mirror of
https://github.com/Novartis/cellxgene-gateway.git
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george-hall-ucl
81c8ce4219
This adds the flag `GATEWAY_ENABLE_GENE_SETS` to enable support for gene sets. To simplify implementation, activating this flag also activates `GATEWAY_ENABLE_ANNOTATIONS`. The gene sets are saved in a file that has the same name as the annotations `csv` but with `_gene_sets` appended to the file name (before the extension). This file is hidden in filecrawler, and the gene sets are loaded when the associated annotations file is loaded. If the annotations file is missing, then an Exception is raised. I have updated one unit test to make it expect `--disable-gene-sets-save` in the default case (i.e. if `GATEWAY_ENABLE_ANNOTATIONS = 0`). All units tests pass. I have updated the README to document `GATEWAY_ENABLE_GENE_SETS`.
107 lines
3.9 KiB
Python
107 lines
3.9 KiB
Python
# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
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# under the Apache License, Version 2.0 (the "License"); you may not use
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# this file except in compliance with the License. You may obtain a copy
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# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
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# required by applicable law or agreed to in writing, software distributed
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# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
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# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
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# the specific language governing permissions and limitations under the License.
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import logging
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import subprocess
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from flask_api import status
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from cellxgene_gateway.cache_entry import CacheEntryStatus
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from cellxgene_gateway.dir_util import make_annotations
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from cellxgene_gateway.env import (
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cellxgene_args,
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enable_annotations,
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enable_backed_mode,
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enable_gene_sets,
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)
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from cellxgene_gateway.process_exception import ProcessException
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logger = logging.getLogger(__name__)
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class SubprocessBackend:
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def __init__(self):
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pass
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def create_cmd(self, cellxgene_loc, file_path, port, scripts, annotation_file_path):
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if enable_annotations and not annotation_file_path is None:
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if annotation_file_path == "":
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extra_args = f" --annotations-dir {make_annotations(file_path)}"
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else:
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extra_args = f" --annotations-file {annotation_file_path}"
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else:
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extra_args = " --disable-annotations"
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if enable_gene_sets and not annotation_file_path is None:
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if annotation_file_path == "":
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raise Exception(
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"GATEWAY_ENABLE_GENE_SETS is true but --annotation_file_path not set"
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)
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else:
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gene_sets_file_path = annotation_file_path[:-4] + "_gene_sets.csv"
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extra_args += f" --gene-sets-file {gene_sets_file_path}"
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else:
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extra_args += " --disable-gene-sets-save"
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if enable_backed_mode:
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extra_args += " --backed"
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if not cellxgene_args is None:
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extra_args += f" {cellxgene_args}"
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cmd = (
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f"yes | {cellxgene_loc} launch {file_path}"
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+ f" --port {port}"
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+ " --host 127.0.0.1"
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+ extra_args
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)
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for s in scripts:
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cmd += f" --scripts {s}"
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return cmd
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def launch(self, cellxgene_loc, scripts, cache_entry):
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cmd = self.create_cmd(
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cellxgene_loc,
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cache_entry.key.file_path,
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cache_entry.port,
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scripts,
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cache_entry.key.annotation_file_path,
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)
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logger.info(f"launching {cmd}")
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process = subprocess.Popen(
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[cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
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)
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while True:
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output = process.stdout.readline().decode()
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if output == "[cellxgene] Type CTRL-C at any time to exit.\n":
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break
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elif output == "":
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stderr = process.stderr.read().decode()
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if (
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"Error while loading file" in stderr
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or "Could not open file" in stderr
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):
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message = "File was invalid."
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http_status = status.HTTP_400_BAD_REQUEST
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else:
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message = "Cellxgene failed to launch dataset."
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http_status = status.HTTP_500_INTERNAL_SERVER_ERROR
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cache_entry.status = CacheEntryStatus.error
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cache_entry.set_error(message, stderr, http_status)
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raise ProcessException.from_cache_entry(cache_entry)
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else:
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cache_entry.append_output(output)
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cache_entry.set_loaded(process.pid)
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for output in process.communicate():
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logger.debug(f"cellxgene:{output}")
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logger.info(f"exiting {cmd}")
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