Mercurial > repos > iuc > idr_download_by_ids
changeset 6:5c743356df83 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bf331f8e60e7bc1daf1cd71d2068062d925e7ffa"
| author | iuc |
|---|---|
| date | Mon, 06 Jul 2020 19:33:59 -0400 |
| parents | e08b1dc0480c |
| children | f067504aa92a |
| files | idr_download_by_ids.py idr_download_by_ids.xml |
| diffstat | 2 files changed, 33 insertions(+), 42 deletions(-) [+] |
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--- a/idr_download_by_ids.py Mon Jun 08 08:36:41 2020 -0400 +++ b/idr_download_by_ids.py Mon Jul 06 19:33:59 2020 -0400 @@ -2,11 +2,10 @@ import os import sys import tarfile -import time -from tempfile import TemporaryFile +from contextlib import ExitStack +from tempfile import TemporaryDirectory from libtiff import TIFF -from PIL import Image from omero.gateway import BlitzGateway # noqa from omero.constants.namespaces import NSBULKANNOTATIONS # noqa @@ -129,17 +128,25 @@ .format(region_spec) ) - # connect to idr - conn = BlitzGateway('public', 'public', - host='idr.openmicroscopy.org', - secure=True) - conn.connect() + with ExitStack() as exit_stack: + # connect to idr + conn = exit_stack.enter_context( + BlitzGateway( + 'public', 'public', + host='idr.openmicroscopy.org', + secure=True + ) + ) + # exit_stack.callback(conn.connect().close) + if download_tar: + # create an archive file to write images to + archive = exit_stack.enter_context( + tarfile.open('images.tar', mode='w') + ) + tempdir = exit_stack.enter_context( + TemporaryDirectory() + ) - if download_tar: - # create an archive file to write images to - archive = tarfile.open('images.tar', mode='w') - - try: for image_id in image_ids: image_warning_id = 'Image-ID: {0}'.format(image_id) try: @@ -271,26 +278,17 @@ im_array = get_image_array(image, tile, z_stack, channel_index, frame) - # pack images into tarball if download_tar: - tar_img = Image.fromarray(im_array) - # Use TemporaryFile() for intermediate storage of images. - # TO DO: could this be improved by using - # SpooledTemporaryFile with a suitable max_size? - with TemporaryFile() as buf: - tar_img.save(buf, format='TIFF') - tarinfo = tarfile.TarInfo(name=fname) - buf.seek(0, 2) - tarinfo.size = buf.tell() - tarinfo.mtime = time.time() - buf.seek(0) - archive.addfile(tarinfo=tarinfo, fileobj=buf) - else: # save image as individual file - try: - tiff = TIFF.open(fname, mode='w') - tiff.write_image(im_array) - finally: - tiff.close() + fname = os.path.join(tempdir, fname) + try: + tiff = TIFF.open(fname, mode='w') + tiff.write_image(im_array) + finally: + tiff.close() + # move image into tarball + if download_tar: + archive.add(fname, os.path.basename(fname)) + os.remove(fname) except Exception as e: if skip_failed: # respect skip_failed on unexpected errors @@ -299,13 +297,6 @@ else: raise - finally: - # close the archive file,if it is created - if download_tar: - archive.close() - # Close the connection - conn.close() - def _center_to_ul(center_x, center_y, width, height): if width > 0:
--- a/idr_download_by_ids.xml Mon Jun 08 08:36:41 2020 -0400 +++ b/idr_download_by_ids.xml Mon Jul 06 19:33:59 2020 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idr_download_by_ids" name="IDR Download" version="0.41" profile="18.09"> +<tool id="idr_download_by_ids" name="IDR Download" version="0.42" profile="18.09"> <description>- download images from the Image Data Resource using image IDs</description> <macros> <xml name="region_spec" token_pos="upper-left corner"> @@ -235,10 +235,10 @@ <assert_contents> <has_size value="1382400" /> <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" > - <has_size value="685884" /> + <has_size value="685896" /> </has_archive_member> <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" > - <has_size value="685884" /> + <has_size value="685896" /> </has_archive_member> </assert_contents> </output>