diff --git a/lib/galaxy/datatypes/annotation.py b/lib/galaxy/datatypes/annotation.py index 9f8074a322f..8d2e70d87b3 100644 --- a/lib/galaxy/datatypes/annotation.py +++ b/lib/galaxy/datatypes/annotation.py @@ -17,7 +17,7 @@ class SnapHmm(Text): file_ext = "snaphmm" edam_data = "data_1364" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = "SNAP HMM model" @@ -46,7 +46,7 @@ class Augustus(CompressedArchive): edam_data = "data_0950" compressed = True - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Augustus model" dataset.blurb = nice_size(dataset.get_size()) diff --git a/lib/galaxy/datatypes/anvio.py b/lib/galaxy/datatypes/anvio.py index f88e9e0c788..9e0d9828b57 100644 --- a/lib/galaxy/datatypes/anvio.py +++ b/lib/galaxy/datatypes/anvio.py @@ -61,7 +61,7 @@ class AnvioComposite(Html): """Returns the mime type of the datatype""" return 'text/html' - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = 'Anvio database (multiple files)' diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index a958b86208c..52f5c1caa4b 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -82,7 +82,7 @@ class Ab1(Binary): edam_format = "format_3000" edam_data = "data_0924" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary ab1 sequence file" dataset.blurb = nice_size(dataset.get_size()) @@ -167,7 +167,7 @@ class Cel(Binary): elif header_bytes.decode("utf8", errors="ignore").startswith('[CEL]'): dataset.metadata.version = "3" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.blurb = f"Cel version: {dataset.metadata.version}" dataset.peek = get_file_peek(dataset.file_name) @@ -196,7 +196,7 @@ class CompressedArchive(Binary): file_ext = "compressed_archive" compressed = True - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Compressed binary file" dataset.blurb = nice_size(dataset.get_size()) @@ -251,7 +251,7 @@ class Bref3(Binary): def sniff_prefix(self, sniff_prefix): return sniff_prefix.startswith_bytes(self._magic) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary bref3 file" dataset.blurb = nice_size(dataset.get_size()) @@ -308,7 +308,7 @@ class CompressedZipArchive(CompressedArchive): """ file_ext = "zip" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Compressed zip file" dataset.blurb = nice_size(dataset.get_size()) @@ -410,7 +410,7 @@ class BamNative(CompressedArchive, _BamOrSam): except Exception: return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary bam alignments file" dataset.blurb = nice_size(dataset.get_size()) @@ -778,7 +778,7 @@ class CRAM(Binary): log.warning('%s, set_index_file Exception: %s', self, exc) return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = 'CRAM binary alignment file' dataset.blurb = 'binary data' @@ -897,7 +897,7 @@ class H5(Binary): except Exception: return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary HDF5 file" dataset.blurb = nice_size(dataset.get_size()) @@ -959,7 +959,7 @@ class Loom(H5): return True return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary Loom file" dataset.blurb = nice_size(dataset.get_size()) @@ -1188,7 +1188,7 @@ class Anndata(H5): if dataset.metadata.shape is None: dataset.metadata.shape = (int(dataset.metadata.obs_size), int(dataset.metadata.var_size)) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: tmp = dataset.metadata @@ -1236,7 +1236,7 @@ class GmxBinary(Binary): # The first 4 bytes of any GROMACS binary file containing the magic number return sniff_prefix.magic_header('>1i') == self.magic_number - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = f"Binary GROMACS {self.file_ext} file" dataset.blurb = nice_size(dataset.get_size()) @@ -1375,7 +1375,7 @@ class Biom2(H5): except Exception as e: log.warning('%s, set_meta Exception: %s', self, util.unicodify(e)) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: lines = ['Biom2 (HDF5) file'] try: @@ -1435,7 +1435,7 @@ class Cool(H5): return True return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Cool (HDF5) file for storing genomic interaction data." dataset.blurb = nice_size(dataset.get_size()) @@ -1495,7 +1495,7 @@ class MCool(H5): return True return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Multi-resolution Cool (HDF5) file for storing genomic interaction data." dataset.blurb = nice_size(dataset.get_size()) @@ -1568,7 +1568,7 @@ class H5MLM(H5): log.warning('%s, get model configuration Except: %s', self, e) return "" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: repr_ = self.get_repr(dataset.file_name) dataset.peek = repr_[:self.max_peek_size] @@ -1656,7 +1656,7 @@ class HexrdMaterials(H5): except Exception as e: log.warning('%s, set_meta Exception: %s', self, e) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: lines = ['Material SpaceGroup Lattice'] if dataset.metadata.materials: @@ -1678,7 +1678,7 @@ class Scf(Binary): edam_data = "data_0924" file_ext = "scf" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary scf sequence file" dataset.blurb = nice_size(dataset.get_size()) @@ -1705,7 +1705,7 @@ class Sff(Binary): # about the format, see http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format return sniff_prefix.startswith_bytes(b'.sff') - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary sff file" dataset.blurb = nice_size(dataset.get_size()) @@ -1741,7 +1741,7 @@ class BigWig(Binary): def sniff_prefix(self, sniff_prefix): return sniff_prefix.magic_header("I") == self._magic - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = f"Binary UCSC {self._name} file" dataset.blurb = nice_size(dataset.get_size()) @@ -1780,7 +1780,7 @@ class TwoBit(Binary): magic = sniff_prefix.magic_header(">L") return magic == TWOBIT_MAGIC_NUMBER or magic == TWOBIT_MAGIC_NUMBER_SWAP - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary TwoBit format nucleotide file" dataset.blurb = nice_size(dataset.get_size()) @@ -1863,7 +1863,7 @@ class SQlite(Binary): log.warning('%s, sniff Exception: %s', self, e) return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "SQLite Database" lines = ['SQLite Database'] @@ -1929,7 +1929,7 @@ class GeminiSQLite(SQlite): return self.sniff_table_names(filename, table_names) return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Gemini SQLite Database, version %s" % (dataset.metadata.gemini_version or 'unknown') dataset.blurb = nice_size(dataset.get_size()) @@ -2005,7 +2005,7 @@ class CuffDiffSQlite(SQlite): return self.sniff_table_names(filename, table_names) return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "CuffDiff SQLite Database, version %s" % (dataset.metadata.cuffdiff_version or 'unknown') dataset.blurb = nice_size(dataset.get_size()) @@ -2250,7 +2250,7 @@ class IdpDB(SQlite): return self.sniff_table_names(filename, table_names) return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "IDPickerDB SQLite file" dataset.blurb = nice_size(dataset.get_size()) @@ -2326,7 +2326,7 @@ class NcbiTaxonomySQlite(SQlite): return self.sniff_table_names(filename, table_names) return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "NCBI Taxonomy SQLite Database, version {} ({} taxons)".format( getattr(dataset.metadata, "ncbitaxonomy_schema_version", "unknown"), @@ -2377,7 +2377,7 @@ class ExcelXls(Binary): """Returns the mime type of the datatype""" return 'application/vnd.ms-excel' - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Microsoft Excel XLS file" dataset.blurb = data.nice_size(dataset.get_size()) @@ -2403,7 +2403,7 @@ class Sra(Binary): """ return sniff_prefix.startswith_bytes(b'NCBI.sra') - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = 'Binary sra file' dataset.blurb = nice_size(dataset.get_size()) @@ -2747,7 +2747,7 @@ class PostgresqlArchive(CompressedArchive): return 'postgresql/db/PG_VERSION' in temptar.getnames() return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = f"PostgreSQL Archive ({nice_size(dataset.get_size())})" dataset.blurb = "PostgreSQL version %s" % (dataset.metadata.version or 'unknown') @@ -2801,7 +2801,7 @@ class Fast5Archive(CompressedArchive): log.warning('%s, sniff Exception: %s', self, e) return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = f"FAST5 Archive ({nice_size(dataset.get_size())})" dataset.blurb = "%s sequences" % (dataset.metadata.fast5_count or 'unknown') @@ -2895,7 +2895,7 @@ class SearchGuiArchive(CompressedArchive): log.warning('%s, sniff Exception: %s', self, e) return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "SearchGUI Archive, version %s" % (dataset.metadata.searchgui_version or 'unknown') dataset.blurb = nice_size(dataset.get_size()) @@ -2917,7 +2917,7 @@ class NetCDF(Binary): edam_format = "format_3650" edam_data = "data_0943" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary netCDF file" dataset.blurb = nice_size(dataset.get_size()) @@ -2972,7 +2972,7 @@ class Dcd(Binary): except Exception: return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary CHARMM/NAMD dcd file" dataset.blurb = nice_size(dataset.get_size()) @@ -3023,7 +3023,7 @@ class Vel(Binary): except Exception: return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary CHARMM velocity file" dataset.blurb = nice_size(dataset.get_size()) @@ -3113,7 +3113,7 @@ class ICM(Binary): file_ext = "icm" edam_data = "data_0950" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary ICM (interpolated context model) file" dataset.blurb = nice_size(dataset.get_size()) @@ -3178,7 +3178,7 @@ class BafTar(CompressedArchive): def get_type(self): return "Bruker BAF directory archive" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = self.get_type() dataset.blurb = nice_size(dataset.get_size()) @@ -3280,7 +3280,7 @@ class Pretext(Binary): # file contains binary data. return sniff_prefix.startswith_bytes(b'pstm') - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary pretext file" dataset.blurb = nice_size(dataset.get_size()) @@ -3322,7 +3322,7 @@ class JP2(Binary): except Exception: return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary JPEG 2000 file" dataset.blurb = nice_size(dataset.get_size()) @@ -3377,7 +3377,7 @@ class Npz(CompressedArchive): except Exception as e: log.warning('%s, set_meta Exception: %s', self, e) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = f"Binary Numpy npz {dataset.metadata.nfiles} files ({nice_size(dataset.get_size())})" dataset.blurb = nice_size(dataset.get_size()) @@ -3438,7 +3438,7 @@ class HexrdImagesNpz(Npz): except Exception as e: log.warning('%s, set_meta Exception: %s', self, e) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: lines = [f"Binary Hexrd Image npz {dataset.metadata.nfiles} files ({nice_size(dataset.get_size())})", f"Panel: {dataset.metadata.panel_id} Frames: {dataset.metadata.nframes} Shape: {dataset.metadata.shape}"] @@ -3495,7 +3495,7 @@ class HexrdEtaOmeNpz(Npz): except Exception as e: log.warning('%s, set_meta Exception: %s', self, e) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: lines = [f"Binary Hexrd Eta-Ome npz {dataset.metadata.nfiles} files ({nice_size(dataset.get_size())})", f"Eta-Ome HKLs: {dataset.metadata.HKLs} Frames: {dataset.metadata.nframes}"] diff --git a/lib/galaxy/datatypes/blast.py b/lib/galaxy/datatypes/blast.py index 09f2f4f0918..7d03e000532 100644 --- a/lib/galaxy/datatypes/blast.py +++ b/lib/galaxy/datatypes/blast.py @@ -56,7 +56,7 @@ class BlastXml(GenericXml): edam_format = "format_3331" edam_data = "data_0857" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) @@ -176,7 +176,7 @@ class BlastXml(GenericXml): class _BlastDb(Data): """Base class for BLAST database datatype.""" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text.""" if not dataset.dataset.purged: dataset.peek = "BLAST database (multiple files)" @@ -314,7 +314,7 @@ class LastDb(Data): file_ext = 'lastdb' composite_type = 'basic' - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text.""" if not dataset.dataset.purged: dataset.peek = "LAST database (multiple files)" diff --git a/lib/galaxy/datatypes/constructive_solid_geometry.py b/lib/galaxy/datatypes/constructive_solid_geometry.py index 4d963bfd063..a51898c8d22 100644 --- a/lib/galaxy/datatypes/constructive_solid_geometry.py +++ b/lib/galaxy/datatypes/constructive_solid_geometry.py @@ -107,7 +107,7 @@ class Ply: element_tuple = (items[1], int(items[2])) dataset.metadata.other_elements.append(element_tuple) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = f"Faces: {str(dataset.metadata.face)}, Vertices: {str(dataset.metadata.vertex)}" @@ -430,7 +430,7 @@ class Vtk: blurb += str(dataset.metadata.dataset_type) return blurb or 'VTK data' - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = self.get_blurb(dataset) diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py index a3a0364ddd8..f7bc205d945 100644 --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -259,12 +259,9 @@ class Data(metaclass=DataMeta): max_optional_metadata_filesize = property(get_max_optional_metadata_filesize, set_max_optional_metadata_filesize) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """ Set the peek and blurb text - - :param is_multi_byte: deprecated - :type is_multi_byte: bool """ if not dataset.dataset.purged: dataset.peek = '' @@ -893,7 +890,7 @@ class Text(Data): return None return data_lines - def set_peek(self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None, line_wrap=True, **kwd): + def set_peek(self, dataset, line_count=None, WIDTH=256, skipchars=None, line_wrap=True, **kwd): """ Set the peek. This method is used by various subclasses of Text. """ @@ -1090,13 +1087,10 @@ def get_test_fname(fname): return full_path -def get_file_peek(file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=None, line_wrap=True): +def get_file_peek(file_name, WIDTH=256, LINE_COUNT=5, skipchars=None, line_wrap=True): """ Returns the first LINE_COUNT lines wrapped to WIDTH. - :param is_multi_byte: deprecated - :type is_multi_byte: bool - >>> def assert_peek_is(file_name, expected, *args, **kwd): ... path = get_test_fname(file_name) ... peek = get_file_peek(path, *args, **kwd) diff --git a/lib/galaxy/datatypes/flow.py b/lib/galaxy/datatypes/flow.py index abe1a9b7b18..48a7a4a2495 100644 --- a/lib/galaxy/datatypes/flow.py +++ b/lib/galaxy/datatypes/flow.py @@ -19,7 +19,7 @@ class FCS(Binary): """Class describing an FCS binary file""" file_ext = "fcs" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Binary FCS file" dataset.blurb = data.nice_size(dataset.get_size()) diff --git a/lib/galaxy/datatypes/gis.py b/lib/galaxy/datatypes/gis.py index adb2d167873..02a5f8931dc 100644 --- a/lib/galaxy/datatypes/gis.py +++ b/lib/galaxy/datatypes/gis.py @@ -46,7 +46,7 @@ class Shapefile(Binary): rval.append('\n') return "\n".join(rval) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text.""" if not dataset.dataset.purged: dataset.peek = "Shapefile data" diff --git a/lib/galaxy/datatypes/graph.py b/lib/galaxy/datatypes/graph.py index c36deb26885..94f0156b1f4 100644 --- a/lib/galaxy/datatypes/graph.py +++ b/lib/galaxy/datatypes/graph.py @@ -22,7 +22,7 @@ class Xgmml(xml.GenericXml): """ file_ext = "xgmml" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """ Set the peek and blurb text """ @@ -68,7 +68,7 @@ class Sif(tabular.Tabular): """ file_ext = "sif" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """ Set the peek and blurb text """ diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py index 3388b60b4c8..a3d24b45346 100644 --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -50,7 +50,7 @@ class Image(data.Data): super().__init__(**kwd) self.image_formats = [self.file_ext.upper()] - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = f'Image in {dataset.extension} format' dataset.blurb = nice_size(dataset.get_size()) @@ -354,7 +354,7 @@ class Gmaj(data.Data): file_ext = "gmaj.zip" copy_safe_peek = False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: if hasattr(dataset, 'history_id'): params = { @@ -540,7 +540,7 @@ class Star(data.Text): https://relion.readthedocs.io/en/latest/Reference/Conventions.html""" file_ext = "star" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -596,7 +596,7 @@ class Laj(data.Text): file_ext = "laj" copy_safe_peek = False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: if hasattr(dataset, 'history_id'): params = { diff --git a/lib/galaxy/datatypes/isa.py b/lib/galaxy/datatypes/isa.py index ee158cc5dc7..66a3338e892 100644 --- a/lib/galaxy/datatypes/isa.py +++ b/lib/galaxy/datatypes/isa.py @@ -141,7 +141,7 @@ class _Isa(data.Data): # Set peek {{{2 ################################################################ - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text. Get first lines of the main file and set it as the peek.""" main_file = self._get_main_file(dataset) diff --git a/lib/galaxy/datatypes/microarrays.py b/lib/galaxy/datatypes/microarrays.py index e690c843371..fc83c051f2e 100644 --- a/lib/galaxy/datatypes/microarrays.py +++ b/lib/galaxy/datatypes/microarrays.py @@ -36,7 +36,7 @@ class GenericMicroarrayFile(data.Text): readonly=True, visible=True, optional=True, no_value=0) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: if dataset.metadata.block_count == 1: dataset.blurb = f"{dataset.metadata.file_type} {dataset.metadata.version_number}: Format {dataset.metadata.file_format}, 1 block, {dataset.metadata.number_of_optional_header_records} headers and {dataset.metadata.number_of_data_columns} columns" diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py index ea44f51daa5..5c95158a9e2 100644 --- a/lib/galaxy/datatypes/molecules.py +++ b/lib/galaxy/datatypes/molecules.py @@ -48,7 +48,7 @@ class GenericMolFile(Text): """ MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: if (dataset.metadata.number_of_molecules == 1): dataset.blurb = "1 molecule" @@ -394,7 +394,7 @@ class OBFS(Binary): self.add_composite_file('molecule.cml', optional=True, is_binary=False, description='Molecule File') - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text.""" if not dataset.dataset.purged: dataset.peek = "OpenBabel Fastsearch Index" @@ -441,7 +441,7 @@ class PHAR(GenericMolFile): """ file_ext = "phar" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = "pharmacophore" @@ -509,7 +509,7 @@ class PDB(GenericMolFile): log.error('Error finding chain_ids: %s', unicodify(e)) raise - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: atom_numbers = count_special_lines("^ATOM", dataset.file_name) hetatm_numbers = count_special_lines("^HETATM", dataset.file_name) @@ -561,7 +561,7 @@ class PDBQT(GenericMolFile): else: return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: root_numbers = count_special_lines("^ROOT", dataset.file_name) branch_numbers = count_special_lines("^BRANCH", dataset.file_name) @@ -662,7 +662,7 @@ class PQR(GenericMolFile): log.error('Error finding chain_ids: %s', unicodify(e)) raise - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: atom_numbers = count_special_lines("^ATOM", dataset.file_name) hetatm_numbers = count_special_lines("^HETATM", dataset.file_name) @@ -677,7 +677,7 @@ class PQR(GenericMolFile): class grd(Text): file_ext = "grd" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = "grids for docking" @@ -689,7 +689,7 @@ class grd(Text): class grdtgz(Binary): file_ext = "grd.tgz" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = 'binary data' dataset.blurb = "compressed grids for docking" @@ -712,7 +712,7 @@ class InChI(Tabular): """ dataset.metadata.number_of_molecules = self.count_data_lines(dataset) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: if (dataset.metadata.number_of_molecules == 1): dataset.blurb = "1 molecule" @@ -762,7 +762,7 @@ class SMILES(Tabular): """ dataset.metadata.number_of_molecules = self.count_data_lines(dataset) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: if dataset.metadata.number_of_molecules == 1: dataset.blurb = "1 molecule" @@ -789,7 +789,7 @@ class CML(GenericXml): """ dataset.metadata.number_of_molecules = count_special_lines(r'^\s* 0: dataset.metadata.number_comp = max(significant_components) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) if (dataset.metadata.number_comp == 1): @@ -165,7 +165,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptortho" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesOrtho, self).set_peek(dataset) # dataset.blurb = "Proteins orthogroup fasta files: %d items" % dataset.metadata.num_files # @@ -177,7 +177,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptorthocs" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesOrthoCodingSequence, self).set_peek(dataset) # dataset.blurb = "Protein and coding sequences orthogroup fasta files: %d items" % dataset.metadata.num_files # @@ -188,7 +188,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "pttgf" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesTargetedGeneFamilies, self).set_peek(dataset) # dataset.blurb = "Targeted gene families" # @@ -200,7 +200,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "pttree" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesPhylogeneticTree, self).set_peek(dataset) # dataset.blurb = "Phylogenetic trees: %d items" % dataset.metadata.num_files # @@ -211,7 +211,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptphylip" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesPhylip, self).set_peek(dataset) # dataset.blurb = "Orthogroup phylip multiple sequence alignments: %d items" % dataset.metadata.num_files # @@ -222,7 +222,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptalign" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset) # dataset.blurb = "Proteins orthogroup alignments: %d items" % dataset.metadata.num_files # @@ -233,7 +233,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptalignca" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset: # super(PlantTribesMultipleSequenceAlignmentCodonAlignment, self).set_peek(dataset) # dataset.blurb = "Protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files # @@ -244,7 +244,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptaligntrimmed" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesMultipleSequenceAlignmentTrimmed, self).set_peek(dataset) # dataset.blurb = "Trimmed proteins orthogroup alignments: %d items" % dataset.metadata.num_files # @@ -255,7 +255,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptaligntrimmedca" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment, self).set_peek(dataset) # dataset.blurb = "Trimmed protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files # @@ -266,7 +266,7 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptalignfiltered" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesMultipleSequenceAlignmentFiltered, self).set_peek(dataset) # dataset.blurb = "Filtered proteins orthogroup alignments: %d items" % dataset.metadata.num_files # @@ -277,6 +277,6 @@ class PlantTribesKsComponents(Tabular): # """ # file_ext = "ptalignfilteredca" # -# def set_peek(self, dataset, is_multi_byte=False): +# def set_peek(self, dataset): # super(PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment, self).set_peek(dataset) # dataset.blurb = "Filtered protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py index a01a35ef662..93a1dfa2f02 100644 --- a/lib/galaxy/datatypes/proteomics.py +++ b/lib/galaxy/datatypes/proteomics.py @@ -83,7 +83,7 @@ class MzTab(Text): def __init__(self, **kwd): super().__init__(**kwd) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -133,7 +133,7 @@ class MzTab2(MzTab): def __init__(self, **kwd): super().__init__(**kwd) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -601,7 +601,7 @@ class ProteomicsXml(GenericXml): pattern = r'<(\w*:)?%s' % self.root return re.search(pattern, line) is not None - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -759,7 +759,7 @@ class Mgf(Text): edam_format = "format_3651" file_ext = "mgf" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -787,7 +787,7 @@ class MascotDat(Text): edam_format = "format_3713" file_ext = "mascotdat" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -829,7 +829,7 @@ class ThermoRAW(Binary): except Exception: return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Thermo Finnigan RAW file" dataset.blurb = nice_size(dataset.get_size()) @@ -869,7 +869,7 @@ class SPLibNoIndex(Text): """SPlib without index file """ file_ext = "splib_noindex" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -910,7 +910,7 @@ class SPLib(Msp): rval.append('') return "\n".join(rval) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index b134d36f294..6bea2db62fc 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -55,7 +55,7 @@ class SequenceSplitLocations(data.Text): """ file_ext = "fqtoc" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: try: parsed_data = json.load(open(dataset.file_name)) @@ -109,7 +109,7 @@ class Sequence(data.Text): dataset.metadata.data_lines = data_lines dataset.metadata.sequences = sequences - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) if dataset.metadata.sequences: @@ -611,7 +611,7 @@ class Fastg(Sequence): return return Sequence.set_meta(self, dataset, **kwd) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) if dataset.metadata.sequences: @@ -932,7 +932,7 @@ class Maf(Alignment): indexes.write(open(index_file.file_name, 'wb')) dataset.metadata.maf_index = index_file - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method dataset.peek = data.get_file_peek(dataset.file_name) @@ -1144,7 +1144,7 @@ class RNADotPlotMatrix(data.Data): edam_format = "format_3466" file_ext = "rna_eps" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = 'RNA Dot Plot format (Postscript derivative)' dataset.blurb = nice_size(dataset.get_size()) diff --git a/lib/galaxy/datatypes/spaln.py b/lib/galaxy/datatypes/spaln.py index e95b80e3dd6..19ad30c083d 100644 --- a/lib/galaxy/datatypes/spaln.py +++ b/lib/galaxy/datatypes/spaln.py @@ -94,7 +94,7 @@ class _SpalnDb(Data): f.write("\n".join(rval)) f.write("\n") - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text.""" if not dataset.dataset.purged: dataset.peek = "spaln database (multiple files)" diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 933a9511ef0..d7f6f070abe 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -56,7 +56,7 @@ class TabularData(data.Text): def set_meta(self, dataset, **kwd): raise NotImplementedError - def set_peek(self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None, line_wrap=False, **kwd): + def set_peek(self, dataset, line_count=None, WIDTH=256, skipchars=None, line_wrap=False, **kwd): super().set_peek(dataset, line_count=line_count, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap) if dataset.metadata.comment_lines: dataset.blurb = f"{dataset.blurb}, {util.commaify(str(dataset.metadata.comment_lines))} comments" diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py index 480e6748b61..2f20a120597 100644 --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -34,7 +34,7 @@ class Html(Text): edam_format = "format_2331" file_ext = "html" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "HTML file" dataset.blurb = nice_size(dataset.get_size()) @@ -70,7 +70,7 @@ class Json(Text): edam_format = "format_3464" file_ext = "json" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = "JavaScript Object Notation (JSON)" @@ -148,7 +148,7 @@ class ExpressionJson(Json): class Ipynb(Json): file_ext = "ipynb" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = "Jupyter Notebook" @@ -225,7 +225,7 @@ class Biom1(Json): MetadataElement(name="table_columns", default=[], desc="table_columns", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[]) MetadataElement(name="table_column_metadata_headers", default=[], desc="table_column_metadata_headers", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value=[]) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): super().set_peek(dataset) if not dataset.dataset.purged: dataset.blurb = "Biological Observation Matrix v1" @@ -321,7 +321,7 @@ class ImgtJson(Json): MetadataElement(name="taxon_names", default=[], desc="taxonID: names", readonly=True, visible=True, no_value=[]) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): super().set_peek(dataset) if not dataset.dataset.purged: dataset.blurb = "IMGT Library" @@ -386,7 +386,7 @@ class GeoJson(Json): """ file_ext = "geojson" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): super().set_peek(dataset) if not dataset.dataset.purged: dataset.blurb = "GeoJSON" @@ -435,7 +435,7 @@ class Obo(Text): edam_format = "format_2549" file_ext = "obo" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = "Open Biomedical Ontology (OBO)" @@ -474,7 +474,7 @@ class Arff(Text): MetadataElement(name="comment_lines", default=0, desc="Number of comment lines", readonly=True, optional=True, no_value=0) MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = get_file_peek(dataset.file_name) dataset.blurb = "Attribute-Relation File Format (ARFF)" @@ -704,7 +704,7 @@ class SnpSiftDbNSFP(Text): except Exception as e: log.warning("set_meta fname: %s %s", dataset.file_name if dataset and dataset.file_name else 'Unkwown', unicodify(e)) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = f"{dataset.metadata.reference_name} : {','.join(dataset.metadata.annotation)}" dataset.blurb = f'{dataset.metadata.reference_name}' diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py index 0ee0cfa5835..6d28363c8da 100644 --- a/lib/galaxy/datatypes/tracks.py +++ b/lib/galaxy/datatypes/tracks.py @@ -42,7 +42,7 @@ class UCSCTrackHub(Html): rval.append('') return "\n".join(rval) - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub" else: diff --git a/lib/galaxy/datatypes/triples.py b/lib/galaxy/datatypes/triples.py index 98b66ec67ea..29e9611761c 100644 --- a/lib/galaxy/datatypes/triples.py +++ b/lib/galaxy/datatypes/triples.py @@ -35,7 +35,7 @@ class Triples(data.Data): """ return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -59,7 +59,7 @@ class NTriples(data.Text, Triples): return True return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -82,7 +82,7 @@ class N3(data.Text, Triples): """ return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -109,7 +109,7 @@ class Turtle(data.Text, Triples): return True return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -135,7 +135,7 @@ class Rdf(xml.GenericXml, Triples): return True return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -160,7 +160,7 @@ class Jsonld(text.Json, Triples): return True return False - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -182,7 +182,7 @@ class HDT(binary.Binary, Triples): if f.read(4) == b"$HDT": return True - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) diff --git a/lib/galaxy/datatypes/xml.py b/lib/galaxy/datatypes/xml.py index bb841631d36..18eb4a95409 100644 --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -29,7 +29,7 @@ class GenericXml(data.Text): edam_format = "format_2332" file_ext = "xml" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -79,7 +79,7 @@ class MEMEXml(GenericXml): """MEME XML Output data""" file_ext = "memexml" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -94,7 +94,7 @@ class CisML(GenericXml): """CisML XML data""" # see: http://www.ncbi.nlm.nih.gov/pubmed/15001475 file_ext = "cisml" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -148,7 +148,7 @@ class Dzi(GenericXml): """ Returns a list of visualizations for datatype""" return ['openseadragon'] - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) dataset.blurb = "Deep Zoom Image" @@ -180,7 +180,7 @@ class Phyloxml(GenericXml): edam_format = "format_3159" file_ext = "phyloxml" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) @@ -221,7 +221,7 @@ class Owl(GenericXml): edam_format = "format_3262" file_ext = "owl" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) dataset.blurb = "Web Ontology Language OWL" @@ -245,7 +245,7 @@ class Sbml(GenericXml): edam_data = "data_2024" edam_format = "format_2585" - def set_peek(self, dataset, is_multi_byte=False): + def set_peek(self, dataset): if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name) dataset.blurb = "System Biology Markup Language SBML" diff --git a/lib/galaxy/tool_util/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py index a4f8c6ea9b5..98173f44aec 100644 --- a/lib/galaxy/tool_util/parser/interface.py +++ b/lib/galaxy/tool_util/parser/interface.py @@ -18,7 +18,6 @@ class ToolSource(metaclass=ABCMeta): """ This interface represents an abstract source to parse tool information from. """ - default_is_multi_byte = False language: str @abstractmethod @@ -71,12 +70,6 @@ class ToolSource(metaclass=ABCMeta): def parse_xrefs(self) -> List[Dict[str, str]]: """Parse list of external resource URIs and types.""" - def parse_is_multi_byte(self): - """ Parse is_multi_byte from tool - TODO: figure out what this is and - document. - """ - return self.default_is_multi_byte - def parse_display_interface(self, default): """ Parse display_interface - fallback to default for the tool type (supplied as default parameter) if not specified. diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py index ff16177864a..3a91ab59364 100644 --- a/lib/galaxy/tool_util/parser/xml.py +++ b/lib/galaxy/tool_util/parser/xml.py @@ -117,9 +117,6 @@ class XmlToolSource(ToolSource): def parse_description(self): return xml_text(self.root, "description") - def parse_is_multi_byte(self): - return self._get_attribute_as_bool("is_multi_byte", self.default_is_multi_byte) - def parse_display_interface(self, default): return self._get_attribute_as_bool("display_interface", default) diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py index e8c5e74b246..44c91bfbb44 100644 --- a/lib/galaxy/tool_util/parser/yaml.py +++ b/lib/galaxy/tool_util/parser/yaml.py @@ -58,9 +58,6 @@ class YamlToolSource(ToolSource): xrefs = self.root_dict.get("xrefs", []) return [dict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]] - def parse_is_multi_byte(self): - return self.root_dict.get("is_multi_byte", self.default_is_multi_byte) - def parse_sanitize(self): return self.root_dict.get("sanitize", True) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index ef8cef1d5db..3d5d9008319 100644 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -844,8 +844,6 @@ class Tool(Dictifiable): else: raise Exception(f"Missing tool 'version' for tool with id '{self.id}' at '{tool_source}'") - # Support multi-byte tools - self.is_multi_byte = tool_source.parse_is_multi_byte() # Legacy feature, ignored by UI. self.force_history_refresh = False diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/view_tool_metadata.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/view_tool_metadata.mako index 8ee9cd4dcf2..8297007c323 100644 --- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/view_tool_metadata.mako +++ b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/view_tool_metadata.mako @@ -136,11 +136,6 @@ ${render_galaxy_repository_actions( repository )} ${tool.interpreter|h}
-
- - ${tool.is_multi_byte|h} -
-
${tool.force_history_refresh|h} diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako index fad4e51e036..9ec498046b6 100644 --- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako +++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako @@ -197,11 +197,6 @@ ${tool.interpreter | h}
-
- - ${tool.is_multi_byte | h} -
-
${tool.force_history_refresh | h} diff --git a/templates/admin/tool_shed_repository/view_tool_metadata.mako b/templates/admin/tool_shed_repository/view_tool_metadata.mako index 8ee9cd4dcf2..8297007c323 100644 --- a/templates/admin/tool_shed_repository/view_tool_metadata.mako +++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako @@ -136,11 +136,6 @@ ${render_galaxy_repository_actions( repository )} ${tool.interpreter|h}
-
- - ${tool.is_multi_byte|h} -
-
${tool.force_history_refresh|h} diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py index b6845c91caa..5d806b45ee4 100644 --- a/test/unit/tool_util/test_parsing.py +++ b/test/unit/tool_util/test_parsing.py @@ -11,7 +11,7 @@ from galaxy.util import galaxy_directory TOOL_XML_1 = """ -