You can verify the integrity of the data with the MD5 (Message Digest Algorithm 5) checksum. It is a widely used cryptographic hash function that generates a fixed-size, 128-bit hash value from any input data. This hash value is unique to the content of the data, meaning even a slight change in the data will result in a significantly different MD5 checksum.

For files smaller than 16 MB, you can directly retrieve the MD5 checksum using our API endpoints. Make an API GET call to the https://ica.illumina.com/ica/rest/api/projects/{projectId}/data/{dataId} endpoint specifying the data Id you want to check and the corresponding project ID. The response you receive will be in JSON format, containing various file metadata. Within the JSON response, look for the objectETag field. This value is the MD5 checksum for the file you have queried. You can compare this checksum with the one you compute locally ot ensure the file's integrity.

For larger files, the process is different due to computation limitations. In these cases, we recommend using a dedicated pipeline on our platform to explicitly calculate the MD5 checksum. Below you can find both a main.nf file and the corresponding XML for a possible Nextflow pipeline to calculate the MD5 checksum for FASTQ files.

nextflow.enable.dsl = 2


process md5sum {
    
    container "public.ecr.aws/lts/ubuntu:22.04"
    pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-small'
    
    input:
        file txt

    output:
        stdout emit: result
        path '*', emit: output

    publishDir "out", mode: 'symlink'

    script:
        txt_file_name = txt.getName()
        id = txt_file_name.takeWhile { it != '.'}

        """
        set -ex
        echo "File: $txt_file_name"
        echo "Sample: $id"
        md5sum ${txt} > ${id}_md5.txt
        """
    }

workflow {
    txt_ch = Channel.fromPath(params.in)
    txt_ch.view()
    md5sum(txt_ch).result.view()
}

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<pd:pipeline xmlns:pd="xsd://www.illumina.com/ica/cp/pipelinedefinition">
    <pd:dataInputs>
        <pd:dataInput code="in" format="FASTQ" type="FILE" required="true" multiValue="true">
            <pd:label>Input</pd:label>
            <pd:description>FASTQ files input</pd:description>
        </pd:dataInput>
    </pd:dataInputs>
    <pd:steps/>
</pd:pipeline>

The Data section gives you access to the files and folders stored in the project as well as those linked to the project. Here, you can perform searches and data management operations such as moving, copying, deleting and (un)archiving.

Recommended Practices

File/Folder Naming

ICA supports UTF-8 characters in file and folder names for data. Please follow the guidelines detailed below. (For more information about recommended approaches to file naming that can be applicable across platforms, please refer to the AWS S3 documentation.)

Data Formats

See the list of supported Data Formats

Data Privacy

Data privacy should be carefully considered when adding data in ICA, either through storage configurations (ie, AWS S3) or ICA data upload. Be aware that when adding data from cloud storage providers by creating a storage configuration, ICA will provide access to the data. Ensure the storage configuration source settings are correct and ensure uploads do not include unintended data in order to avoid unintentional privacy breaches. More guidance can be found in the ICA Security and Compliance section.

Data Integrity

See Data Integrity

Data Management

Viewing Data

On the Projects > your_project > Data page, you can view file information and preview files.

To view file details click on the filename to see the file details.

• Run input tags identify the last 100 pipelines which used this file as input.

• Connector tags indicate if the file was added via browser upload or connector.

To view file contents, select the checkbox at the begining of the line and then select View from the top menu. Alternatively, you can first click on the filename to see the details and then click view to preview the file.

Secondary Data

When Secondary Data is added to a data record, those secondary data records are mounted in the same parent folder path as the primary data file when the primary data file is provided as an input to a pipeline. Secondary data is intended to work with the CWL secondaryFiles feature. This is commonly used with genomic data such as BAM files with companion BAM index files (refer to https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/ for an example).

Hyperlinking to Data

To hyperlink to data, use the following syntax:

https://<ServerURL>/ica/link/project/<ProjectID>/data/<FolderID>

https://<ServerURL>/ica/link/project/<ProjectID>/analysis/<AnalysisID>

Uploading Data

Uploading data to the platform makes it available for consumption by analysis workflows and tools.

UI Upload

To upload data manually via the drag-and-drop interface in the platform UI, go to Projects > your_project > Data and either

• Drag a file from your system into Choose a file or drag it here box.

• Select the Choose a file or drag it here box, and then choose a file. Select Open to upload the file.

Your file or files are added to the Data page when upload completes.

Upload Data via CLI

For instructions on uploading/downloading data via CLI, see CLI Data Transfer.

Copying Data

You can copy data from the same project to a different folder or from another project to which you have access.

In order to copy data, the following rights must be assigned to the person copying the data:

The following restrictions apply when copying data:

To use data copy:

1. Go to the destination project for your data copy and proceed to Projects > your_project > Data > Manage > Copy Data From.

2. Optionally, use the filters (Type, Name, Status, Format or additional filters) to filter out the data or search with the search box.

3. Select the data (individual files or folders with data) you want to copy.

4. Select any meta data which you want to keep with the copied data (user tags, technical system tags or instrument information).

5. Select which action to take if the data already exists (overwrite exsiting data, don't copy or keep both the original and the new copy by appending a number to the copied data).

6. Select Copy Data to copy the data to your project. You can see the progress in Projects > your_project > Activity > Batch Jobs and if your browser permits it, a pop-up message will be displayed whan the copy process completes.

The outcome can be

• INITIALIZED

• WAITING_FOR_RESOURCES

• RUNNING

• STOPPED - When choosing to stop the batch job.

• SUCCEEDED - All files and folders are copied.

• PARTIALLY_SUCCEEDED - Some files and folders could be copied, but not all. Partially succeeded will typically occur when files were being modified or unavailable while the copy process was running.

• FAILED - None of the files and folders could be copied.

There is a difference in copy type behavior between copying files and folders. The behavior is designed for files and it is best practice to not copy folders if there already is a folder with the same name in the destination location.

Move Data

You can move data both within a project and between different projects to which you have access. If you allow notifications from your browser, a pop-up will appear when the move is completed.

• Move Data From is used when you are in the destination location.

• Move Data To is used when you are in the source location. Before moving the data, pre-checks are performed to verify that the data can be moved and no currently running operations are being performed on the folder. Conflicting jobs and missing permissions will be reported. Once the move has started, no other operation should be performed on the data being moved to avoid potential data loss or duplication. Adding or (un)archiving files during the move may result in duplicate folders and files with different identifiers. If this happens, you will need to manually delete the duplicate files and move the files which were skipped during the initial move.

There are a number of rights and restrictions related to data move as this will delete the data in the source location.

Move Data From

Move Data From is used when you are in the destination location.

1. Navigate to Projects > your_project > Data > your_destination_location > Manage > Move Data From.

2. Select the files and folders which you want to move.

3. Select the Move button. Moving large amounts of data can take considerable time. You can monitor the progress at Projects > your_project > Activity > Batch Jobs.

Move Data To

Move Data To is used when you are in the source location. You will need to select the data you want to move from to current location and the destination to move it to.

1. Navigate to Projects > your_project > Data > your_source_location.

2. Select the files and folders which you want to move.

3. Select to Projects > your_project > Data > your_source_location > Manage > Move Data To.

4. Select your target project and location.

   1. Note: You can create a new folder to move data to by filling in the "New folder name (optional)" field. This does NOT rename an existing folder. To rename an existing folder, please see File/Folder Naming.

5. Select the Move button. Moving large amounts of data can take considerable time. You can monitor the progress at Projects > your_project > Activity > Batch Jobs.

Move Status

• INITIALIZED

• WAITING_FOR_RESOURCES

• RUNNING

• STOPPED - When choosing to stop the batch job.

• SUCCEEDED - All files and folders are moved.

• PARTIALLY_SUCCEEDED - Some files and folders could be moved, but not all. Partially succeeded will typically occur when files were being modified or unavailable while the move process was running.

• FAILED - None of the files and folders could be moved.

Download Data

Single files can be downloaded directly from within the UI.

• Select the checkbox next to the file which you want to download, followed by Download > Download file.

• Files for which ICA can display the contents can be viewed by clicking on the filename, followed by the View tab. Select the download action on the view tab to download the file. Note that larger files may take some time to load.

Schedule for Download

You can trigger an asynchronous download via service connector using the Schedule for Download button with one or more files selected.

1. Select a file or files to download.

2. Select Download > Download files or folders using a service connector. This will display a list of all available connectors.

3. Select a connector, and then select Schedule for Download. If you do not find the connector you need or you do not have a connector, you can click the Don't have a connector yet? option to create a new connector. You must then install this new connector and return to the file selection in step 1 to use it.

You can view the progress of the download or stop the download on the Activity page for the project.

Export Project Data Information

The data records contained in a project can be exported in CSV, JSON, and excel format.

1. Select one or more files to export.

2. Select Export.

3. Select the following export options:

   • To export only the selected file, select the Selected rows as the Rows to export option. To export all files on the page, select Current page.

   • To export only the columns present for the file, select the Visible columns as the Columns to export option.

4. Select the export format.

Archiving and Deleting files

To manually archive or delete files, do as follows:

1. Select the checkbox next to the file or files to delete or archive.

2. Select Manage, and then select one of the following options:

   • Archive — Move the file or files to long-term storage (event code ICA_DATA_110).

   • Unarchive — Return the file or files from long-term storage. Unarchiving can take up to 48 hours, regardless of file size. Unarchived files can be used in analysis (event code ICA_DATA_114).

   • Delete — Remove the file completely (event code ICA_DATA_106).

When attempting concurrent archiving or unarchiving of the same file, a message will inform you to wait for the currently running (un)archiving to finish first.

To archive or delete files programmatically, you can use ICA's API endpoints:

1. GET the file's information.

2. Modify the dates of the file to be deleted/archived.

3. PUT the updated information back in ICA.

import requests
import json

from config import PROJECT_ID, DATA_ID, API_KEY

url_get="https://ica.illumina.com/ica/rest/api/projects/" + PROJECT_ID + "/data/" + DATA_ID

# set the API get headers
headers = {
            'X-API-Key': API_KEY,
            'accept': 'application/vnd.illumina.v3+json'
            }

# set the API put headers
headers_put = {
            'X-API-Key': API_KEY,
            'accept': 'application/vnd.illumina.v3+json',
            'Content-Type': 'application/vnd.illumina.v3+json'
            }

# Helper function to insert willBeArchivedAt after field named 'region'
def insert_after_region(details_dict, timestamp):
    new_dict = {}
    for k, v in details_dict.items():
        new_dict[k] = v
        if k == 'region':
            new_dict['willBeArchivedAt'] = timestamp
    if 'willBeArchivedAt' in details_dict:
        new_dict['willBeArchivedAt'] = timestamp
    return new_dict

# 1. Make the GET request
response = requests.get(url_get, headers=headers)
response_data = response.json()

# 2. Modify the JSON data
timestamp = "2024-01-26T12:00:04Z"  # Replace with the provided timestamp
response_data['data']['details'] = insert_after_region(response_data['data']['details'], timestamp)

# 3. Make the PUT request
put_response = requests.put(url_get, data=json.dumps(response_data), headers=headers_put)
print(put_response.status_code)

Link Project Data

Linking a folder creates a dynamic read-only view of the source data. You can use this to get access to data without running the risk of modifying the source material and to share data between projects. In addition, linking ensures changes to the source data are immediately visible and no additional storage is required.

You can recognise linked data by the green color and see the owning project as part of the details.

Since this is read-only access, you cannot perform actions on linked data that need to write access. Actions like (un)archiving, linking, creating, deleting, adding or moving data and folders, and copying data into the linked data are not possible.

You can perform analysis on data from other projects by linking data from that project.

1. Select Projects > your_project > Data > Manage, and then select Link Data.

2. To view data by project, select the funnel symbol, and then select Owning Project. If you only know which project the data is linked to, you can choose to filter on linked projects.

3. Select the checkbox next to the file or files to add.

4. Select Select Data.

Your files are added to the Data page. To view the linked data file, select Add filter, and then select Links.

Linking Folders

If you link a folder instead of individual files, a warning is displayed indicating that, depending on the size of the folder, linking may take considerable time. The linking process will run in the background and the progress can be monitored on the Projects > your_project > activity > Batch Jobs screen.

To see more details, double-click the batch job.

To see how many individual files are already linked, double-click the item.

Unlinking Project Data

To unlink the data, go to the root level of your project and select the linked folder or if you have linked individual files separately, then you can select those linked files (limited to 100 at a time) and select Manage > Unlink Data. As during linking a folder, when unlinking, the progress can be monitored at Projects > your_project > activity > Batch Jobs.