{"lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "title": "4DN DCIC, HMS", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "To download multiple files at one time you first need to get a metadata.tsv file that contains the information necessary for download as well as additional helpful information about the selected files. First select and filter the file(s) from either the `browse Experiment Sets `_ page, the `search Files `_ page, or from the page of an Experiment Set containing the desired files using the selector check boxes and facet filters. The Download button will generate and download a file 'metadata.tsv' to your local machine.\n\nInstructions to download the files included in the metadata.tsv file as well as some general statistics on the files you selected are included at the bottom of the file itself.\n\nYou will need to create a new access key, if you don't have an access key already. **Note** that access keys created for Jupyterhub can't be used for the rest of the portal.\n\nTo create a new access key, first log in to the data portal, then click on your account in the upper right and click on Profile from the dropdown menu. There will be a button near the bottom of the page to add an access key. Save the key and secret; typically this is done by creating a file in your home directory called ``keypairs.json`` with the following contents/format (replacing the x\u2019s with the appropriate key and secret, of course): ::\n\n {\n \"default\": {\n \"key\": \"XXXXXXXX\",\n \"secret\": \"xxxxxxxxxxxxxxxx\",\n \"server\": \"https://data.4dnucleome.org\"\n }\n }\n\nOnce the access key is created and stored, a file can be downloaded via curl with the following command: ::\n\n curl -O -L --user : \n", "name": "help.downloading-files.batch-downloading", "award": {"@type": ["Award", "Item"], "@id": "/awards/2U01CA200059-06/", "status": "current", "project": "4DN", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "name": "2U01CA200059-06", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "center_title": "DCIC - Park", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Batch Download", "status": "released", "aliases": ["4dn-dcic-lab:batch_downloading"], "options": {"filetype": "rst", "collapsible": false, "default_open": true, "convert_ext_links": true}, "date_created": "2021-04-12T18:16:34.432712+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-08-19T20:54:56.486279+00:00"}, "schema_version": "2", "@id": "/static-sections/83644f6c-1114-4d13-9382-4e90e5b43e3a/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "83644f6c-1114-4d13-9382-4e90e5b43e3a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}, "display_title": "Batch Download", "external_references": [], "content": "To download multiple files at one time you first need to get a metadata.tsv file that contains the information necessary for download as well as additional helpful information about the selected files. First select and filter the file(s) from either the `browse Experiment Sets `_ page, the `search Files `_ page, or from the page of an Experiment Set containing the desired files using the selector check boxes and facet filters. The Download button will generate and download a file 'metadata.tsv' to your local machine.\n\nInstructions to download the files included in the metadata.tsv file as well as some general statistics on the files you selected are included at the bottom of the file itself.\n\nYou will need to create a new access key, if you don't have an access key already. **Note** that access keys created for Jupyterhub can't be used for the rest of the portal.\n\nTo create a new access key, first log in to the data portal, then click on your account in the upper right and click on Profile from the dropdown menu. There will be a button near the bottom of the page to add an access key. Save the key and secret; typically this is done by creating a file in your home directory called ``keypairs.json`` with the following contents/format (replacing the x\u2019s with the appropriate key and secret, of course): ::\n\n {\n \"default\": {\n \"key\": \"XXXXXXXX\",\n \"secret\": \"xxxxxxxxxxxxxxxx\",\n \"server\": \"https://data.4dnucleome.org\"\n }\n }\n\nOnce the access key is created and stored, a file can be downloaded via curl with the following command: ::\n\n curl -O -L --user : \n", "filetype": "rst", "content_as_html": "

To download multiple files at one time you first need to get a metadata.tsv file that contains the information necessary for download as well as additional helpful information about the selected files. First select and filter the file(s) from either the browse Experiment Sets page, the search Files page, or from the page of an Experiment Set containing the desired files using the selector check boxes and facet filters. The Download button will generate and download a file 'metadata.tsv' to your local machine.

Instructions to download the files included in the metadata.tsv file as well as some general statistics on the files you selected are included at the bottom of the file itself.

You will need to create a new access key, if you don't have an access key already. Note that access keys created for Jupyterhub can't be used for the rest of the portal.

To create a new access key, first log in to the data portal, then click on your account in the upper right and click on Profile from the dropdown menu. There will be a button near the bottom of the page to add an access key. Save the key and secret; typically this is done by creating a file in your home directory called keypairs.json with the following contents/format (replacing the x\u2019s with the appropriate key and secret, of course):

\n{\n    \"default\": {\n        \"key\": \"XXXXXXXX\",\n        \"secret\": \"xxxxxxxxxxxxxxxx\",\n        \"server\": \"https://data.4dnucleome.org\"\n    }\n}\n

Once the access key is created and stored, a file can be downloaded via curl with the following command:

\ncurl -O -L --user <key>:<secret> <download-url>\n
", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}