| Previous changeset 2:17b1cd0f4812 (2020-04-14) Next changeset 4:11036f6197d6 (2020-05-15) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70" |
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modified:
idr_download_by_ids.py idr_download_by_ids.xml |
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added:
test-data/test_output.log |
| b |
| diff -r 17b1cd0f4812 -r 381f248febba idr_download_by_ids.py --- a/idr_download_by_ids.py Tue Apr 14 10:27:25 2020 -0400 +++ b/idr_download_by_ids.py Wed Apr 22 11:43:18 2020 -0400 |
| [ |
| b'@@ -7,10 +7,22 @@\n from omero.constants.namespaces import NSBULKANNOTATIONS # noqa\n \n \n-def warn(message, image_identifier):\n+def warn(message, image_identifier, warn_skip=False):\n+ message = message.rstrip()\n+ if warn_skip:\n+ if message[-1] in [\'.\', \'!\', \'?\']:\n+ skip_msg = \' Skipping download!\'\n+ else:\n+ skip_msg = \'. Skipping download!\'\n+ else:\n+ skip_msg = \'\'\n print(\n- \'ImageSpecWarning for {0}: {1}\'\n- .format(image_identifier, message),\n+ \'ImageSpecWarning for {0}: {1}{2}\'\n+ .format(\n+ image_identifier,\n+ message,\n+ skip_msg\n+ ),\n file=sys.stderr\n )\n \n@@ -93,6 +105,7 @@\n if fname[-5:] != \'.tiff\':\n fname += \'.tiff\'\n try:\n+ fname = fname.replace(\' \', \'_\')\n tiff = TIFF.open(fname, mode=\'w\')\n tiff.write_image(selection)\n finally:\n@@ -105,6 +118,19 @@\n coord=(0, 0), width=0, height=0, region_spec=\'rectangle\',\n skip_failed=False\n ):\n+ # basic argument sanity checks and adjustments\n+ prefix = \'image-\'\n+ # normalize image ids by stripping off prefix if it exists\n+ image_ids = [\n+ iid[len(prefix):] if iid[:len(prefix)] == prefix else iid\n+ for iid in image_ids\n+ ]\n+\n+ if region_spec not in [\'rectangle\', \'center\']:\n+ raise ValueError(\n+ \'Got unknown value "{0}" as region_spec argument\'\n+ .format(region_spec)\n+ )\n \n # connect to idr\n conn = BlitzGateway(\'public\', \'public\',\n@@ -113,20 +139,30 @@\n conn.connect()\n \n try:\n- prefix = \'image-\'\n for image_id in image_ids:\n- if image_id[:len(prefix)] == prefix:\n- image_id = image_id[len(prefix):]\n- image_id = int(image_id)\n- image = conn.getObject("Image", image_id)\n+ image_warning_id = \'Image-ID: {0}\'.format(image_id)\n+ try:\n+ image_id = int(image_id)\n+ except ValueError:\n+ image = None\n+ else:\n+ try:\n+ image = conn.getObject("Image", image_id)\n+ except Exception as e:\n+ # respect skip_failed on unexpected errors\n+ if skip_failed:\n+ warn(str(e), image_warning_id, warn_skip=True)\n+ continue\n+ else:\n+ raise\n \n if image is None:\n- image_warning_id = \'Image-ID: {0}\'.format(image_id)\n if skip_failed:\n warn(\n \'Unable to find an image with this ID in the \'\n- \'database. Skipping download!\',\n- image_warning_id\n+ \'database.\',\n+ image_warning_id,\n+ warn_skip=True\n )\n continue\n raise ValueError(\n@@ -135,23 +171,39 @@\n .format(image_warning_id)\n )\n \n- image_name = os.path.splitext(image.getName())[0]\n- image_warning_id = \'{0} (ID: {1})\'.format(\n- image_name, image_id\n- )\n+ try:\n+ # try to extract image properties\n+ # if anything goes wrong here skip the image\n+ # or abort.\n+ image_name = os.path.splitext(image.getName())[0]\n+ image_warning_id = \'{0} (ID: {1})\'.format(\n+ image_name, image_id\n+ )\n+\n+ if region_spec == \'rectangle\':\n+ tile = get_clipping_region(image, *coord, width, height)\n+ elif region_spec == \'center\':\n+ tile = get_clipping_region(\n+ image,\n+ *_center_to_ul(*coord, width, height)\n+ )\n \n- if region_spec == \'rectangle\':\n-'..b'_spec argument\'\n- .format(region_spec)\n- )\n+ ori_z, z_stack = z_stack, confine_plane(image, z_stack)\n+ ori_frame, frame = frame, confine_frame(image, frame)\n+ num_channels = image.getSizeC()\n+ if channel is None:\n+ channel_index = 0\n+ else:\n+ channel_index = find_channel_index(image, channel)\n+ except Exception as e:\n+ # respect skip_failed on unexpected errors\n+ if skip_failed:\n+ warn(str(e), image_warning_id, warn_skip=True)\n+ continue\n+ else:\n+ raise\n+\n+ # region sanity checks and warnings\n if tile[2] < width or tile[3] < height:\n # The downloaded image region will have smaller dimensions\n # than the specified width x height.\n@@ -162,7 +214,7 @@\n image_warning_id\n )\n \n- ori_z, z_stack = z_stack, confine_plane(image, z_stack)\n+ # z-stack sanity checks and warnings\n if z_stack != ori_z:\n warn(\n \'Specified image plane ({0}) is out of bounds. Using {1} \'\n@@ -171,7 +223,7 @@\n image_warning_id\n )\n \n- ori_frame, frame = frame, confine_frame(image, frame)\n+ # frame sanity checks and warnings\n if frame != ori_frame:\n warn(\n \'Specified image frame ({0}) is out of bounds. Using \'\n@@ -179,10 +231,9 @@\n .format(ori_frame, frame),\n image_warning_id\n )\n- # Get the channel index. If the index is not valid, skip the image\n+\n+ # channel index sanity checks and warnings\n if channel is None:\n- channel_index = 0\n- num_channels = image.getSizeC()\n if num_channels > 1:\n warn(\n \'No specific channel selected for multi-channel \'\n@@ -191,18 +242,35 @@\n image_warning_id\n )\n else:\n- channel_index = find_channel_index(image, channel)\n- if channel_index == -1 or channel_index >= image.getSizeC():\n- raise ValueError(\n- \'"{0}" is not a known channel name for image {1}\'\n- .format(channel, image.getName())\n- )\n+ if channel_index == -1 or channel_index >= num_channels:\n+ if skip_failed:\n+ warn(\n+ str(channel)\n+ + \' is not a known channel name for this image.\',\n+ image_warning_id,\n+ warn_skip=True\n+ )\n+ continue\n+ else:\n+ raise ValueError(\n+ \'"{0}" is not a known channel name for image {1}. \'\n+ \'Aborting!\'\n+ .format(channel, image_warning_id)\n+ )\n \n # download and save the region as TIFF\n fname = \'__\'.join(\n [image_name, str(image_id)] + [str(x) for x in tile]\n )\n- download_plane_as_tiff(image, tile, z_stack, channel_index, frame, fname)\n+ try:\n+ download_plane_as_tiff(image, tile, z_stack, channel_index, frame, fname)\n+ except Exception as e:\n+ if skip_failed:\n+ # respect skip_failed on unexpected errors\n+ warn(str(e), image_warning_id, warn_skip=True)\n+ continue\n+ else:\n+ raise\n finally:\n # Close the connection\n conn.close()\n' |
| b |
| diff -r 17b1cd0f4812 -r 381f248febba idr_download_by_ids.xml --- a/idr_download_by_ids.xml Tue Apr 14 10:27:25 2020 -0400 +++ b/idr_download_by_ids.xml Wed Apr 22 11:43:18 2020 -0400 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idr_download_by_ids" name="IDR Download" version="0.20" profile="18.09"> +<tool id="idr_download_by_ids" name="IDR Download" version="0.30" 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"> @@ -218,10 +218,13 @@ A set of image IDs as can be obtained from the IDR webclient_ like this: -1. select the images you want to download -2. click on the 'Link' button on the top right of the page and copy the provided - URL -3. paste the URL into the input field of this tool, for example: :: +1. Select the wells you want to download in the thumbnails. + +2. Select at the bottom the images in those wells that you want to download (one well might contain several images). + +3. Click on the 'Link' button on the top right of the page and copy the provided URL. + +4. Paste the URL into the input field of this tool, for example: https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711 |
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| diff -r 17b1cd0f4812 -r 381f248febba test-data/test_output.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output.log Wed Apr 22 11:43:18 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +ImageSpecWarning for Image-ID: 9036708999: Some random error |