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Upload Metaphase Images

Sign into AWS Management Console

An e-mail is sent to the user containing a temporary password and a SHA-256 hash of their UserName. The SHA-256 hash will be necessary later in the image upload process, so it should be recorded and set aside for the moment. The user accesses the Amazon Web Services (AWS) webpage and selects “AWS Management Console” from the “My Account” dropdown at the top-right of the page. The credentials provided in the e-mail can now be used to log in.

S3 is a secure storage service provided by AWS. S3 is utilized to store user-specific files which must persist between ADCI_Online streaming sessions. Uploaded metaphase images and files generated by ADCI are stored in S3 and are not visible to other users.

Click the “Services” dropdown at the top-left of the webpage and select “S3” as shown in the image to proceed to S3.

Access User-Specific Home Folder

Click the name of the S3 bucket beginning with “appstream2-”. Navigate through directories stored within the bucket by clicking on the directory name. To go back one or more directories, observe the blue text at the top of the image to the right. This is a list of all parent directories of the folder you are currently visiting, click the name of any of the parent directories to return to it. The goal is to traverse to your user-specific ADCI_Images directory. The directory structure is shown below.

└── userpool/
    └── *SHA-256 hash of UserName/
        └── Persistent_ADCI_Data/
            └── ADCI_Images

*The SHA-256 hash of your UserName was sent in an e-mail to you which contained your AWS login credentials. Please note, although directories named with SHA-256 hashes are visible to other users, each user can access only their own directory.

Upload Samples

Begin Upload from the ADCI_Images directory

Please ensure you have traversed to the ADCI_Images directory before continuing. To do so, consult the image to the right. The directory structure shown in your web browser should be similar to the directory structure shown in the image (blue text at the top of the image). The only differences should be the SHA-256 hash of your UserName, and the name of the S3 Bucket will not contain '*' characters as it does in the image. As noted, if you have navigated to an “ADCI_Images” directory, you are in the right place, as you cannot access the directories of other users.

Click “Upload” to proceed to the next step.

Select Local Files for Upload

An upload page is presented which allows the upload of files or folders. First, we must ensure all samples to be uploaded are present on your local system and that metaphase images associated with each sample are stored in separate directories. For example, a user would like to upload two samples (Sample1 and Sample2) to ADCI_Online to be processed. All metaphase images associated with Sample1 should be placed in a single directory. All metaphase images associated with Sample2 should be placed in a different single directory. The Sample1 and Sample2 directories should contain only metaphase images associated with the particular sample and no other files. An appropriate directory structure on your local system before upload can be seen below:

└── LocalSystem/
    └── Samples/
        ├── Sample1/
        │   ├── img1.png
        │   ├── img2.png
        │   └── ... more images
        └── Sample2/
            ├── img1.png
            ├── img2.png
            └── ... more images

Note: When uploading a folder to S3, the name of the directory on your local system is used as the name of the directory on S3. If desired, you may wish to change the name of the directories containing metaphase images before upload.

When ready to proceed, click the “Add Folder” button. A dialog will pop up allowing you to browse your local system for the folder you would like to upload. Following the example above, we would select the folder 'Sample1'. The filenames of all files within the selected directory will be populated on the screen. This process can be repeated for each sample you would like to upload during this session. It is not necessary to upload all samples simultaneously, more samples can be uploaded later if desired.

Begin Upload

Once all samples you wish to upload have been added using the “Add Folder” button, your screen should look similar to the image to the right. File names of image files should be present under the “Name” heading. The name of each directory to be uploaded is shown in the “Folder” heading. Again following our previously laid out example, the “Folder” heading will contain either 'Sample1' or 'Sample2', and the “Name” heading will contain all files contained in those two folders.

To begin the upload process, click the “Upload” button at the bottom-right of the webpage.

Upload Progress

Progress of the upload can be seen in the banner at the top of the page. Users can ensure all images have been uploaded successfully by observing the “Succeeded” and “Failed” sections.

In this example, 2180 metaphase images (1.77Gb) were uploaded to the S3 Bucket in 17 minutes 33 seconds. This is a rate of ~2 images / second.

If Files/Folders were Uploaded in Error

Files or Folders uploaded in error can be deleted. Please take care to only delete files or folders uploaded by you, and not any of the directory structure which was automatically prepopulated (such as the “Persistent_ADCI_Data” directory itself). Locate the files or folder uploaded in error and click the checkbox beside them. Once you have marked the checkboxes beside the files/folders you wish to delete, click the “Delete” button. A confirmation screen will appear describing the files you have selected for deletion and it prompts you to type out a confirmation you are sure you would like to proceed.

adcionline/imgupload.txt · Last modified: 2021/02/16 19:59 by bshirley