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Source code for galaxy.datatypes.isa

"""
ISA datatype

See https://github.com/ISA-tools
"""
from __future__ import print_function

import io
import json
import logging
import os
import os.path
import re
import shutil
import sys
import tempfile

# Imports isatab after turning off warnings inside logger settings to avoid pandas warning making uploads fail.
logging.getLogger("isatools.isatab").setLevel(logging.ERROR)
from isatools import (
    isajson,
    isatab_meta
)
from markupsafe import escape

from galaxy import util
from galaxy.datatypes import data
from galaxy.util.compression_utils import CompressedFile
from galaxy.util.sanitize_html import sanitize_html

# CONSTANTS {{{1
################################################################

# Main files regex
JSON_FILE_REGEX = re.compile(r"^.*\.json$", flags=re.IGNORECASE)
INVESTIGATION_FILE_REGEX = re.compile(r"^i_\w+\.txt$", flags=re.IGNORECASE)

# The name of the ISA archive (compressed file) as saved inside Galaxy
ISA_ARCHIVE_NAME = "archive"

# Set max number of lines of the history peek
_MAX_LINES_HISTORY_PEEK = 11

# Configure logger {{{1
################################################################

logger = logging.getLogger(__name__)

# Function for opening correctly a CSV file for csv.reader() for both Python 2 and 3 {{{1
################################################################


[docs]def utf8_text_file_open(path): if sys.version_info[0] < 3: fp = open(path, 'rb') else: fp = open(path, 'r', newline='', encoding='utf8') return fp
# ISA class {{{1 ################################################################ class _Isa(data.Data): """ Base class for implementing ISA datatypes """ composite_type = 'auto_primary_file' allow_datatype_change = False is_binary = True _main_file_regex = None # Make investigation instance {{{2 ################################################################ def _make_investigation_instance(self, filename): raise NotImplementedError() # Constructor {{{2 ################################################################ def __init__(self, main_file_regex, **kwd): super(_Isa, self).__init__(**kwd) self._main_file_regex = main_file_regex # Add the archive file as the only composite file self.add_composite_file(ISA_ARCHIVE_NAME, is_binary=True, optional=True) # Get ISA folder path {{{2 ################################################################ def _get_isa_folder_path(self, dataset): isa_folder = dataset.extra_files_path if not isa_folder: raise Exception('Unvalid dataset object, or no extra files path found for this dataset.') return isa_folder # Get main file {{{2 ################################################################ def _get_main_file(self, dataset): """Get the main file of the ISA archive. Either the investigation file i_*.txt for ISA-Tab, or the JSON file for ISA-JSON.""" main_file = None isa_folder = self._get_isa_folder_path(dataset) if os.path.exists(isa_folder): # Get ISA archive older isa_files = os.listdir(isa_folder) # Try to find main file main_file = self._find_main_file_in_archive(isa_files) if main_file is None: raise Exception('Invalid ISA archive. No main file found.') # Make full path main_file = os.path.join(isa_folder, main_file) return main_file # Get investigation {{{2 ################################################################ def _get_investigation(self, dataset): """Create a contained instance specific to the exact ISA type (Tab or Json). We will use it to parse and access information from the archive.""" investigation = None main_file = self._get_main_file(dataset) if main_file is not None: investigation = self._make_investigation_instance(main_file) return investigation # Find main file in archive {{{2 ################################################################ def _find_main_file_in_archive(self, files_list): """Find the main file inside the ISA archive.""" found_file = None for f in files_list: match = self._main_file_regex.match(f) if match: if found_file is None: found_file = match.group() else: raise Exception('More than one file match the pattern "', str(self._main_file_regex), '" to identify the investigation file') return found_file # Set peek {{{2 ################################################################ def set_peek(self, dataset, is_multi_byte=False): """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) if main_file is None: raise RuntimeError("Unable to find the main file within the 'files_path' folder") # Read first lines of main file with io.open(main_file, encoding='utf-8') as f: data = [] for line in f: if len(data) < _MAX_LINES_HISTORY_PEEK: data.append(line) else: break if not dataset.dataset.purged and data: dataset.peek = json.dumps({"data": data}) dataset.blurb = 'data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' # Display peek {{{2 ################################################################ def display_peek(self, dataset): """Create the HTML table used for displaying peek, from the peek text found by set_peek() method.""" out = ['<table cellspacing="0" cellpadding="3">'] try: if not dataset.peek: dataset.set_peek() json_data = json.loads(dataset.peek) for line in json_data["data"]: line = line.strip() if not line: continue out.append('<tr><td>%s</td></tr>' % escape(util.unicodify(line, 'utf-8'))) out.append('</table>') out = "".join(out) except Exception as exc: out = "Can't create peek: %s" % util.unicodify(exc) return out # Generate primary file {{{2 ################################################################ def generate_primary_file(self, dataset=None): """Generate the primary file. It is an HTML file containing description of the composite dataset as well as a list of the composite files that it contains.""" if dataset: rval = ['<html><head><title>ISA Dataset </title></head><p/>'] if hasattr(dataset, "extra_files_path"): rval.append('<div>ISA Dataset composed of the following files:<p/><ul>') for cmp_file in os.listdir(dataset.extra_files_path): rval.append('<li><a href="%s" type="text/plain">%s</a></li>' % (cmp_file, escape(cmp_file))) rval.append('</ul></div></html>') else: rval.append('<div>ISA Dataset is empty!<p/><ul>') return "\n".join(rval) return "<div>No dataset available</div>" # Dataset content needs grooming {{{2 ################################################################ def dataset_content_needs_grooming(self, file_name): """This function is called on an output dataset file after the content is initially generated.""" return os.path.basename(file_name) == ISA_ARCHIVE_NAME # Groom dataset content {{{2 ################################################################ def groom_dataset_content(self, file_name): """This method is called by Galaxy to extract files contained in a composite data type.""" # XXX Is the right place to extract files? Should this step not be a cleaning step instead? # Could extracting be done earlier and composite files declared as files contained inside the archive # instead of the archive itself? # extract basename and folder of the current file whose content has to be groomed basename = os.path.basename(file_name) output_path = os.path.dirname(file_name) # extract archive if the file corresponds to the ISA archive if basename == ISA_ARCHIVE_NAME: # perform extraction # For some ZIP files CompressedFile::extract() extract the file inside <output_folder>/<file_name> instead of outputing it inside <output_folder>. So we first create a temporary folder, extract inside it, and move content to final destination. temp_folder = tempfile.mkdtemp() CompressedFile(file_name).extract(temp_folder) shutil.rmtree(output_path) extracted_files = os.listdir(temp_folder) logger.debug(' '.join(extracted_files)) if len(extracted_files) == 0: os.makedirs(output_path) shutil.rmtree(temp_folder) elif len(extracted_files) == 1 and os.path.isdir(os.path.join(temp_folder, extracted_files[0])): shutil.move(os.path.join(temp_folder, extracted_files[0]), output_path) shutil.rmtree(temp_folder) else: shutil.move(temp_folder, output_path) # Display data {{{2 ################################################################ def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd): """Downloads the ISA dataset if `preview` is `False`; if `preview` is `True`, it returns a preview of the ISA dataset as a HTML page. The preview is triggered when user clicks on the eye icon of the composite dataset.""" # if it is not required a preview use the default behaviour of `display_data` if not preview: return super(_Isa, self).display_data(trans, dataset, preview, filename, to_ext, **kwd) # prepare the preview of the ISA dataset investigation = self._get_investigation(dataset) if investigation is None: html = """<html><header><title>Error while reading ISA archive.</title></header> <body> <h1>An error occurred while reading content of ISA archive.</h1> <p>If you have tried to load your archive with the uploader by selecting isa-tab as composite data type, then try to load it again with isa-json instead. Conversely, if you have tried to load your archive with the uploader by selecting isa-json as composite data type, then try isa-tab instead.</p> <p>You may also try to look into your zip file in order to find out if this is a proper ISA archive. If you see a file i_Investigation.txt inside, then it is an ISA-Tab archive. If you see a file with extension .json inside, then it is an ISA-JSON archive. If you see nothing like that, then either your ISA archive is corrupted, or it is not an ISA archive.</p> </body></html>""" else: html = '<html><body>' html += '<h1>{0} {1}</h1>'.format(investigation.title, investigation.identifier) # Loop on all studies for study in investigation.studies: html += '<h2>Study %s</h2>' % study.identifier html += '<h3>%s</h3>' % study.title html += '<p>%s</p>' % study.description html += '<p>Submitted the %s</p>' % study.submission_date html += '<p>Released on %s</p>' % study.public_release_date html += '<p>Experimental factors used: %s</p>' % ', '.join([x.name for x in study.factors]) # Loop on all assays of this study for assay in study.assays: html += '<h3>Assay %s</h3>' % assay.filename html += '<p>Measurement type: %s</p>' % assay.measurement_type.term # OntologyAnnotation html += '<p>Technology type: %s</p>' % assay.technology_type.term # OntologyAnnotation html += '<p>Technology platform: %s</p>' % assay.technology_platform if assay.data_files is not None: html += '<p>Data files:</p>' html += '<ul>' for data_file in assay.data_files: if data_file.filename != '': html += '<li>' + escape(util.unicodify(str(data_file.filename), 'utf-8')) + ' - ' + escape(util.unicodify(str(data_file.label), 'utf-8')) + '</li>' html += '</ul>' html += '</body></html>' # Set mime type mime = 'text/html' self._clean_and_set_mime_type(trans, mime) return sanitize_html(html).encode('utf-8') # ISA-Tab class {{{1 ################################################################
[docs]class IsaTab(_Isa): file_ext = "isa-tab" # Constructor {{{2 ################################################################
[docs] def __init__(self, **kwd): super(IsaTab, self).__init__(main_file_regex=INVESTIGATION_FILE_REGEX, **kwd)
# Make investigation instance {{{2 ################################################################ def _make_investigation_instance(self, filename): # Parse ISA-Tab investigation file parser = isatab_meta.InvestigationParser() isa_dir = os.path.dirname(filename) fp = utf8_text_file_open(filename) parser.parse(fp) for study in parser.isa.studies: s_parser = isatab_meta.LazyStudySampleTableParser(parser.isa) s_parser.parse(os.path.join(isa_dir, study.filename)) for assay in study.assays: a_parser = isatab_meta.LazyAssayTableParser(parser.isa) a_parser.parse(os.path.join(isa_dir, assay.filename)) isa = parser.isa return isa
# ISA-JSON class {{{1 ################################################################
[docs]class IsaJson(_Isa): file_ext = "isa-json" # Constructor {{{2 ################################################################
[docs] def __init__(self, **kwd): super(IsaJson, self).__init__(main_file_regex=JSON_FILE_REGEX, **kwd)
# Make investigation instance {{{2 ################################################################ def _make_investigation_instance(self, filename): # Parse JSON file fp = utf8_text_file_open(filename) isa = isajson.load(fp) return isa