Mercurial > repos > iuc > idr_download_by_ids
changeset 10:4aed70472589 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
| author | iuc |
|---|---|
| date | Wed, 24 Nov 2021 21:01:02 +0000 |
| parents | 80af973c5277 |
| children | cbd605a24336 |
| files | idr_download_by_ids.py idr_download_by_ids.xml |
| diffstat | 2 files changed, 97 insertions(+), 15 deletions(-) [+] |
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--- a/idr_download_by_ids.py Fri Feb 26 20:12:11 2021 +0000 +++ b/idr_download_by_ids.py Wed Nov 24 21:01:02 2021 +0000 @@ -110,7 +110,7 @@ def download_image_data( - image_ids, + image_ids_or_dataset_id, dataset=False, channel=None, z_stack=0, frame=0, coord=(0, 0), width=0, height=0, region_spec='rectangle', skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None @@ -129,14 +129,6 @@ omero_username = 'public' omero_password = 'public' - # basic argument sanity checks and adjustments - prefix = 'image-' - # normalize image ids by stripping off prefix if it exists - image_ids = [ - iid[len(prefix):] if iid[:len(prefix)] == prefix else iid - for iid in image_ids - ] - if region_spec not in ['rectangle', 'center']: raise ValueError( 'Got unknown value "{0}" as region_spec argument' @@ -160,6 +152,47 @@ TemporaryDirectory() ) + if dataset: + dataset_warning_id = 'Dataset-ID: {0}'.format(image_ids_or_dataset_id[0]) + try: + dataset_id = int(image_ids_or_dataset_id[0]) + except ValueError: + image_ids = None + else: + try: + dataset = conn.getObject("Dataset", dataset_id) + except Exception as e: + # respect skip_failed on unexpected errors + if skip_failed: + warn(str(e), dataset_warning_id, warn_skip=True) + else: + raise + else: + image_ids = [image.id for image in dataset.listChildren()] + + if image_ids is None: + if skip_failed: + warn( + 'Unable to find a dataset with this ID in the ' + 'database.', + dataset_warning_id, + warn_skip=True + ) + else: + raise ValueError( + '{0}: Unable to find a dataset with this ID in the ' + 'database. Aborting!' + .format(dataset_warning_id) + ) + + else: + # basic argument sanity checks and adjustments + prefix = 'image-' + # normalize image ids by stripping off prefix if it exists + image_ids = [ + iid[len(prefix):] if iid[:len(prefix)] == prefix else iid + for iid in image_ids_or_dataset_id + ] for image_id in image_ids: image_warning_id = 'Image-ID: {0}'.format(image_id) try: @@ -330,8 +363,9 @@ if __name__ == "__main__": p = argparse.ArgumentParser() p.add_argument( - 'image_ids', nargs='*', default=[], - help='one or more IDR image ids for which to retrieve data (default: ' + 'image_ids_or_dataset_id', nargs='*', default=[], + help='one or more IDR image ids or a single dataset id' + 'for which to retrieve data (default: ' 'read ids from stdin).' ) p.add_argument( @@ -378,9 +412,14 @@ p.add_argument( '-cf', '--config-file', dest='config_file', default=None ) + p.add_argument( + '--dataset', action='store_true' + ) args = p.parse_args() - if not args.image_ids: - args.image_ids = sys.stdin.read().split() + if not args.image_ids_or_dataset_id: + args.image_ids_or_dataset_id = sys.stdin.read().split() + if args.dataset and len(args.image_ids_or_dataset_id) > 1: + warn("Multiple dataset ids provided. Only the first one will be used.") if 'center' in args: args.coord, args.width, args.height = ( args.center[:2], args.center[2], args.center[3]
--- a/idr_download_by_ids.xml Fri Feb 26 20:12:11 2021 +0000 +++ b/idr_download_by_ids.xml Wed Nov 24 21:01:02 2021 +0000 @@ -16,7 +16,7 @@ </xml> </macros> <requirements> - <requirement type="package" version="5.7.1">python-omero</requirement> + <requirement type="package" version="5.10.1">omero-py</requirement> <requirement type="package" version="0.4.2">pylibtiff</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -37,10 +37,15 @@ #if str($image_ids.source) == 'link': python -c 'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\n"))' ## https://idr.openmicroscopy.org/webclient/?show=image-3426274|image-3426275|image-3426276|image-3426277 + #elif str($image_ids.source) == 'dataset': + cat '${image_ids.id_spec}' #else: - cat '${image_ids.id_spec}' + echo '${image_ids.id_dataset_omero}' #end if | python '$__tool_directory__/idr_download_by_ids.py' + #if str($image_ids.source) == 'omeroDatasetID': + --dataset + #end if #set $channel = str($channel).strip() #if $channel: -c '$channel' @@ -100,6 +105,7 @@ <param name="source" type="select" label="How would you like to specify the IDs of images to download?"> <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option> <option value="dataset">As a dataset (one image ID per line)</option> + <option value="omeroDatasetID">All images from a single Dataset ID</option> </param> <when value="link"> <param name="id_spec" type="text" @@ -114,6 +120,9 @@ <param name="id_spec" type="data" format="txt" label="Select a dataset with image IDs (one per line)" /> </when> + <when value="omeroDatasetID"> + <param name="id_dataset_omero" type="integer" min = "0" value = "9059" label="Dataset ID"/> + </when> </conditional> <param name="channel" type="text" label="Name of the channel to download" @@ -362,6 +371,37 @@ <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" /> </assert_stderr > </test> + <test> + <conditional name="omero_instance_type"> + <param name="omero_instance" value="idr" /> + </conditional> + <!-- Test for download all images from a dataset --> + <param name="source" value="omeroDatasetID" /> + <param name="id_dataset_omero" value="9059" /> + <param name="download_tar" value="false" /> + <output_collection name="output_file" type="list" count="4"> + <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> + <assert_contents> + <has_size value="2097286" /> + </assert_contents> + </element> + <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024"> + <assert_contents> + <has_size value="2097286" /> + </assert_contents> + </element> + <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024"> + <assert_contents> + <has_size value="2097286" /> + </assert_contents> + </element> + <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024"> + <assert_contents> + <has_size value="2097286" /> + </assert_contents> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ Download image data from the IDR_ (Image Data Resource) - a public repository @@ -391,6 +431,9 @@ input field (comma or '|'-separated ), or as an input file (each ID on a separate line). +Finally, if you want to download all images of a single dataset. Specify the id as +All images from a single Dataset ID. + Most images in the IDR have more than two dimensions. Thus, there are parameters available which allow you to select a particular recording channel, z-plane or time frame to download.