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Create a manifest
Upload files in bulk
Modify files in bulk using a manifest
Download files in bulk
Uploading
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Data in
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Bulk
Creating a
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Manifest
Files to be uploaded are specified in a tab separated (.tsv) manifest. The manifest has columns that contain information about each file to be uploaded along with annotations that will be associated with the file in Synapse.
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The path and parent columns are required
The name is only necessary if the displayed name in Synapse should be different than the name of the uploaded file
Used and executed are optional for provenance (but helpful!),
Emotion and species are optional annotations (but also helpful!)
Download the template.
Validate the
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Manifest and
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Upload Files
The format of the manifest file (called filesToUpload.tsv in this example) can be validated prior to upload by using the parameter dryRun in syncToSynapse. The dryRun parameter will not upload the data specified in the manifest file. Instead, the client checks that: the manifest file format is correct, all file paths exist, all files are unique, provenance can be set (optional), and the parent synID exists. The number of files and total upload size is also summarized in the dryRun output. This helps ensure your data upload does not end prematurely due to a typo in the file path or parent synID.
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After validating the manifest, you can now upload the files to Synapse by removing the dryRun parameter. Once the upload is complete, you will receive an email notification. This notification will also show any errors from the upload.
Downloading
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Data in
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Bulk
Files can be downloaded in bulk using the syncFromSynapse function. This function allows you to download all the files in a folder or project along with all the annotations and provenance on those files. A manifest file called SYNAPSE_METADATA_MANIFEST.tsv that contains the metadata will also be added in the path.
Download files in the Python client or command line.
Download files in the R client.
Editing in
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Bulk
You can modify values in the manifest and re-upload them to Synapse using syncToSynapse to edit files in bulk. The manifest allows you to modify everything: file path, provenance, annotations, and versions. If the files have not changed and you only want to update the file annotations, add a column called forceVersion to the manifest with the value False for each row. This will stop syncToSynapse from uploading new versions of the files.
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Note: Changing the parent synID in a manifest creates a copy of the file. It does not move it. |
See also:
Downloading dataData, /wiki/spaces/DOCS/pages/1972470373, Annotations and queriesQueries, /wiki/spaces/DOCS/pages/2011070739, /wiki/spaces/DOCS/pages/2668134540
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