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Source code for galaxy.datatypes.text
# -*- coding: utf-8 -*-
""" Clearing house for generic text datatypes that are not XML or tabular.
"""
import gzip
import json
import logging
import os
import re
import subprocess
import tempfile
from six.moves import shlex_quote
from galaxy.datatypes.data import get_file_peek, Text
from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
from galaxy.datatypes.sniff import build_sniff_from_prefix, iter_headers
from galaxy.util import nice_size, string_as_bool
log = logging.getLogger(__name__)
[docs]@build_sniff_from_prefix
class Html(Text):
"""Class describing an html file"""
edam_format = "format_2331"
file_ext = "html"
[docs] def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = "HTML file"
dataset.blurb = nice_size(dataset.get_size())
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
[docs] def sniff_prefix(self, file_prefix):
"""
Determines whether the file is in html format
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'complete.bed' )
>>> Html().sniff( fname )
False
>>> fname = get_test_fname( 'file.html' )
>>> Html().sniff( fname )
True
"""
headers = iter_headers(file_prefix, None)
for i, hdr in enumerate(headers):
if hdr and hdr[0].lower().find('<html>') >= 0:
return True
return False
[docs]@build_sniff_from_prefix
class Json(Text):
edam_format = "format_3464"
file_ext = "json"
[docs] def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "JavaScript Object Notation (JSON)"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
[docs] def sniff_prefix(self, file_prefix):
"""
Try to load the string with the json module. If successful it's a json file.
"""
return self._looks_like_json(file_prefix)
def _looks_like_json(self, file_prefix):
# Pattern used by SequenceSplitLocations
if file_prefix.file_size < 50000 and not file_prefix.truncated:
# If the file is small enough - don't guess just check.
try:
item = json.loads(file_prefix.contents_header)
# exclude simple types, must set format in these cases
assert isinstance(item, (list, dict))
return True
except Exception:
return False
else:
start = file_prefix.string_io().read(100).strip()
if start:
# simple types are valid JSON as well,
# but if necessary format has to be set explicitly
return start.startswith("[") or start.startswith("{")
return False
[docs] def display_peek(self, dataset):
try:
return dataset.peek
except Exception:
return "JSON file (%s)" % (nice_size(dataset.get_size()))
[docs]@build_sniff_from_prefix
class Ipynb(Json):
file_ext = "ipynb"
[docs] def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "Jupyter Notebook"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
[docs] def sniff_prefix(self, file_prefix):
"""
Try to load the string with the json module. If successful it's a json file.
"""
if self._looks_like_json(file_prefix):
try:
with open(file_prefix.filename) as f:
ipynb = json.load(f)
if ipynb.get('nbformat', False) is not False and ipynb.get('metadata', False):
return True
else:
return False
except Exception:
return False
[docs] def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
config = trans.app.config
trust = getattr(config, 'trust_jupyter_notebook_conversion', False)
if trust:
return self._display_data_trusted(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, **kwd)
else:
return super(Ipynb, self).display_data(trans, dataset, preview=preview, filename=filename, to_ext=to_ext, **kwd)
def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
preview = string_as_bool(preview)
if to_ext or not preview:
return self._serve_raw(trans, dataset, to_ext, **kwd)
else:
with tempfile.NamedTemporaryFile(delete=False) as ofile_handle:
ofilename = ofile_handle.name
try:
cmd = ['jupyter', 'nbconvert', '--to', 'html', '--template', 'full', dataset.file_name, '--output', ofilename]
subprocess.check_call(cmd)
ofilename = '%s.html' % ofilename
except subprocess.CalledProcessError:
ofilename = dataset.file_name
log.exception('Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.', ' '.join(map(shlex_quote, cmd)))
return open(ofilename, mode='rb')
[docs]@build_sniff_from_prefix
class Biom1(Json):
"""
BIOM version 1.0 file format description
http://biom-format.org/documentation/format_versions/biom-1.0.html
"""
file_ext = "biom1"
edam_format = "format_3746"
MetadataElement(name="table_rows", default=[], desc="table_rows", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
MetadataElement(name="table_matrix_element_type", default="", desc="table_matrix_element_type", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="")
MetadataElement(name="table_format", default="", desc="table_format", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="")
MetadataElement(name="table_generated_by", default="", desc="table_generated_by", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="")
MetadataElement(name="table_matrix_type", default="", desc="table_matrix_type", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="")
MetadataElement(name="table_shape", default=[], desc="table_shape", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[])
MetadataElement(name="table_format_url", default="", desc="table_format_url", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="")
MetadataElement(name="table_date", default="", desc="table_date", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="")
MetadataElement(name="table_type", default="", desc="table_type", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="")
MetadataElement(name="table_id", default=None, desc="table_id", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value=None)
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=[])
[docs] def set_peek(self, dataset, is_multi_byte=False):
super(Biom1, self).set_peek(dataset)
if not dataset.dataset.purged:
dataset.blurb = "Biological Observation Matrix v1"
[docs] def sniff_prefix(self, file_prefix):
is_biom = False
if self._looks_like_json(file_prefix):
is_biom = self._looks_like_biom(file_prefix)
return is_biom
def _looks_like_biom(self, file_prefix, load_size=50000):
"""
@param filepath: [str] The path to the evaluated file.
@param load_size: [int] The size of the file block load in RAM (in
bytes).
"""
is_biom = False
segment_size = int(load_size / 2)
try:
with open(file_prefix.filename, "r") as fh:
prev_str = ""
segment_str = fh.read(segment_size)
if segment_str.strip().startswith('{'):
while segment_str:
current_str = prev_str + segment_str
if '"format"' in current_str:
current_str = re.sub(r'\s', '', current_str)
if '"format":"BiologicalObservationMatrix' in current_str:
is_biom = True
break
prev_str = segment_str
segment_str = fh.read(segment_size)
except Exception:
pass
return is_biom
[docs] def set_meta(self, dataset, **kwd):
"""
Store metadata information from the BIOM file.
"""
if dataset.has_data():
with open(dataset.file_name) as fh:
try:
json_dict = json.load(fh)
except Exception:
return
def _transform_dict_list_ids(dict_list):
if dict_list:
return [x.get('id', None) for x in dict_list]
return []
b_transform = {'rows': _transform_dict_list_ids, 'columns': _transform_dict_list_ids}
for (m_name, b_name) in [('table_rows', 'rows'),
('table_matrix_element_type', 'matrix_element_type'),
('table_format', 'format'),
('table_generated_by', 'generated_by'),
('table_matrix_type', 'matrix_type'),
('table_shape', 'shape'),
('table_format_url', 'format_url'),
('table_date', 'date'),
('table_type', 'type'),
('table_id', 'id'),
('table_columns', 'columns')]:
try:
metadata_value = json_dict.get(b_name, None)
if b_name == "columns" and metadata_value:
keep_columns = set()
for column in metadata_value:
if column['metadata'] is not None:
for k, v in column['metadata'].items():
if v is not None:
keep_columns.add(k)
final_list = sorted(list(keep_columns))
dataset.metadata.table_column_metadata_headers = final_list
if b_name in b_transform:
metadata_value = b_transform[b_name](metadata_value)
setattr(dataset.metadata, m_name, metadata_value)
except Exception:
log.exception("Something in the metadata detection for biom1 went wrong.")
pass
[docs]@build_sniff_from_prefix
class Obo(Text):
"""
OBO file format description
https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html
"""
edam_data = "data_0582"
edam_format = "format_2549"
file_ext = "obo"
[docs] def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.blurb = "Open Biomedical Ontology (OBO)"
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
[docs] def sniff_prefix(self, file_prefix):
"""
Try to guess the Obo filetype.
It usually starts with a "format-version:" string and has several stanzas which starts with "id:".
"""
stanza = re.compile(r'^\[.*\]$')
handle = file_prefix.string_io()
first_line = handle.readline()
if not first_line.startswith('format-version:'):
return False
for line in handle:
if stanza.match(line.strip()):
# a stanza needs to begin with an ID tag
if next(handle).startswith('id:'):
return True
return False
[docs]@build_sniff_from_prefix
class Arff(Text):
"""
An ARFF (Attribute-Relation File Format) file is an ASCII text file that describes a list of instances sharing a set of attributes.
http://weka.wikispaces.com/ARFF
"""
edam_format = "format_3581"
file_ext = "arff"
"""Add metadata elements"""
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)
[docs] 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'
[docs] def sniff_prefix(self, file_prefix):
"""
Try to guess the Arff filetype.
It usually starts with a "format-version:" string and has several stanzas which starts with "id:".
"""
handle = file_prefix.string_io()
relation_found = False
attribute_found = False
for line_count, line in enumerate(handle):
if line_count > 1000:
# only investigate the first 1000 lines
return False
line = line.strip()
if not line:
continue
start_string = line[:20].upper()
if start_string.startswith("@RELATION"):
relation_found = True
elif start_string.startswith("@ATTRIBUTE"):
attribute_found = True
elif start_string.startswith("@DATA"):
# @DATA should be the last data block
if relation_found and attribute_found:
return True
return False
[docs] def set_meta(self, dataset, **kwd):
"""
Trying to count the comment lines and the number of columns included.
A typical ARFF data block looks like this:
@DATA
5.1,3.5,1.4,0.2,Iris-setosa
4.9,3.0,1.4,0.2,Iris-setosa
"""
comment_lines = column_count = 0
if dataset.has_data():
first_real_line = False
data_block = False
with open(dataset.file_name) as handle:
for line in handle:
line = line.strip()
if not line:
continue
if line.startswith('%') and not first_real_line:
comment_lines += 1
else:
first_real_line = True
if data_block:
if line.startswith('{'):
# Sparse representation
"""
@data
0, X, 0, Y, "class A", {5}
or
@data
{1 X, 3 Y, 4 "class A"}, {5}
"""
token = line.split('}', 1)
first_part = token[0]
last_column = first_part.split(',')[-1].strip()
numeric_value = last_column.split()[0]
column_count = int(numeric_value)
if len(token) > 1:
# we have an additional weight
column_count -= 1
else:
columns = line.strip().split(',')
column_count = len(columns)
if columns[-1].strip().startswith('{'):
# we have an additional weight at the end
column_count -= 1
# We have now the column_count and we know the initial comment lines. So we can terminate here.
break
if line[:5].upper() == "@DATA":
data_block = True
dataset.metadata.comment_lines = comment_lines
dataset.metadata.columns = column_count
[docs]class SnpEffDb(Text):
"""Class describing a SnpEff genome build"""
edam_format = "format_3624"
file_ext = "snpeffdb"
MetadataElement(name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None)
MetadataElement(name="snpeff_version", default="SnpEff4.0", desc="SnpEff Version", readonly=True, visible=True, no_value=None)
MetadataElement(name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[], optional=True)
MetadataElement(name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[], optional=True)
# The SnpEff version line was added in SnpEff version 4.1
[docs] def getSnpeffVersionFromFile(self, path):
snpeff_version = None
try:
with gzip.open(path, 'rb') as fh:
buf = fh.read(100)
lines = buf.splitlines()
m = re.match(r'^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip())
if m:
snpeff_version = m.groups()[0] + m.groups()[1]
except Exception:
pass
return snpeff_version
[docs] def set_meta(self, dataset, **kwd):
Text.set_meta(self, dataset, **kwd)
data_dir = dataset.extra_files_path
# search data_dir/genome_version for files
regulation_pattern = 'regulation_(.+).bin'
# annotation files that are included in snpEff by a flag
annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif', 'interactions.bin': '-interaction'}
regulations = []
annotations = []
genome_version = None
snpeff_version = None
if data_dir and os.path.isdir(data_dir):
for root, dirs, files in os.walk(data_dir):
for fname in files:
if fname.startswith('snpEffectPredictor'):
# if snpEffectPredictor.bin download succeeded
genome_version = os.path.basename(root)
dataset.metadata.genome_version = genome_version
# read the first line of the gzipped snpEffectPredictor.bin file to get the SnpEff version
snpeff_version = self.getSnpeffVersionFromFile(os.path.join(root, fname))
if snpeff_version:
dataset.metadata.snpeff_version = snpeff_version
else:
m = re.match(regulation_pattern, fname)
if m:
name = m.groups()[0]
regulations.append(name)
elif fname in annotations_dict:
value = annotations_dict[fname]
name = value.lstrip('-')
annotations.append(name)
dataset.metadata.regulation = regulations
dataset.metadata.annotation = annotations
try:
with open(dataset.file_name, 'w') as fh:
fh.write("%s\n" % genome_version if genome_version else 'Genome unknown')
fh.write("%s\n" % snpeff_version if snpeff_version else 'SnpEff version unknown')
if annotations:
fh.write("annotations: %s\n" % ','.join(annotations))
if regulations:
fh.write("regulations: %s\n" % ','.join(regulations))
except Exception:
pass
[docs]class SnpSiftDbNSFP(Text):
"""Class describing a dbNSFP database prepared fpr use by SnpSift dbnsfp """
MetadataElement(name='reference_name', default='dbSNFP', desc='Reference Name', readonly=True, visible=True, set_in_upload=True, no_value='dbSNFP')
MetadataElement(name="bgzip", default=None, desc="dbNSFP bgzip", readonly=True, visible=True, no_value=None)
MetadataElement(name="index", default=None, desc="Tabix Index File", readonly=True, visible=True, no_value=None)
MetadataElement(name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[])
file_ext = "snpsiftdbnsfp"
composite_type = 'auto_primary_file'
allow_datatype_change = False
"""
## The dbNSFP file is a tabular file with 1 header line
## The first 4 columns are required to be: chrom pos ref alt
## These match columns 1,2,4,5 of the VCF file
## SnpSift requires the file to be block-gzipped and the indexed with samtools tabix
## Example:
## Compress using block-gzip algorithm
bgzip dbNSFP2.3.txt
## Create tabix index
tabix -s 1 -b 2 -e 2 dbNSFP2.3.txt.gz
"""
[docs] def __init__(self, **kwd):
Text.__init__(self, **kwd)
self.add_composite_file('%s.gz', description='dbNSFP bgzip', substitute_name_with_metadata='reference_name', is_binary=True)
self.add_composite_file('%s.gz.tbi', description='Tabix Index File', substitute_name_with_metadata='reference_name', is_binary=True)
[docs] def init_meta(self, dataset, copy_from=None):
Text.init_meta(self, dataset, copy_from=copy_from)
[docs] def generate_primary_file(self, dataset=None):
"""
This is called only at upload to write the html file
cannot rename the datasets here - they come with the default unfortunately
"""
return '<html><head><title>SnpSiftDbNSFP Composite Dataset</title></head></html>'
[docs] def regenerate_primary_file(self, dataset):
"""
cannot do this until we are setting metadata
"""
annotations = "dbNSFP Annotations: %s\n" % ','.join(dataset.metadata.annotation)
with open(dataset.file_name, 'a') as f:
if dataset.metadata.bgzip:
bn = dataset.metadata.bgzip
f.write(bn)
f.write('\n')
f.write(annotations)
[docs] def set_meta(self, dataset, overwrite=True, **kwd):
try:
efp = dataset.extra_files_path
if os.path.exists(efp):
flist = os.listdir(efp)
for i, fname in enumerate(flist):
if fname.endswith('.gz'):
dataset.metadata.bgzip = fname
try:
with gzip.open(os.path.join(efp, fname), 'r') as fh:
buf = fh.read(5000)
lines = buf.splitlines()
headers = lines[0].split('\t')
dataset.metadata.annotation = headers[4:]
except Exception as e:
log.warning("set_meta fname: %s %s" % (fname, str(e)))
if fname.endswith('.tbi'):
dataset.metadata.index = fname
self.regenerate_primary_file(dataset)
except Exception as e:
log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = '%s : %s' % (dataset.metadata.reference_name, ','.join(dataset.metadata.annotation))
dataset.blurb = '%s' % dataset.metadata.reference_name
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
[docs]@build_sniff_from_prefix
class IQTree(Text):
"""IQ-TREE format"""
file_ext = 'iqtree'
[docs] def sniff_prefix(self, file_prefix):
"""
Detect the IQTree file
Scattered text file containing various headers and data
types.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('example.iqtree')
>>> IQTree().sniff(fname)
True
>>> fname = get_test_fname('temp.txt')
>>> IQTree().sniff(fname)
False
>>> fname = get_test_fname('test_tab1.tabular')
>>> IQTree().sniff(fname)
False
"""
return file_prefix.startswith("IQ-TREE")