Merge pull request #17517 from astrovsky01/add_npy

add npy datatype

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

@@ -220,6 +220,7 @@
     <datatype extension="ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
     <datatype extension="hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
     <datatype extension="prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
+    <datatype extension="npy" type="galaxy.datatypes.binary:Numpy" description="Standard format for saving numpy arrays" display_in_upload="true" description_url="https://numpy.org/devdocs/reference/generated/numpy.lib.format.html"/>
 
     <!-- ISA data types -->
     <datatype extension="isa-tab" type="galaxy.datatypes.isa:IsaTab" mimetype="application/isa-tools" display_in_upload="true" description="ISA-Tab data type." description_url="https://isa-tools.org"/>
@@ -1075,6 +1076,7 @@
     <sniffer type="galaxy.datatypes.binary:Edr"/>
     <sniffer type="galaxy.datatypes.binary:Vel"/>
     <sniffer type="galaxy.datatypes.binary:Xlsx"/>
+    <sniffer type="galaxy.datatypes.binary:Numpy"/>    
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Metadata"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Artifact"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Visualization"/>

lib/galaxy/datatypes/binary.py

@@ -4538,3 +4538,58 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
             return dataset.peek
         except Exception:
             return f"Binary FITS file size ({nice_size(dataset.get_size())})"
+
+
+@build_sniff_from_prefix
+class Numpy(Binary):
+    """
+    Class defining a numpy data file
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.npy')
+    >>> Numpy().sniff(fname)
+    True
+    """
+
+    file_ext = "npy"
+
+    MetadataElement(
+        name="version_str",
+        default="",
+        param=MetadataParameter,
+        desc="Version string for the numpy file format",
+        readonly=True,
+        visible=True,
+        no_value=0,
+        optional=True,
+    )
+
+    def _numpy_version_string(self, filename):
+        magic_string = open(filename, "rb").read(8)
+        version_str = f"{magic_string[6]}.{magic_string[7]}"
+        return version_str
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        try:
+            dataset.metadata.version_str = self._numpy_version_string(dataset.get_file_name())
+        except Exception as e:
+            log.warning("%s, set_meta Exception: %s", self, e)
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        # The first 6 bytes of any numpy file is '\x93NUMPY', with following bytes for version
+        # number of file formats, and info about header data. The rest of the file contains binary data.
+        return file_prefix.startswith_bytes(b"\x93NUMPY")
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.peek = f"Binary numpy file version {dataset.metadata.version_str}"
+            dataset.blurb = nice_size(dataset.get_size())
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def display_peek(self, dataset: DatasetProtocol) -> str:
+        try:
+            return dataset.peek
+        except Exception:
+            return "Binary numpy file (%s)" % (nice_size(dataset.get_size()))