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`.
76 lines
2.9 KiB
Python
76 lines
2.9 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 os
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import urllib.parse
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from cellxgene_gateway import env, flask_util
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from cellxgene_gateway.cache_key import CacheKey
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from cellxgene_gateway.dir_util import annotations_suffix, make_annotations, make_h5ad
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def render_annotations(item, item_source):
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url = flask_util.view_url(
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item_source.get_annotations_subpath(item), item_source.name
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)
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new_annotation = f"<a class='new' href='{url}'>new</a>"
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non_gene_set_files = []
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if item.annotations is not None:
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# Do not also display files to store gene_sets. These should be loaded
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# by clicking on the associated annotations file (i.e. without the
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# appended "_gene_sets")
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for a in item.annotations:
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if (len(a.name) < 10) or (a.name[-10:] != "_gene_sets"):
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non_gene_set_files.append(a)
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annotations = (
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", ".join(
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[
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f"<a href='{CacheKey(item, item_source, a).view_url}/'>{a.name}</a>"
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for a in non_gene_set_files
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]
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)
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+ ", "
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if non_gene_set_files
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else ""
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)
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return " | annotations: " + annotations + new_annotation
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def render_item(item, item_source):
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item_string = f"<li> <a href='{ CacheKey(item, item_source).view_url }/'>{item.name}</a> {render_annotations(item, item_source)}</li>"
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return item_string
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def render_item_tree(item_tree, item_source):
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items = (
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"\n".join([render_item(i, item_source) for i in item_tree.items])
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if item_tree.items
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else ""
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)
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branches = (
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"\n".join([render_item_tree(b, item_source) for b in item_tree.branches])
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if item_tree.branches
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else ""
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)
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html = "<ul>" + items + branches + "</ul>"
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if item_tree.descriptor:
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descriptor = item_tree.descriptor.lstrip("/")
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url = f"/filecrawl/{descriptor}?source={item_source.name}"
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name = descriptor.rsplit("/", 1)[-1]
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return f"<li><a href='{url}'>{name}</a>{html}</li>"
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else:
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return html
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def render_item_source(item_source, filter=None):
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item_tree = item_source.list_items(filter)
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filterpart = "" if filter is None else ":" + filter
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heading = f"<h6><a href='/filecrawl.html?source={urllib.parse.quote_plus(item_source.name)}'>{item_source.name}</a>{filterpart}</h6>"
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return heading + render_item_tree(item_tree, item_source)
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