 'b', 'c', 'd', 'b-1', 'b-2'], dtype='object')
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"""
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if index.is_unique:
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return index
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from collections import defaultdict
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values = index.values
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values_set = set(values)
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indices_dup = index.duplicated(keep="first")
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values_dup = values[indices_dup]
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counter = defaultdict(lambda: 0)
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for i, v in enumerate(values_dup):
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while True:
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counter[v] += 1
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tentative_new_name = v + join + str(counter[v])
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if tentative_new_name not in values_set:
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values_set.add(tentative_new_name)
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values_dup[i] = tentative_new_name
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break
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values[indices_dup] = values_dup
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index = pd.Index(values)
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return index
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