diff imagej2_base_utils.py @ 0:ab54024c0a88 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_base_utils.py	Tue Sep 17 17:02:18 2019 -0400
@@ -0,0 +1,169 @@
+import os
+import shutil
+import sys
+import tempfile
+
+BUFF_SIZE = 1048576
+
+
+def cleanup_before_exit(tmp_dir):
+    """
+    Remove temporary files and directories prior to tool exit.
+    """
+    if tmp_dir and os.path.exists(tmp_dir):
+        shutil.rmtree(tmp_dir)
+
+
+def get_base_cmd_bunwarpj(jvm_memory):
+    if jvm_memory in [None, 'None']:
+        jvm_memory_str = ''
+    else:
+        jvm_memory_str = '-Xmx%s' % jvm_memory
+    # The following bunwarpj_base_cmd string will look something like this:
+    # "java %s -cp $JAR_DIR/ij-1.49k.jar:$PLUGINS_DIR/bUnwarpJ_-2.6.1.jar \
+    # bunwarpj.bUnwarpJ_" % (jvm_memory_str)
+    # See the bunwarpj.sh script for the fiji 20151222
+    # bioconda recipe in github.
+    bunwarpj_base_cmd = "bunwarpj %s" % jvm_memory_str
+    return bunwarpj_base_cmd
+
+
+def get_base_command_imagej2(memory_size=None, macro=None, jython_script=None):
+    imagej2_executable = get_imagej2_executable()
+    if imagej2_executable is None:
+        return None
+    cmd = '%s --ij2 --headless --debug' % imagej2_executable
+    if memory_size is not None:
+        memory_size_cmd = ' -DXms=%s -DXmx=%s' % (memory_size, memory_size)
+        cmd += memory_size_cmd
+    if macro is not None:
+        cmd += ' --macro %s' % os.path.abspath(macro)
+    if jython_script is not None:
+        cmd += ' --jython %s' % os.path.abspath(jython_script)
+    return cmd
+
+
+def get_file_extension(image_format):
+    """
+    Return a valid bioformats file extension based on the received
+    value of image_format(e.g., "gif" is returned as ".gif".
+    """
+    return '.%s' % image_format
+
+
+def get_file_name_without_extension(file_path):
+    """
+    Eliminate the .ext from the received file name, assuming that
+    the file name consists of only a single '.'.
+    """
+    if os.path.exists(file_path):
+        path, name = os.path.split(file_path)
+        name_items = name.split('.')
+        return name_items[0]
+    return None
+
+
+def get_imagej2_executable():
+    """
+    Fiji names the ImageJ executable different names for different
+    architectures, but our bioconda recipe allows us to do this.
+    """
+    return 'ImageJ'
+
+
+def get_input_image_path(tmp_dir, input_file, image_format):
+    """
+    Bioformats uses file extensions (e.g., .job, .gif, etc)
+    when reading and writing image files, so the Galaxy dataset
+    naming convention of setting all file extensions as .dat
+    must be handled.
+    """
+    image_path = get_temporary_image_path(tmp_dir, image_format)
+    # Remove the file so we can create a symlink.
+    os.remove(image_path)
+    os.symlink(input_file, image_path)
+    return image_path
+
+
+def get_platform_info_dict():
+    '''Return a dict with information about the current platform.'''
+    platform_dict = {}
+    sysname, nodename, release, version, machine = os.uname()
+    platform_dict['os'] = sysname.lower()
+    platform_dict['architecture'] = machine.lower()
+    return platform_dict
+
+
+def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
+    tmp_stderr.close()
+    """
+    Return a stderr string of reasonable size.
+    """
+    # Get stderr, allowing for case where it's very large.
+    tmp_stderr = open(tmp_err, 'rb')
+    stderr_str = ''
+    buffsize = BUFF_SIZE
+    try:
+        while True:
+            stderr_str += tmp_stderr.read(buffsize)
+            if not stderr_str or len(stderr_str) % buffsize != 0:
+                break
+    except OverflowError:
+        pass
+    tmp_stderr.close()
+    if include_stdout:
+        tmp_stdout = open(tmp_out, 'rb')
+        stdout_str = ''
+        buffsize = BUFF_SIZE
+        try:
+            while True:
+                stdout_str += tmp_stdout.read(buffsize)
+                if not stdout_str or len(stdout_str) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+    tmp_stdout.close()
+    if include_stdout:
+        return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str)
+    return stderr_str
+
+
+def get_temp_dir(prefix='tmp-imagej-', dir=None):
+    """
+    Return a temporary directory.
+    """
+    return tempfile.mkdtemp(prefix=prefix, dir=dir)
+
+
+def get_tempfilename(dir=None, suffix=None):
+    """
+    Return a temporary file name.
+    """
+    fd, name = tempfile.mkstemp(suffix=suffix, dir=dir)
+    os.close(fd)
+    return name
+
+
+def get_temporary_image_path(tmp_dir, image_format):
+    """
+    Return the path to a temporary file with a valid image format
+    file extension that can be used with bioformats.
+    """
+    file_extension = get_file_extension(image_format)
+    return get_tempfilename(tmp_dir, file_extension)
+
+
+def handle_none_type(val, val_type='float'):
+    if val is None:
+        return ' None'
+    else:
+        if val_type == 'float':
+            return ' %.3f' % val
+        elif val_type == 'int':
+            return ' %d' % val
+    return ' %s' % val
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)