Add new ODV datatype

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

@@ -463,6 +463,7 @@
     <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="netcdf" type="galaxy.datatypes.binary:NetCDF" mimetype="application/octet-stream" display_in_upload="true" description="Format used by netCDF software library for writing and reading chromatography-MS data files."/>
+    <datatype extension="odv" type="galaxy.datatypes.text:ODV" display_in_upload="true" description="Ocean Data View format file"/>
     <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>
     <datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/>
     <datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
@@ -1379,6 +1380,7 @@
     <sniffer type="galaxy.datatypes.text:PithyaResult"/>
     <sniffer type="galaxy.datatypes.text:BCSLts"/>
     <sniffer type="galaxy.datatypes.text:Json"/>
+    <sniffer type="galaxy.datatypes.text:ODV"/>
     <sniffer type="galaxy.datatypes.genetics:GenotypeMatrix"/>
     <sniffer type="galaxy.datatypes.genetics:DataIn"/>
     <sniffer type="galaxy.datatypes.genetics:MarkerMap"/>

lib/galaxy/datatypes/text.py

@@ -1532,3 +1532,55 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         False
         """
         return file_prefix.startswith("RBT_PARAMETER_FILE_V1.00")
+
+
+class ODV(Text):
+    file_ext = "odv"
+
+    MetadataElement(name="meta_var_count", default=0, desc="Number of Meta Variables", readonly=True)
+    MetadataElement(name="var_count", default=0, desc="Number of Variables", readonly=True)
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        """
+        Determines whether the file is has some required details in General section
+        """
+        header = file_prefix.contents_header.lower()
+        keywords = ["collectionformat", "odvcf"]
+        return all(keyword in header for keyword in keywords)
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd):
+        dataset.metadata.meta_var_count = 0
+        dataset.metadata.var_count = 0
+
+        section = None
+        try:
+            with open(dataset.get_file_name(), encoding="utf-8") as f:
+                for line in f:
+                    line = line.strip()
+
+                    if line.startswith("[") and line.endswith("]"):
+                        section = line[1:-1].strip()
+                        if section != "General":
+                            # Stop after [General] section
+                            break
+                        continue
+
+                    if section != "General" or not line or "=" not in line:
+                        continue
+
+                    key, value = map(str.strip, line.split("=", 1))
+                    if key == "NumberOfMetaVariables":
+                        dataset.metadata.meta_var_count = int(value)
+                    elif key == "NumberOfVariables":
+                        dataset.metadata.var_count = int(value)
+
+        except Exception:
+            log.exception("Error in set_meta")
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.get_file_name())
+            dataset.blurb = f"ODV Collection Format: {dataset.metadata.meta_var_count} meta variables, {dataset.metadata.var_count} variables"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disc"