Merge pull request #20466 from pvanheus/add_auspicejson_datatype (f33eb423) · Commits · NDIP / Galaxy

lib/galaxy/config/sample/datatypes_conf.xml.sample

+2 −0

Original line number	Diff line number	Diff line
		@@ -148,6 +148,7 @@
		<datatype extension="vitessce.json" type="galaxy.datatypes.text:VitessceJson" mimetype="application/json" display_in_upload="True">
		<visualization plugin="vitessce" />
		</datatype>
		<datatype extension="auspice.json" type="galaxy.datatypes.text:AuspiceJson" mimetype="application/json" display_in_upload="True" />
		<datatype extension="data_manager_json" type="galaxy.datatypes.text:DataManagerJson" mimetype="application/json" subclass="true" display_in_upload="false"/>
		<datatype extension="dbn" type="galaxy.datatypes.sequence:DotBracket" display_in_upload="true" description="Dot-Bracket format is a text-based format for storing both an RNA sequence and its corresponding 2D structure." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Dbn"/>
		<datatype extension="fai" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true" description="A Fasta Index File is a text file consisting of lines each with five TAB-delimited columns : Name, Length, offset, linebases, Linewidth" description_url="http://www.htslib.org/doc/faidx.html"/>
		@@ -1387,6 +1388,7 @@
		<sniffer type="galaxy.datatypes.text:CytoscapeJson"/>
		<sniffer type="galaxy.datatypes.text:GeoJson"/>
		<sniffer type="galaxy.datatypes.text:VitessceJson"/>
		<snipper type="galaxy.datatypes.text:AuspiceJson"/>
		<sniffer type="galaxy.datatypes.text:PithyaResult"/>
		<sniffer type="galaxy.datatypes.text:BCSLts"/>
		<sniffer type="galaxy.datatypes.text:Json"/>

lib/galaxy/datatypes/test/1.auspicejson

0 → 100644

+14 −0

Original line number	Diff line number	Diff line
		{
		"version": "v2",
		"meta": {
		"title": "Minimal AuspiceJSON",
		"updated": "2025-02-05",
		"panels": ["tree"]
		},
		"tree": {
		"name": "1",
		"node_attrs": {
		"div": 1
		}
		}
		}

lib/galaxy/datatypes/text.py

+51 −0

Original line number	Diff line number	Diff line
		@@ -695,6 +695,57 @@ class VitessceJson(Json):
		return False


		@build_sniff_from_prefix
		class AuspiceJson(Json):
		"""
		Auspice is a visualization tool for phylogenetic trees and associated data.
		It uses JSON format to represent the tree structure and metadata.
		"""

		file_ext = "auspice.json"

		def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
		super().set_peek(dataset)
		if not dataset.dataset.purged:
		dataset.blurb = "AuspiceJSON"

		def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
		"""
		Determines whether the file is in Auspice v2 JSON by looking for keys
		like "version", "meta" and "updated" that are both required by the
		https://docs.nextstrain.org/projects/auspice/en/stable/releases/v2.html format
		and also will be in the first part of the file

		>>> from galaxy.datatypes.sniff import get_test_fname
		>>> fname = get_test_fname( '1.json' )
		>>> AuspiceJson().sniff( fname )
		False
		>>> fname = get_test_fname( '1.auspicejson' )
		>>> AuspiceJson().sniff( fname )
		True
		"""
		is_auspicejson = False
		if self._looks_like_json(file_prefix):
		is_auspicejson = self._looks_like_is_auspicejson(file_prefix)
		return is_auspicejson

		def _looks_like_is_auspicejson(self, file_prefix: FilePrefix, load_size: int = 20000) -> bool:
		"""
		Expects JSON to start with { and 'meta', 'tree', 'updated' and 'nodes' to be present as keys in the JSON structure.
		"""
		try:
		with open(file_prefix.filename) as fh:
		segment_str = fh.read(load_size)

		if segment_str.startswith("{") and all(
		x in segment_str for x in ["version", "meta", "updated", "panels"]
		):
		return True
		except Exception:
		pass
		return False


		@build_sniff_from_prefix
		class Obo(Text):
		"""