Unverified Commit c85db3fd authored by E Rasche's avatar E Rasche
Browse files

Some more command refactoring

parent 73337725

lib/galaxy/datatypes/binary.py

+15 −22
Original line number Diff line number Diff line
@@ -253,18 +253,17 @@ class Bam(Binary): 
            raise Exception(message)



        # Get the version of samtools via --version-only, if available

        p = subprocess.Popen(['samtools', '--version-only'],

                             stdout=subprocess.PIPE,

                             stderr=subprocess.PIPE)

        output, error = p.communicate()



        try:

            output = subprocess.check_output(['samtools', '--version-only'])

            # --version-only is available

            # Format is <version x.y.z>+htslib-<a.b.c>

        if p.returncode == 0:

            version = output.split('+')[0]

            return version

        except subprocess.CalledProcessError:

            # --version-only not available

            pass



        output = subprocess.Popen(['samtools'], stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()[1]

        output = subprocess.check_output(['samtools'])

        lines = output.split('\n')

        for line in lines:

            if line.lower().startswith('version'):
@@ -294,10 +293,8 @@ class Bam(Binary): 


    def _is_coordinate_sorted(self, file_name):

        """See if the input BAM file is sorted from the header information."""

        params = ["samtools", "view", "-H", file_name]

        output = subprocess.Popen(params, stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()[0]

        # find returns -1 if string is not found

        return output.find("SO:coordinate") != -1 or output.find("SO:sorted") != -1

        output = subprocess.check_output(["samtools", "view", "-H", file_name])

        return 'SO:coordinate' in output or 'SO:sorted' in output



    def dataset_content_needs_grooming(self, file_name):

        """See if file_name is a sorted BAM file"""
@@ -322,8 +319,7 @@ class Bam(Binary): 
                return False

            index_name = tempfile.NamedTemporaryFile(prefix="bam_index").name

            stderr_name = tempfile.NamedTemporaryFile(prefix="bam_index_stderr").name

            command = 'samtools index %s %s' % (file_name, index_name)

            proc = subprocess.Popen(args=command, shell=True, stderr=open(stderr_name, 'wb'))

            proc = subprocess.Popen(['samtools', 'index', file_name, index_name], stderr=open(stderr_name, 'wb'))

            proc.wait()

            stderr = open(stderr_name).read().strip()

            if stderr:
@@ -366,8 +362,8 @@ class Bam(Binary): 
        tmp_sorted_dataset_file_name_prefix = os.path.join(tmp_dir, 'sorted')

        stderr_name = tempfile.NamedTemporaryFile(dir=tmp_dir, prefix="bam_sort_stderr").name

        samtools_created_sorted_file_name = "%s.bam" % tmp_sorted_dataset_file_name_prefix  # samtools accepts a prefix, not a filename, it always adds .bam to the prefix

        command = "samtools sort %s %s" % (file_name, tmp_sorted_dataset_file_name_prefix)

        proc = subprocess.Popen(args=command, shell=True, cwd=tmp_dir, stderr=open(stderr_name, 'wb'))

        proc = subprocess.Popen(['samtools', 'sort', file_name, tmp_sorted_dataset_file_name_prefix],

                                cwd=tmp_dir, stderr=open(stderr_name, 'wb'))

        exit_code = proc.wait()

        # Did sort succeed?

        stderr = open(stderr_name).read().strip()
@@ -1309,11 +1305,8 @@ class ExcelXls(Binary): 
    edam_format = "format_3468"



    def sniff(self, filename):

        mime_type = subprocess.check_output("file --mime-type '{}'".format(filename), shell=True).rstrip()

        if mime_type.find("application/vnd.ms-excel") != -1:

            return True

        else:

            return False

        mime_type = subprocess.check_output(['file', '--mime-type', filename]).strip()

        return "application/vnd.ms-excel" in mime_type



    def get_mime(self):

        """Returns the mime type of the datatype"""

lib/galaxy/tools/deps/mulled/mulled_build.py

+5 −10
Original line number Diff line number Diff line
@@ -116,17 +116,12 @@ def get_affected_packages(args): 
    """

    recipes_dir = args.recipes_dir

    hours = args.diff_hours

    cmd = """cd '%s' && git log --diff-filter=ACMRTUXB --name-only --pretty="" --since="%s hours ago" | grep -E '^recipes/.*/meta.yaml' | sort | uniq""" % (recipes_dir, hours)

    pkg_list = check_output(cmd, shell=True)

    ret = list()

    for pkg in pkg_list.strip().split('\n'):

    cmd = ['git', 'log', '--diff-filter=ACMRTUXB', '--name-only', '--pretty=""', '--since="%s hours ago"' % hours]

    changed_files = subprocess.check_output(cmd, cwd=recipes_dir).strip().split('\n')

    pkg_list = set([x for x in changed_files if x.startswith('recipes/') and x.endswith('meta.yaml')])

    for pkg in pkg_list:

        if pkg and os.path.exists(os.path.join(recipes_dir, pkg)):

            ret.append((get_pkg_name(args, pkg), get_tests(args, pkg)))

    return ret





def check_output(cmd, shell=True):

    return subprocess.check_output(cmd, shell=shell)

            yield (get_pkg_name(args, pkg), get_tests(args, pkg))





def conda_versions(pkg_name, file_name):

lib/galaxy/tools/deps/mulled/mulled_build_channel.py

+1 −2
Original line number Diff line number Diff line
@@ -55,8 +55,7 @@ def _new_versions(quay, conda): 


def run_channel(args, build_last_n_versions=1):

    """Build list of involucro commands (as shell snippet) to run."""

    pkgs = get_affected_packages(args)

    for pkg_name, pkg_tests in pkgs:

    for pkg_name, pkg_tests in get_affected_packages(args):

        repo_data = _fetch_repo_data(args)

        c = conda_versions(pkg_name, repo_data)

        # only package the most recent N versions