Merge pull request #10862 from mvdbeek/refactor_mkstemp

Replace usage of mkstemp with NamedTemporaryFile

lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py

@@ -34,22 +34,18 @@ def timenow():
 def pruneLD(plinktasks=[], cd='./', vclbase=[]):
     """
     """
-    fd, plog = tempfile.mkstemp()
-    os.close(fd)
-    alog = []
-    alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
-    for task in plinktasks:  # each is a list
-        vcl = vclbase + task
-        with open(plog, 'w') as sto:
-            subprocess.check_call(vcl, stdout=sto, stderr=sto, cwd=cd)
-        try:
-            lplog = open(plog).readlines()
-            lplog = [elem for elem in lplog if elem.find('Pruning SNP') == -1]
-            alog += lplog
-            alog.append('\n')
-            os.unlink(plog)  # no longer needed
-        except Exception:
-            alog.append('### {} Strange - no std out from plink when running command line\n{}\n'.format(timenow(), ' '.join(vcl)))
+    alog = ['## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n']
+    with tempfile.NamedTemporaryFile(mode='r+') as plog:
+        for task in plinktasks:  # each is a list
+            vcl = vclbase + task
+            subprocess.check_call(vcl, stdout=plog, stderr=plog, cwd=cd)
+            try:
+                plog.seek(0)
+                lplog = [elem for elem in plog.readlines() if elem.find('Pruning SNP') == -1]
+                alog += lplog
+                alog.append('\n')
+            except Exception:
+                alog.append('### {} Strange - no std out from plink when running command line\n{}\n'.format(timenow(), ' '.join(vcl)))
     return alog
 
 

lib/galaxy/datatypes/sniff.py

@@ -50,8 +50,8 @@ def stream_url_to_file(path, file_sources=None):
     prefix = "url_paste"
     if file_sources and file_sources.looks_like_uri(path):
         file_source_path = file_sources.get_file_source_path(path)
-        _, temp_name = tempfile.mkstemp(prefix=prefix)
-        os.close(_)
+        with tempfile.NamedTemporaryFile(prefix=prefix, delete=False) as temp:
+            temp_name = temp.name
         file_source_path.file_source.realize_to(file_source_path.path, temp_name)
         return temp_name
     else:
@@ -118,11 +118,10 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload",
     Converts in place a file from universal line endings
     to Posix line endings.
     """
-    fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
     i = 0
     NEWLINE_BYTE = 10
     CR_BYTE = 13
-    with open(fd, mode="wb") as fp, open(fname, mode="rb") as fi:
+    with tempfile.NamedTemporaryFile(mode='wb', prefix=tmp_prefix, dir=tmp_dir, delete=False) as fp, open(fname, mode='rb') as fi:
         last_char = None
         block = fi.read(block_size)
         last_block = b""
@@ -144,11 +143,11 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload",
             i += 1
             fp.write(b"\n")
     if in_place:
-        shutil.move(temp_name, fname)
+        shutil.move(fp.name, fname)
         # Return number of lines in file.
         return (i, None)
     else:
-        return (i, temp_name)
+        return (i, fp.name)
 
 
 def convert_newlines_sep2tabs(fname, in_place=True, patt=br"[^\S\n]+", tmp_dir=None, tmp_prefix="gxupload"):
@@ -678,21 +677,20 @@ def handle_compressed_file(
             keep_compressed = getattr(datatype, 'compressed', False)
     # don't waste time decompressing if we sniff invalid contents
     if is_compressed and is_valid and auto_decompress and not keep_compressed:
-        fd, uncompressed = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
-        compressed_file = DECOMPRESSION_FUNCTIONS[compressed_type](filename)
-        # TODO: it'd be ideal to convert to posix newlines and space-to-tab here as well
-        while True:
-            try:
-                chunk = compressed_file.read(CHUNK_SIZE)
-            except OSError as e:
-                os.close(fd)
-                os.remove(uncompressed)
-                compressed_file.close()
-                raise OSError('Problem uncompressing {} data, please try retrieving the data uncompressed: {}'.format(compressed_type, util.unicodify(e)))
-            if not chunk:
-                break
-            os.write(fd, chunk)
-        os.close(fd)
+        with tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir, delete=False) as uncompressed:
+            compressed_file = DECOMPRESSION_FUNCTIONS[compressed_type](filename)
+            # TODO: it'd be ideal to convert to posix newlines and space-to-tab here as well
+            while True:
+                try:
+                    chunk = compressed_file.read(CHUNK_SIZE)
+                except OSError as e:
+                    os.remove(uncompressed.name)
+                    compressed_file.close()
+                    raise OSError('Problem uncompressing {} data, please try retrieving the data uncompressed: {}'.format(compressed_type, util.unicodify(e)))
+                if not chunk:
+                    break
+                uncompressed.write(chunk)
+        uncompressed = uncompressed.name
         compressed_file.close()
         if in_place:
             # Replace the compressed file with the uncompressed file

lib/galaxy/datatypes/util/maf_utilities.py

@@ -353,12 +353,11 @@ def build_maf_index_species_chromosomes(filename, index_species=None):
 
 # builds and returns ( index, index_filename ) for specified maf_file
 def build_maf_index(maf_file, species=None):
-    indexes, found_species, species_chromosomes, blocks = build_maf_index_species_chromosomes(maf_file, species)
+    indexes, *_ = build_maf_index_species_chromosomes(maf_file, species)
     if indexes is not None:
-        fd, index_filename = tempfile.mkstemp()
-        with os.fdopen(fd, 'w') as out:
-            indexes.write(out)
-        return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), index_filename)
+        with tempfile.NamedTemporaryFile(mode='w', delete=False) as index:
+            indexes.write(index)
+        return (bx.align.maf.Indexed(maf_file, index_filename=index.name, keep_open=True, parse_e_rows=False), index.name)
     return (None, None)
 
 

lib/galaxy/metadata/__init__.py

@@ -373,11 +373,9 @@ class JobExternalOutputMetadataWrapper(MetadataCollectionStrategy):
         assert not use_bin
         if include_command:
             # return command required to build
-            fd, fp = tempfile.mkstemp(suffix='.py', dir=tmp_dir, prefix="set_metadata_")
-            metadata_script_file = abspath(fp)
-            with os.fdopen(fd, 'w') as f:
-                f.write(SET_METADATA_SCRIPT)
-            return 'python "{}" {}'.format(metadata_path_on_compute(metadata_script_file), args)
+            with tempfile.NamedTemporaryFile(mode='w', suffix='.py', dir=tmp_dir, prefix="set_metadata_", delete=False) as temp:
+                temp.write(SET_METADATA_SCRIPT)
+            return 'python "{}" {}'.format(metadata_path_on_compute(temp.name), args)
         else:
             # return args to galaxy_ext.metadata.set_metadata required to build
             return args

lib/galaxy/tool_util/deps/conda_util.py

@@ -428,8 +428,8 @@ def hash_conda_packages(conda_packages, conda_target=None):
 # shell makes sense for planemo, in Galaxy this should just execute
 # these commands as Python
 def install_conda(conda_context, force_conda_build=False):
-    f, script_path = tempfile.mkstemp(suffix=".sh", prefix="conda_install")
-    os.close(f)
+    with tempfile.NamedTemporaryFile(suffix=".sh", prefix="conda_install", delete=False) as temp:
+        script_path = temp.name
     download_cmd = commands.download_command(conda_link(), to=script_path)
     install_cmd = ['bash', script_path, '-b', '-p', conda_context.conda_prefix]
     package_targets = [

lib/galaxy/tool_util/locations/__init__.py

@@ -1,4 +1,3 @@
-import os
 import tempfile
 from abc import (
     ABCMeta,
@@ -20,6 +19,5 @@ class ToolLocationResolver(metaclass=ABCMeta):
 
     def _temp_path(self, uri_like):
         """Create an abstraction for this so we can configure and cache later."""
-        handle, filename = tempfile.mkstemp(suffix=uri_like.split("/")[-1])
-        os.close(handle)
-        return filename
+        with tempfile.NamedTemporaryFile(suffix=uri_like.split("/")[-1], delete=False) as temp:
+            return temp.name

lib/galaxy/tool_util/verify/__init__.py

@@ -176,27 +176,25 @@ def verify(
 def make_temp_fname(fname=None):
     """Safe temp name - preserve the file extension for tools that interpret it."""
     suffix = os.path.split(fname)[-1]  # ignore full path
-    fd, temp_prefix = tempfile.mkstemp(prefix='tmp', suffix=suffix)
-    os.close(fd)
-    return temp_prefix
+    with tempfile.NamedTemporaryFile(prefix='tmp', suffix=suffix, delete=False) as temp:
+        return temp.name
 
 
 def _bam_to_sam(local_name, temp_name):
     temp_local = tempfile.NamedTemporaryFile(suffix='.sam', prefix='local_bam_converted_to_sam_')
-    fd, temp_temp = tempfile.mkstemp(suffix='.sam', prefix='history_bam_converted_to_sam_')
-    os.close(fd)
-    try:
-        pysam.view('-h', '-o%s' % temp_local.name, local_name)
-    except Exception as e:
-        msg = "Converting local (test-data) BAM to SAM failed: %s" % unicodify(e)
-        raise Exception(msg)
-    try:
-        pysam.view('-h', '-o%s' % temp_temp, temp_name)
-    except Exception as e:
-        msg = "Converting history BAM to SAM failed: %s" % unicodify(e)
-        raise Exception(msg)
+    with tempfile.NamedTemporaryFile(suffix='.sam', prefix='history_bam_converted_to_sam_', delete=False) as temp:
+        try:
+            pysam.view('-h', '-o%s' % temp_local.name, local_name)
+        except Exception as e:
+            msg = "Converting local (test-data) BAM to SAM failed: %s" % unicodify(e)
+            raise Exception(msg)
+        try:
+            pysam.view('-h', '-o%s' % temp.name, temp_name)
+        except Exception as e:
+            msg = "Converting history BAM to SAM failed: %s" % unicodify(e)
+            raise Exception(msg)
     os.remove(temp_name)
-    return temp_local, temp_temp
+    return temp_local, temp.name
 
 
 def _verify_checksum(data, checksum_type, expected_checksum_value):

lib/galaxy/tools/evaluation.py

@@ -518,8 +518,8 @@ class ToolEvaluator:
                 directory = os.path.join(self.local_working_directory, "working")
                 config_filename = os.path.join(directory, filename)
             else:
-                fd, config_filename = tempfile.mkstemp(dir=directory)
-                os.close(fd)
+                with tempfile.NamedTemporaryFile(dir=directory, delete=False) as temp:
+                    config_filename = temp.name
             self.__write_workdir_file(config_filename, config_text, param_dict, is_template=is_template)
             self.__register_extra_file(name, config_filename)
             config_filenames.append(config_filename)
@@ -542,8 +542,8 @@ class ToolEvaluator:
                 is_template = False
             else:
                 is_template = True
-            fd, config_filename = tempfile.mkstemp(dir=directory)
-            os.close(fd)
+            with tempfile.NamedTemporaryFile(dir=directory, delete=False) as temp:
+                config_filename = temp.name
             self.__write_workdir_file(config_filename, environment_variable_template, param_dict, is_template=is_template, strip=environment_variable_def.get("strip", False))
             config_file_basename = os.path.basename(config_filename)
             # environment setup in job file template happens before `cd $working_directory`
@@ -571,17 +571,15 @@ class ToolEvaluator:
         directory = self.local_working_directory
         command = self.tool.command
         if self.tool.profile < 16.04 and command and "$param_file" in command:
-            fd, param_filename = tempfile.mkstemp(dir=directory)
-            os.close(fd)
-            with open(param_filename, "w") as f:
+            with tempfile.NamedTemporaryFile(mode='w', dir=directory, delete=False) as param:
                 for key, value in param_dict.items():
                     # parameters can be strings or lists of strings, coerce to list
                     if not isinstance(value, list):
                         value = [value]
                     for elem in value:
-                        f.write(f'{key}={elem}\n')
-            self.__register_extra_file('param_file', param_filename)
-            return param_filename
+                        param.write(f'{key}={elem}\n')
+            self.__register_extra_file('param_file', param.name)
+            return param.name
         else:
             return None
 

lib/galaxy/visualization/data_providers/genome.py

@@ -8,11 +8,9 @@ import os
 import random
 import re
 import sys
-import tempfile
 from contextlib import contextmanager
 from json import loads
 
-import packaging.version
 import pysam
 from bx.bbi.bigbed_file import BigBedFile
 from bx.bbi.bigwig_file import BigWigFile
@@ -30,7 +28,6 @@ from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and
 # pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
 # Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
 pysam.set_verbosity(0)
-PYSAM_INDEX_SYMLINK_NECESSARY = packaging.version.parse(pysam.__version__) <= packaging.version.parse('0.13.0')
 
 
 def float_nan(n):
@@ -327,17 +324,9 @@ class TabixDataProvider(GenomeDataProvider, FilterableMixin):
     def open_data_file(self):
         # We create a symlink to the index file. This is
         # required until https://github.com/pysam-developers/pysam/pull/586 is merged.
-        if PYSAM_INDEX_SYMLINK_NECESSARY:
-            fd, index_path = tempfile.mkstemp(suffix='.tbi')
-            os.close(fd)
-            os.unlink(index_path)
-            os.symlink(self.converted_dataset.file_name, index_path)
-        else:
-            index_path = self.converted_dataset.file_name
+        index_path = self.converted_dataset.file_name
         with pysam.TabixFile(self.dependencies['bgzip'].file_name, index=index_path) as f:
             yield f
-        if PYSAM_INDEX_SYMLINK_NECESSARY:
-            os.unlink(index_path)
 
     def get_iterator(self, data_file, chrom, start, end, **kwargs):
         # chrom must be a string, start/end integers.

lib/tool_shed/util/commit_util.py

@@ -130,24 +130,23 @@ def get_upload_point(repository, **kwd):
 
 
 def handle_bz2(repository, uploaded_file_name):
-    fd, uncompressed = tempfile.mkstemp(prefix='repo_%d_upload_bunzip2_' % repository.id,
-                                        dir=os.path.dirname(uploaded_file_name),
-                                        text=False)
-    bzipped_file = bz2.BZ2File(uploaded_file_name, 'rb')
-    while 1:
-        try:
-            chunk = bzipped_file.read(basic_util.CHUNK_SIZE)
-        except OSError:
-            os.close(fd)
-            os.remove(uncompressed)
-            log.exception('Problem uncompressing bz2 data "%s"', uploaded_file_name)
-            return
-        if not chunk:
-            break
-        os.write(fd, chunk)
-    os.close(fd)
-    bzipped_file.close()
-    shutil.move(uncompressed, uploaded_file_name)
+    with tempfile.NamedTemporaryFile(
+        mode='wb',
+        prefix=f'repo_{repository.id}_upload_bunzip2_',
+        dir=os.path.dirname(uploaded_file_name),
+        delete=False,
+    ) as uncompressed, bz2.BZ2File(uploaded_file_name, 'rb') as bzipped_file:
+        while 1:
+            try:
+                chunk = bzipped_file.read(basic_util.CHUNK_SIZE)
+            except OSError:
+                os.remove(uncompressed.name)
+                log.exception(f'Problem uncompressing bz2 data "{uploaded_file_name}"')
+                return
+            if not chunk:
+                break
+            uncompressed.write(chunk)
+    shutil.move(uncompressed.name, uploaded_file_name)
 
 
 def handle_directory_changes(app, host, username, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar,
@@ -230,24 +229,23 @@ def handle_directory_changes(app, host, username, repository, full_path, filenam
 
 
 def handle_gzip(repository, uploaded_file_name):
-    fd, uncompressed = tempfile.mkstemp(prefix='repo_%d_upload_gunzip_' % repository.id,
-                                        dir=os.path.dirname(uploaded_file_name),
-                                        text=False)
-    gzipped_file = gzip.GzipFile(uploaded_file_name, 'rb')
-    while 1:
-        try:
-            chunk = gzipped_file.read(basic_util.CHUNK_SIZE)
-        except OSError:
-            os.close(fd)
-            os.remove(uncompressed)
-            log.exception('Problem uncompressing gz data "%s"', uploaded_file_name)
-            return
-        if not chunk:
-            break
-        os.write(fd, chunk)
-    os.close(fd)
-    gzipped_file.close()
-    shutil.move(uncompressed, uploaded_file_name)
+    with tempfile.NamedTemporaryFile(
+        mode='wb',
+        prefix=f'repo_{repository.id}_upload_gunzip_',
+        dir=os.path.dirname(uploaded_file_name),
+        delete=False
+    ) as uncompressed, gzip.GzipFile(uploaded_file_name, 'rb') as gzipped_file:
+        while 1:
+            try:
+                chunk = gzipped_file.read(basic_util.CHUNK_SIZE)
+            except OSError:
+                os.remove(uncompressed.name)
+                log.exception(f'Problem uncompressing gz data "{uploaded_file_name}"')
+                return
+            if not chunk:
+                break
+            uncompressed.write(chunk)
+    shutil.move(uncompressed.name, uploaded_file_name)
 
 
 def uncompress(repository, uploaded_file_name, uploaded_file_filename, isgzip=False, isbz2=False):

lib/tool_shed/webapp/controllers/upload.py

@@ -79,13 +79,12 @@ class UploadController(BaseUIController):
                     status = 'error'
                     uploaded_file = None
                 if valid_url:
-                    fd, uploaded_file_name = tempfile.mkstemp()
-                    os.close(fd)
-                    uploaded_file = open(uploaded_file_name, 'wb')
-                    for chunk in stream.iter_content(chunk_size=util.CHUNK_SIZE):
-                        if chunk:
-                            uploaded_file.write(chunk)
-                    uploaded_file.flush()
+                    with tempfile.NamedTemporaryFile(mode='wb', delete=False) as uploaded_file:
+                        uploaded_file_name = uploaded_file.name
+                        for chunk in stream.iter_content(chunk_size=util.CHUNK_SIZE):
+                            if chunk:
+                                uploaded_file.write(chunk)
+                        uploaded_file.flush()
                     uploaded_file_filename = url.split('/')[-1]
                     isempty = os.path.getsize(os.path.abspath(uploaded_file_name)) == 0
             elif file_data not in ('', None):

test/functional/tools/directory_uri_copy_to.py

@@ -28,10 +28,9 @@ def main(argv=None):
         target_uri = directory_uri + "/helloworld"
     file_source_path = file_sources.get_file_source_path(target_uri)
     file_source = file_source_path.file_source
-    fd, temp_name = tempfile.mkstemp()
-    with open(fd, 'w') as f:
+    with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
         f.write('hello world!\n')
-    file_source.write_from(file_source_path.path, temp_name)
+    file_source.write_from(file_source_path.path, f.name)
 
 
 def _parser():

test/integration/test_work_queue_put_failure.py

@@ -26,10 +26,9 @@ class WorkQueuePutFailureTestCase(integration_util.IntegrationTestCase):
     @classmethod
     def handle_galaxy_config_kwds(cls, config, ):
         # config["jobs_directory"] = cls.jobs_directory
-        fd, path = tempfile.mkstemp(suffix='job_conf.yml')
-        with open(path, 'w') as job_conf:
+        with tempfile.NamedTemporaryFile(mode='w', suffix='job_conf.yml', delete=False) as job_conf:
             job_conf.write(job_conf_yaml)
-        config["job_config_file"] = path
+        config["job_config_file"] = job_conf.name
         # Disable tool dependency resolution.
         config["tool_dependency_dir"] = "none"
 

test/integration/test_workflow_handler_configuration.py

@@ -81,13 +81,11 @@ steps:
 
 
 def config_file(template, assign_with=''):
-    fd, path = tempfile.mkstemp(suffix=".xml", prefix="workflow_handler_config_")
-    os.close(fd)
-    with open(path, 'w') as config:
+    with tempfile.NamedTemporaryFile(mode='w', suffix=".xml", prefix="workflow_handler_config_", delete=False) as config:
         if assign_with:
             assign_with = f'assign_with="{assign_with}"'
         config.write(template.substitute(assign_with=assign_with))
-    return path
+    return config.name
 
 
 class BaseWorkflowHandlerConfigurationTestCase(integration_util.IntegrationTestCase):

test/unit/data/datatypes/util.py

@@ -24,14 +24,10 @@ def get_dataset(filename, index_attr='bam_index', dataset_id=1, has_data=True):
 
 @contextmanager
 def get_tmp_path(should_exist=False, suffix=''):
-    _, path = tempfile.mkstemp(suffix=suffix)
-    if not should_exist:
-        os.remove(path)
-    yield path
-    try:
-        os.remove(path)
-    except Exception:
-        pass
+    with tempfile.NamedTemporaryFile(suffix=suffix) as temp:
+        if not should_exist:
+            os.remove(temp.name)
+        yield temp.name
 
 
 @contextmanager

test/unit/files/_util.py

@@ -62,11 +62,9 @@ def user_context_fixture(user_ftp_dir=None):
 
 def assert_realizes_as(file_sources, uri, expected, user_context=None):
     file_source_path = file_sources.get_file_source_path(uri)
-    _, temp_name = tempfile.mkstemp()
-    file_source_path.file_source.realize_to(file_source_path.path, temp_name, user_context=user_context)
-    try:
-        with open(temp_name) as f:
-            realized_contents = f.read()
+    with tempfile.NamedTemporaryFile(mode='r') as temp:
+        file_source_path.file_source.realize_to(file_source_path.path, temp.name, user_context=user_context)
+        realized_contents = temp.read()
         if realized_contents != expected:
             message = "Expected to realize contents at [{}] as [{}], instead found [{}]".format(
                 uri,
@@ -74,14 +72,10 @@ def assert_realizes_as(file_sources, uri, expected, user_context=None):
                 realized_contents,
             )
             raise AssertionError(message)
-    finally:
-        os.remove(temp_name)
-    return temp_name
 
 
 def write_from(file_sources, uri, content, user_context=None):
     file_source_path = file_sources.get_file_source_path(uri)
-    fd, temp_name = tempfile.mkstemp()
-    with open(fd, 'w') as f:
+    with tempfile.NamedTemporaryFile(mode='w') as f:
         f.write(content)
-    file_source_path.file_source.write_from(file_source_path.path, temp_name, user_context=user_context)
+        file_source_path.file_source.write_from(file_source_path.path, f.name, user_context=user_context)

test/unit/queue_worker/conftest.py

@@ -22,10 +22,8 @@ def create_base_test(connection, amqp_type, amqp_connection=None):
 
 @pytest.fixture()
 def sqlite_connection(request):
-    fd, path = tempfile.mkstemp()
-    os.close(fd)
-    request.addfinalizer(lambda: os.remove(path))
-    return 'sqlite:////%s' % path
+    with tempfile.NamedTemporaryFile() as temp:
+        yield f'sqlite:////{temp.name}'
 
 
 @pytest.fixture()

test/unit/test_verify.py

@@ -1,5 +1,4 @@
 import collections
-import os
 import tempfile
 
 import pytest
@@ -24,10 +23,9 @@ TestFile = collections.namedtuple('TestFile', 'value path')
 def test_file_list():
     files = []
     for b, ext in [(F1, '.txt'), (F2, '.txt'), (F3, '.pdf'), (F4, '.txt'), (MULTILINE_MATCH, '.txt')]:
-        fd, path = tempfile.mkstemp(suffix=ext)
-        with os.fdopen(fd, 'wb') as out:
+        with tempfile.NamedTemporaryFile(mode='wb', suffix=ext, delete=False) as out:
             out.write(b)
-        files.append(TestFile(b, path))
+        files.append(TestFile(b, out.name))
     return files
 
 

test/unit/tools/test_history_imp_exp.py

@@ -1,11 +1,8 @@
 import json
 import os
 import tarfile
+import tempfile
 from shutil import rmtree
-from tempfile import (
-    mkdtemp,
-    mkstemp,
-)
 
 from galaxy import model
 from galaxy.exceptions import MalformedContents
@@ -53,31 +50,32 @@ def _mock_app(store_by="id"):
 def _run_jihaw_cleanup_check_secure(history_archive, msg):
     malformed = False
     try:
-        app, _ = _run_jihaw_cleanup(history_archive.arc_directory)
+        _run_jihaw_cleanup(history_archive.arc_directory)
     except MalformedContents:
         malformed = True
     assert malformed
 
 
 def test_create_archive():
-    tempdir = mkdtemp()
-    _, out_file = mkstemp()
-    dataset = os.path.join(tempdir, 'datasets/Pasted_Entry_1.txt')
-    history_attrs_file = os.path.join(tempdir, 'history_attrs.txt')
-    datasets_attrs_file = os.path.join(tempdir, 'datasets_attrs.txt')
-    jobs_attrs_file = os.path.join(tempdir, 'jobs_attrs.txt')
-    os.makedirs(os.path.join(tempdir, 'datasets'))
-    with open(dataset, 'w') as out:
-        out.write('Hello\n')
-    with open(history_attrs_file, 'w') as out:
-        out.write(HISTORY_ATTRS)
-    with open(datasets_attrs_file, 'w') as out:
-        out.write(DATASETS_ATTRS_EXPORT.format(file_name=dataset))
-    with open(jobs_attrs_file, 'w') as out:
-        out.write(JOBS_ATTRS)
-    create_archive(tempdir, out_file, gzip=True)
-    with tarfile.open(out_file) as t:
-        assert sorted(t.getnames()) == sorted(['datasets', 'datasets/Pasted_Entry_1.txt', 'history_attrs.txt', 'datasets_attrs.txt', 'jobs_attrs.txt']), t.getnames()
+    tempdir = tempfile.mkdtemp()
+    with tempfile.NamedTemporaryFile() as temp:
+        out_file = temp.name
+        dataset = os.path.join(tempdir, 'datasets/Pasted_Entry_1.txt')
+        history_attrs_file = os.path.join(tempdir, 'history_attrs.txt')
+        datasets_attrs_file = os.path.join(tempdir, 'datasets_attrs.txt')
+        jobs_attrs_file = os.path.join(tempdir, 'jobs_attrs.txt')
+        os.makedirs(os.path.join(tempdir, 'datasets'))
+        with open(dataset, 'w') as out:
+            out.write('Hello\n')
+        with open(history_attrs_file, 'w') as out:
+            out.write(HISTORY_ATTRS)
+        with open(datasets_attrs_file, 'w') as out:
+            out.write(DATASETS_ATTRS_EXPORT.format(file_name=dataset))
+        with open(jobs_attrs_file, 'w') as out:
+            out.write(JOBS_ATTRS)
+        create_archive(tempdir, out_file, gzip=True)
+        with tarfile.open(out_file) as t:
+            assert sorted(t.getnames()) == sorted(['datasets', 'datasets/Pasted_Entry_1.txt', 'history_attrs.txt', 'datasets_attrs.txt', 'jobs_attrs.txt']), t.getnames()
 
 
 def test_history_import_symlink():
@@ -620,7 +618,7 @@ def _setup_history_for_export(history_name):
 
 def _import_export(app, h, dest_export=None):
     if dest_export is None:
-        dest_parent = mkdtemp()
+        dest_parent = tempfile.mkdtemp()
         dest_export = os.path.join(dest_parent, "moo.tgz")
 
     dataset = model.Dataset(id=100)
@@ -681,7 +679,7 @@ def test_import_1901_default():
 
 
 def import_archive(archive_path, app=None):
-    dest_parent = mkdtemp()
+    dest_parent = tempfile.mkdtemp()
     dest_dir = os.path.join(dest_parent, 'dest')
 
     options = Dummy()
@@ -715,7 +713,7 @@ def test_history_import_relpath_in_archive():
     """ Ensure that a history import archive cannot reference a relative path
     outside the archive
     """
-    dest_parent = mkdtemp()
+    dest_parent = tempfile.mkdtemp()
     with HistoryArchive(arcname_prefix='../insecure') as history_archive:
 
         history_archive.write_metafiles()
@@ -728,7 +726,7 @@ def test_history_import_abspath_in_archive():
     """ Ensure that a history import archive cannot reference a absolute path
     outside the archive
     """
-    dest_parent = mkdtemp()
+    dest_parent = tempfile.mkdtemp()
     arcname_prefix = os.path.abspath(os.path.join(dest_parent, 'insecure'))
 
     with HistoryArchive(arcname_prefix=arcname_prefix) as history_archive:
@@ -740,7 +738,7 @@ def test_history_import_abspath_in_archive():
 
 class HistoryArchive:
     def __init__(self, arcname_prefix=None):
-        self.temp_directory = mkdtemp()
+        self.temp_directory = tempfile.mkdtemp()
         self.arc_directory = os.path.join(self.temp_directory, 'archive')
         self.arcname_prefix = arcname_prefix
         self.tar_file_path = os.path.join(self.temp_directory, 'archive.tar.gz')

test/unit/util/test_utils.py

@@ -1,5 +1,4 @@
 import errno
-import os
 import tempfile
 
 import pytest
@@ -76,9 +75,8 @@ def test_xml_to_string_pretty():
 
 
 def test_parse_xml_enoent():
-    fd, path = tempfile.mkstemp()
-    os.close(fd)
-    os.remove(path)
+    with tempfile.NamedTemporaryFile() as temp:
+        path = temp.name
     with pytest.raises(IOError) as excinfo:
         util.parse_xml(path)
     assert excinfo.value.errno == errno.ENOENT

tools/extract/liftOver_wrapper.py

@@ -25,14 +25,12 @@ def safe_bed_file(infile):
     https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html
     """
     fix_pat = re.compile("^(track|browser)")
-    fd, fname = tempfile.mkstemp()
-    os.close(fd)
-    with open(infile) as in_handle, open(fname, 'w') as out_handle:
+    with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'w') as in_handle:
         for line in in_handle:
             if fix_pat.match(line):
                 line = "#" + line
             out_handle.write(line)
-    return fname
+    return out_handle.name
 
 
 if len(sys.argv) < 9: