Merge pull request #17482 from brsynth/feature_datatypes_sbol

Feature SBOL datatypes

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

@@ -573,6 +573,7 @@
     <datatype extension="ttl" type="galaxy.datatypes.triples:Turtle" display_in_upload="true"/>
     <datatype extension="rdf" type="galaxy.datatypes.triples:Rdf" display_in_upload="true"/>
     <datatype extension="jsonld" type="galaxy.datatypes.triples:Jsonld" display_in_upload="true"/>
+    <datatype extension="sbol" type="galaxy.datatypes.triples:Sbol" description="The SBOL (Synthetic Biology Open Language) standard was developed by the synthetic biology community to create a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs." description_url="https://sbolstandard.org" display_in_upload="true"/>
     <!-- Excel datatypes -->
     <datatype extension="excel.xls" type="galaxy.datatypes.binary:ExcelXls" display_in_upload="true"/>
     <datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true"/>
@@ -1130,6 +1131,7 @@
     <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
     <sniffer type="galaxy.datatypes.proteomics:PEFF"/>
     <sniffer type="galaxy.datatypes.molecules:CML"/>
+    <sniffer type="galaxy.datatypes.triples:Sbol"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
     <sniffer type="galaxy.datatypes.triples:HDT"/>
     <sniffer type="galaxy.datatypes.triples:Turtle"/>

lib/galaxy/datatypes/triples.py

@@ -5,6 +5,7 @@ Triple format classes
 import logging
 import re
 
+from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.protocols import DatasetProtocol
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
@@ -21,6 +22,7 @@ log = logging.getLogger(__name__)
 
 TURTLE_PREFIX_PATTERN = re.compile(r"@prefix\s+[^:]*:\s+<[^>]*>\s\.")
 TURTLE_BASE_PATTERN = re.compile(r"@base\s+<[^>]*>\s\.")
+SBOL_PATTERN = re.compile(r"http[s]?://[w\.]*sbol[s]?.org/v(\d{1})#")
 
 
 class Triples(data.Data):
@@ -202,3 +204,38 @@ class HDT(binary.Binary, Triples):
         else:
             dataset.peek = "file does not exist"
             dataset.blurb = "file purged from disk"
+
+
+@build_sniff_from_prefix
+class Sbol(data.Text, Triples):
+    """
+    The SBOL data format (https://sbolstandard.org).
+    """
+
+    MetadataElement(name="version", default="", readonly=True, visible=True, optional=True)
+    edam_format = "format_3725"
+    file_ext = "sbol"
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        file_prefix = FilePrefix(filename=dataset.get_file_name())
+        match = file_prefix.search(SBOL_PATTERN)
+        if match and match.group(1):
+            dataset.metadata.version = match.group(1)
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        # http://sbols.org/v2#
+        if file_prefix.search(SBOL_PATTERN):
+            return True
+        return False
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.get_file_name())
+            msg = "SBOL data"
+            if dataset.metadata.version != "":
+                msg += " v" + dataset.metadata.version
+            dataset.blurb = msg
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"

test/unit/data/datatypes/test_sbol.py

@@ -0,0 +1,22 @@
+from galaxy.datatypes.triples import Sbol
+from .util import (
+    get_dataset,
+    get_input_files,
+)
+
+
+def test_sbol_sniff():
+    sbol_datatype = Sbol()
+    with get_input_files("sbol.v2.crispr_example.xml") as input_files:
+        assert sbol_datatype.sniff(input_files[0]) is True
+
+
+def test_sbol_set_meta():
+    sbol_datatype = Sbol()
+    with get_input_files("sbol.v2.crispr_example.xml") as input_files, get_dataset(input_files[0]) as dataset:
+        sbol_datatype.set_meta(dataset)
+        assert dataset.metadata.version == "2"
+
+    with get_input_files("sbol.v3.circuit.nt") as input_files, get_dataset(input_files[0]) as dataset:
+        sbol_datatype.set_meta(dataset)
+        assert dataset.metadata.version == "3"