Python get_file_peek示例

示例#1

文件： molecules.py 项目： Ahsanzia/galaxytools

 def set_peek( self, dataset, is_multi_byte=False ):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
         if (dataset.metadata.number_of_molecules == 1):
             dataset.blurb = "1 molecule"
         else:
             dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
         dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#2

文件： msa.py 项目： eteriSokhoyan/galaxy

 def set_peek( self, dataset, is_multi_byte=False ):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
         if (dataset.metadata.number_of_models == 1):
             dataset.blurb = "1 alignment"
         else:
             dataset.blurb = "%s alignments" % dataset.metadata.number_of_models
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#3

文件： genbank.py 项目： Ahsanzia/galaxytools

 def set_peek( self, dataset, is_multi_byte=False ):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
         if (dataset.metadata.number_of_sequences == 1):
             dataset.blurb = "1 sequence [%s]" % dataset.metadata.name_of_sequences[0]
         else:
             seq_list = ', '.join(dataset.metadata.name_of_sequences[0:10])
             if len(dataset.metadata.name_of_sequences) > 10:
                 seq_list += ', ...'
             dataset.blurb = "%s sequences [%s]" % ( dataset.metadata.number_of_sequences,
                                                    seq_list )
         dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#4

文件： constructive_solid_geometry.py 项目： brandeis-nlp/Galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
         dataset.blurb = "Faces: %s, Vertices: %s" % (str(dataset.metadata.face), str(dataset.metadata.vertex))
     else:
         dataset.peek = 'File does not exist'
         dataset.blurb = 'File purged from disc'

示例#5

文件： constructive_solid_geometry.py 项目： brandeis-nlp/Galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
         dataset.blurb = self.get_blurb(dataset)
     else:
         dataset.peek = 'File does not exist'
         dataset.blurb = 'File purged from disc'

示例#6

文件： molecules.py 项目： msauria/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "pharmacophore"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#7

文件： molecules.py 项目： msauria/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "grids for docking"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#8

文件： text.py 项目： manisha-sapre/Trinity_CTAT_galaxy

 def set_peek( self, dataset, is_multi_byte=False ):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
         dataset.blurb = "Open Biomedical Ontology (OBO)"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#9

文件： annotation.py 项目： ImmPortDB/immport-galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "SNAP HMM model"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#10

文件： text.py 项目： manisha-sapre/Trinity_CTAT_galaxy

 def set_peek( self, dataset, is_multi_byte=False ):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
         dataset.blurb = "JavaScript Object Notation (JSON)"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#11

文件： compressed.py 项目： TianhuaHe/galaxy-tools

 def set_peek( self, dataset, is_multi_byte=False ):
     """Set the peek and blurb text"""
     if not dataset.dataset.purged:
         dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#12

文件： text.py 项目： manisha-sapre/Trinity_CTAT_galaxy

 def set_peek( self, dataset, is_multi_byte=False ):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
         dataset.blurb = "IPython Notebook"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#13

文件： plant_tribes.py 项目： osallou/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "ESTScan scores matrices"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#14

文件： text.py 项目： manisha-sapre/Trinity_CTAT_galaxy

 def set_peek( self, dataset, is_multi_byte=False ):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
         dataset.blurb = "Attribute-Relation File Format (ARFF)"
         dataset.blurb += ", %s comments, %s attributes" % ( dataset.metadata.comment_lines, dataset.metadata.columns )
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#15

文件： proteomics.py 项目： ImmPortDB/immport-galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     """Set the peek and blurb text"""
     if not dataset.dataset.purged:
         dataset.peek = data.get_file_peek(dataset.file_name)
         dataset.blurb = 'splib Spectral Library Format'
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#16

文件： proteomics.py 项目： PeterKoza/Galaxy-fmfi

 def set_peek(self, dataset, is_multi_byte=False):
     """Set the peek and blurb text"""
     if not dataset.dataset.purged:
         dataset.peek = data.get_file_peek(dataset.file_name,
                                           is_multi_byte=is_multi_byte)
         dataset.blurb = 'Spectral Library without index files'
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#17

文件： molecules.py 项目： lappsgrid-incubator/Galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         atom_numbers = count_special_lines("^ATOM", dataset.file_name)
         hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#18

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         root_numbers = count_special_lines("^ROOT", dataset.file_name)
         branch_numbers = count_special_lines("^BRANCH", dataset.file_name)
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = f"{root_numbers} roots and {branch_numbers} branches"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#19

文件： molecules.py 项目： manabuishii/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         atom_numbers = count_special_lines("^ATOM", dataset.file_name)
         hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
         dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
         dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#20

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "Attribute-Relation File Format (ARFF)"
         dataset.blurb += ", %s comments, %s attributes" % (
             dataset.metadata.comment_lines, dataset.metadata.columns)
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#21

 def set_peek(self, dataset, is_multi_byte=False):
     """Set the peek and blurb text"""
     if not dataset.dataset.purged:
         dataset.peek = data.get_file_peek(dataset.file_name,
                                           is_multi_byte=is_multi_byte)
         dataset.blurb = self.blurb
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#22

文件： molecules.py 项目： msauria/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         root_numbers = count_special_lines("^ROOT", dataset.file_name)
         branch_numbers = count_special_lines("^BRANCH", dataset.file_name)
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "%s roots and %s branches" % (root_numbers, branch_numbers)
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#23

文件： constructive_solid_geometry.py 项目： avengerpb/Galaxyondocker

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name,
                                      is_multi_byte=is_multi_byte)
         dataset.blurb = "Faces: %s, Vertices: %s" % (str(
             dataset.metadata.face), str(dataset.metadata.vertex))
     else:
         dataset.peek = 'File does not exist'
         dataset.blurb = 'File purged from disc'

示例#24

文件： plant_tribes.py 项目： mvdbeek/galaxy

 def set_peek(self, dataset):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         if (dataset.metadata.number_comp == 1):
             dataset.blurb = "1 significant component"
         else:
             dataset.blurb = f"{dataset.metadata.number_comp} significant components"
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#25

文件： molecules.py 项目： msauria/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         atom_numbers = count_special_lines("^ATOM", dataset.file_name)
         hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
         chain_ids = ','.join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else 'None'
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "%s atoms and %s HET-atoms\nchain_ids: %s" % (atom_numbers, hetatm_numbers, str(chain_ids))
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#26

文件： msa.py 项目： mvdbeek/galaxy

 def set_peek(self, dataset):
     if not dataset.dataset.purged:
         if (dataset.metadata.number_of_models == 1):
             dataset.blurb = "1 alignment"
         else:
             dataset.blurb = f"{dataset.metadata.number_of_models} alignments"
         dataset.peek = get_file_peek(dataset.file_name)
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#27

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         if (dataset.metadata.number_comp == 1):
             dataset.blurb = "1 significant component"
         else:
             dataset.blurb = "%s significant components" % dataset.metadata.number_comp
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#28

文件： stockholm_1_0.py 项目： zph001/tools-iuc

 def set_peek( self, dataset, is_multi_byte=False ):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
         if (dataset.metadata.number_of_models == 1):
             dataset.blurb = "1 alignment"
         else:
             dataset.blurb = "%s alignments" % dataset.metadata.number_of_models
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disc'

示例#29

文件： phylip.py 项目： ImmPortDB/immport-galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
         if dataset.metadata.sequences:
             dataset.blurb = "%s sequences" % util.commaify(str(dataset.metadata.sequences))
         else:
             dataset.blurb = nice_size(dataset.get_size())
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#30

 def set_peek(self, dataset):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         if dataset.metadata.sequences:
             dataset.blurb = f"{util.commaify(str(dataset.metadata.sequences))} sequences"
         else:
             dataset.blurb = nice_size(dataset.get_size())
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#31

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         if (dataset.metadata.number_of_molecules == 1):
             dataset.blurb = "1 molecule"
         else:
             dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
         dataset.peek = get_file_peek(dataset.file_name)
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#32

文件： plant_tribes.py 项目： osallou/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name)
         if (dataset.metadata.number_comp == 1):
             dataset.blurb = "1 significant component"
         else:
             dataset.blurb = "%s significant components" % dataset.metadata.number_comp
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#33

 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"
         else:
             dataset.blurb = f"{dataset.metadata.file_type} {dataset.metadata.version_number}: Format {dataset.metadata.file_format}, {dataset.metadata.block_count} blocks, {dataset.metadata.number_of_optional_header_records} headers and {dataset.metadata.number_of_data_columns} columns"
         dataset.peek = get_file_peek(dataset.file_name)
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#34

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         atom_numbers = count_special_lines("^ATOM", dataset.file_name)
         hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
         chain_ids = ','.join(dataset.metadata.chain_ids) if len(dataset.metadata.chain_ids) > 0 else 'None'
         dataset.peek = get_file_peek(dataset.file_name)
         dataset.blurb = "%s atoms and %s HET-atoms\nchain_ids: %s" % (atom_numbers, hetatm_numbers, str(chain_ids))
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#35

文件： phylip.py 项目： scrathat/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         dataset.peek = get_file_peek(dataset.file_name,
                                      is_multi_byte=is_multi_byte)
         if dataset.metadata.sequences:
             dataset.blurb = "%s sequences" % util.commaify(
                 str(dataset.metadata.sequences))
         else:
             dataset.blurb = nice_size(dataset.get_size())
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#36

文件： microarrays.py 项目： yin-max/galaxy

 def set_peek(self, dataset, is_multi_byte=False):
     if not dataset.dataset.purged:
         if dataset.metadata.block_count == 1:
             dataset.blurb = "{} {}: Format {}, 1 block, {} headers and {} columns".format(
                 dataset.metadata.file_type,
                 dataset.metadata.version_number,
                 dataset.metadata.file_format,
                 dataset.metadata.number_of_optional_header_records,
                 dataset.metadata.number_of_data_columns)
         else:
             dataset.blurb = "{} {}: Format {}, {} blocks, {} headers and {} columns".format(
                 dataset.metadata.file_type,
                 dataset.metadata.version_number,
                 dataset.metadata.file_format, dataset.metadata.block_count,
                 dataset.metadata.number_of_optional_header_records,
                 dataset.metadata.number_of_data_columns)
         dataset.peek = get_file_peek(dataset.file_name)
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'

示例#37

def test_get_file_peek():
    # should get the first 5 lines of the file without a trailing newline character
    assert get_file_peek(
        'test-data/1.tabular', line_wrap=False
    ) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11'

示例#38

文件： test_data.py 项目： scrathat/galaxy

def test_get_file_peek():
    # should get the first 5 lines of the file without a trailing newline character
    assert get_file_peek(os.path.join(galaxy_directory(), 'test-data/1.tabular'), line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11\n'

示例#39

文件： test_data.py 项目： ImmPortDB/immport-galaxy

def test_get_file_peek():
    # should get the first 5 lines of the file without a trailing newline character
    assert get_file_peek('test-data/1.tabular', line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11'