Skip to content

Only render paths whose taxon matches the map being built. #103

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dbrnz merged 1 commit into from
Nov 1, 2024
Merged

Only render paths whose taxon matches the map being built. #103

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ Command line help

usage: mapmaker [-h] [-v]
[--log LOG_FILE] [--show-deprecated] [--silent] [--verbose]
[--clean-connectivity] [--background-tiles] [--disconnected-paths]
[--all-path-taxons] [--background-tiles] [--clean-connectivity] [--disconnected-paths]
[--force] [--id ID] [--ignore-git] [--ignore-sckan] [--invalid-neurons]
[--no-path-layout] [--publish SPARC_DATASET] [--sckan-version {production,staging}]
[--authoring] [--debug]
Expand All @@ -130,9 +130,10 @@ Command line help
--verbose Show progress bars

Map generation:
--clean-connectivity Refresh local connectivity knowledge from SciCrunch
--all-path-taxons Include paths whose taxons don't match the map's taxon
--background-tiles Generate image tiles of map's layers (may take a
while...)
--clean-connectivity Refresh local connectivity knowledge from SciCrunch
--disconnected-paths Include paths that are disconnected in the map
--force Generate the map even if it already exists
--id ID Set explicit ID for flatmap, overriding manifest
Expand Down
6 changes: 4 additions & 2 deletions mapmaker/__main__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,10 +43,12 @@ def arg_parser():
help="Show progress bars")

generation_options = parser.add_argument_group('Map generation')
generation_options.add_argument('--clean-connectivity', dest='cleanConnectivity', action='store_true',
help='Refresh local connectivity knowledge from SciCrunch')
generation_options.add_argument('--all-path-taxons', dest='allPathTaxons', action='store_true',
help="Include paths whose taxons don't match the map's taxon")
generation_options.add_argument('--background-tiles', dest='backgroundTiles', action='store_true',
help="Generate image tiles of map's layers (may take a while...)")
generation_options.add_argument('--clean-connectivity', dest='cleanConnectivity', action='store_true',
help='Refresh local connectivity knowledge from SciCrunch')
generation_options.add_argument('--disconnected-paths', dest='disconnectedPaths', action='store_true',
help="Include paths that are disconnected in the map")
generation_options.add_argument('--force', action='store_true',
Expand Down
11 changes: 10 additions & 1 deletion mapmaker/properties/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,10 @@

#===============================================================================

MAMMALIAN_TAXON = 'NCBITaxon:40674'

#===============================================================================

class PropertiesStore(object):
def __init__(self, flatmap: "FlatMap", manifest: "Manifest"):
self.__flatmap = flatmap
Expand Down Expand Up @@ -94,7 +98,12 @@ def __init__(self, flatmap: "FlatMap", manifest: "Manifest"):
if (path_knowledge.get('pathDisconnected', False) and not settings.get('disconnectedPaths', False)):
continue
phenotype_sex = path_knowledge.get('biologicalSex')
if manifest.biological_sex is None or phenotype_sex is None or (manifest.biological_sex == phenotype_sex):
path_taxons = path_knowledge.get('taxons')
if ((manifest.biological_sex is None or phenotype_sex is None
or manifest.biological_sex == phenotype_sex)
and (settings.get('allPathTaxons', False)
or manifest.models is None or path_taxons is None
or manifest.models in path_taxons or MAMMALIAN_TAXON in path_taxons)):
self.__pathways.add_connectivity_path(connectivity_path,
self, path_filter=path_filter, traced_paths=traced_paths)

Expand Down