Download C97 Txt
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Download C97 txt
A convenient way to download multiple files from the GDC is to use a manifest file generated by the GDC Data Portal. After generating a manifest file (see Preparing for Data Download and Upload for instructions), initiate the download using the GDC Data Transfer Tool by supplying the -m or --manifest option, followed by the location and name of the manifest file. OS X users can drag and drop the manifest file into Terminal to provide its location.
The GDC Data Transfer Tool supports resumption of interrupted downloads. To resume an incomplete download, repeat the download of the manifest or UUID(s) in the same folder as the initial download. Failed downloads will appear in the destination folder with a .partial extension. This feature allows users the ability to identify quickly where the download stopped. For large downloads this feature can let the user identify where the download was interrupted and edit the manifest accordingly.
The GDC Data Transfer Tool supports file versioning. Our backend data storage supports multiple file versions so older and current versions can be accessible to our users. For information about accessing file versioning information with our API and finding older UUID information from current UUIDs please check out the the API User Guide section in our API documentation. When working with older manifests or older lists of UUIDs the latest version of a file can always be download with the --latest flag.
Shell Output gdc-client download 426de656-7e34-4a49-b87e-6e2563fa3cdd --latest -t gdc-user-token.2018.txt Downloading LATEST versions of filesLatest version for 426de656-7e34-4a49-b87e-6e2563fa3cdd ==> 6633bfbd-87f1-4d3a-a475-7ad1e8c2017a100% [#############################################################################################################################] Time: 0:01:16 14.10 MB/sSuccessfully downloaded: 1
A user authentication token is required for downloading Controlled-Access Data from GDC. Tokens can be obtained from the GDC Data Portal (see instructions in Obtaining an Authentication Token). Once downloaded, the token file can be passed to the GDC Data Transfer Tool using the -t or --token-file option:
The directory in which the files are downloaded will include folders named by the file UUID. Inside these folders, along with the the data and zipped metadata or index files, will exist a logs folder. The logs folder contains state files that insure that downloads are accurate and allow for resumption of failed or prematurely stopped downloads. While a download is in progress a file will have a .partial extension. This will also remain if a download failed. Once a file is finished downloading the extension will be removed. If an identical manifest is retried another attempt will be made to download files containing a .partial extension.
Shell Output gdc-client --help usage: gdc-client [-h] [--version] download,upload,settings ...The Genomic Data Commons Command Line Clientoptional arguments: -h, --help show this help message and exit --version show program's version number and exitcommands: download,upload,settings for more information, specify -h after a command download download data from the GDC upload upload data to the GDC settings display default settings The available menus are provided below.
Shell Output gdc-client download --help usage: gdc-client download [-h] [--debug] [--log-file LOG_FILE] [--color_off] [-t TOKEN_FILE] [-d DIR] [-s server] [--no-segment-md5sums] [--no-file-md5sum] [-n N_PROCESSES] [--http-chunk-size HTTP_CHUNK_SIZE] [--save-interval SAVE_INTERVAL] [--no-verify] [--no-related-files] [--no-annotations] [--no-auto-retry] [--retry-amount RETRY_AMOUNT] [--wait-time WAIT_TIME] [--latest] [--config FILE] [-u] [-m MANIFEST] [file_id [file_id ...]]positional arguments:file_id The GDC UUID of the file(s) to downloadoptional arguments:-h, --help show this help message and exit--debug Enable debug logging. If a failure occurs, the program will stop.--log-file LOG_FILE Save logs to file. Amount logged affected by --debug--color_off Disable colored output-t TOKEN_FILE, --token-file TOKEN_FILE GDC API auth token file-d DIR, --dir DIR Directory to download files to. Defaults to current dir-s server, --server server The TCP server address server[:port]--no-segment-md5sums Do not calculate inbound segment md5sums and/or do not verify md5sums on restart--no-file-md5sum Do not verify file md5sum after download-n N_PROCESSES, --n-processes N_PROCESSES Number of client connections.--http-chunk-size HTTP_CHUNK_SIZE, -c HTTP_CHUNK_SIZE Size in bytes of standard HTTP block size.--save-interval SAVE_INTERVAL The number of chunks after which to flush state file. A lower save interval will result in more frequent printout but lower performance.--no-verify Perform insecure SSL connection and transfer--no-related-files Do not download related files.--no-annotations Do not download annotations.--no-auto-retry Ask before retrying to download a file--retry-amount RETRY_AMOUNT Number of times to retry a download--wait-time WAIT_TIME Amount of seconds to wait before retrying--latest Download latest version of a file if it exists--config FILE Path to INI-type config file-u, --udt Use the UDT protocol.-m MANIFEST, --manifest MANIFEST GDC download manifest file
The DTT has the ability to save and reuse configuration parameters in the format of a flat text file via a command line argument. A simple text file needs to be created first with an extension of either txt or dtt. The supported section headers are upload and download which can be used independently of each other or used in the same configuration file. Each section header corresponds to the main functions of the application which are to either download data from the GDC portals or to upload data to the submission system of the GDC. The configurable parameters are those listed in the help menus under either download or upload displayed under the output tabs.
You are allowed to download and use these files for your own use, however the content remains the copyright of the author. You may not sell, rent or lease these files or any part of them without prior written consent of the copyright owner.
I have a file URL for a PDF that I want to download using Chrome. wget is not an option, because Chrome is seemingly sending headers and cookies that I can't replicate. So what I need is to be able to run
Functionally it is the same as opening a window in Chrome with the given URL, then right-clicking and hitting "Save as...". But I have a list of many PDFs that I need to download, so it has to be automated somehow.
Instead wget you can use cURL in conjuction with chrome. Open chrome dev tools (F12), enter network tab and start your download. Now in network tab you will see new request. Click on it with mouse right button and select "Copy as cURL (cmd)". Open command line and paste clipboard. It should look something like this:
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