{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","results":{"codes":[]},"settings":"","params":[]},"next":{"description":"","pages":[]},"title":"Import from a DRS server","type":"basic","slug":"import-from-a-drs-server","excerpt":"","body":"## OVERVIEW\n\nCAVATICA Powered by Seven Bridges allows you to import DRS files from either open external sources or known ones such as the following compatible Seven Bridges environments:\n\n* [CGC Powered by Seven Bridges](https://cgc.sbgenomics.com)\n* [BioData Catalyst Powered by Seven Bridges](https://platform.sb.biodatacatalyst.nhlbi.nih.gov/)\n\nAfter importing the files, you can then use them as any other file on CAVATICA. Please note that files imported via DRS are only linked, meaning that they're not physically transferred to CAVATICA, but instead they remain hosted on the source platform. However, after importing the files, you can then use them as any other file on CAVATICA.\n\n## PREREQUISITE\n\nIn order to be able to import a DRS file, your account on CAVATICA has to be connected to the DRS server of the environment you are importing data from.\n\n[Learn more](doc:connect-to-biodata-catalyst-drs-server) about this procedure.\n\n## PROCEDURE\n1. [Open](doc:view-a-project) the project to which you're importing files.\n2. Select the **Files** tab and then click **+ Add Files**.\n3. Click **Add Files** > **GA4GH Data Repository Service (DRS)**.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/418c2b3-cavatica-import-from-a-drs-server-1.png\",\n        \"cavatica-import-from-a-drs-server-1.png\",\n        447,\n        543,\n        \"#333\"\n      ]\n    }\n  ]\n}\n[/block]\n4. Enter DRS URIs into the text area (see [Form a DRS URI](#section-form-a-drs-uri-on-a-compatible-seven-bridges-environment) below) or click **Browse file** to navigate to a text file on your computer containing DRS URIs.\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"The maximum number of links you can put inside the text area is 500. To import again, you will have to wait for 5 minutes. In addition, please bear in mind that all other API calls you make within this time frame will also count toward this limit. URLs should be entered one per row.\",\n  \"title\": \"Important notes:\"\n}\n[/block]\n5. _Optional:_ Enter tags in the **Tag files** box. This makes it easier to visually identify and organize files. Separate tags with commas or hit the return key. All tags which are already in the selected project are autosuggested in the drop-down menu. Learn more about [tagging your files](doc:tag-your-files). \n6. **Resolve naming conflicts**-  Select the action to be taken if a naming conflict occurs. Available actions are **Skip**(default option), **Auto-rename**and **Overwrite**. Read more about naming conflicts resolution [below](#section-resolving-naming-conflicts). \n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"Allowed characters in **file names** are all alphanumerics and special characters except slash (/). File names can’t be longer than 255 characters.Allowed characters in **folder names** are a-z, A-Z, 0-9, and special characters (_), (-), and (.). Folder names can’t be longer than 255 characters.\"\n}\n[/block]\n7. Give your consent regarding importing sensitive data by checking the related option.\n8. Click **Import** to start the upload.\n\n### Form a DRS URI on a compatible Seven Bridges environment\n\n_This step takes place on [CGC Powered by Seven Bridges](https://cgc.sbgenomics.com) or [BioData Catalyst Powered by Seven Bridges](https://platform.sb.biodatacatalyst.nhlbi.nih.gov/)_.\n\nA DRS URI is formed by appending the ID of the file you want to import, to the DRS endpoint of the environment you are importing the files from.\n\nTo form a DRS URI for importing a file:\n1. Use the DRS endpoint for the environment you are importing the file from:\n    * CGC Powered by Seven Bridges: `drs://cgc-ga4gh-api.sbgenomics.com`\n    * BioData Catalyst Powered by Seven Bridges: `drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov`\nYou can also find the endpoint when logged in to the chosen environment, in the **Account Settings** page under **Dataset Access**.\n2. Get the ID of the file from the URL, once you have clicked on a file to see its details.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/81d7bbf-cavatica-import-from-a-drs-server-2.png\",\n        \"cavatica-import-from-a-drs-server-2.png\",\n        878,\n        296,\n        \"#333\"\n      ]\n    }\n  ]\n}\n[/block]\n3. Form the DRS URI by following the `<drs-endpoint>/<file-id>` pattern. For example, a full DRS URI for a file you want to import from BioData Catalyst Powered by Seven Bridges would be: `drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5cd573bce4b0359df2c239ae`.\n4. (Optional) In the **Add tags** field add the keywords (tags) that describe the imported items.\n5. **Resolve naming conflicts** - Select the action to be taken if a naming conflict occurs. Available actions are **Skip** (default option), **Auto-rename** and **Overwrite**. Read more about [naming conflicts resolution](#section-resolving-naming-conflicts).\n6. Click the checkbox to confirm that you understand the terms of use.\n7. Click **Import**. The file import process starts.\n\n## DURING UPLOAD\n\nTrack the import progress under the import status icon on the right-hand side of the main menu. When the upload completes, review your files in the **Files** tab of your project.\n\n## RESOLVING NAMING CONFLICTS\n\nNaming conflicts happen when you try to import an item (file or folder) from a DRS server to a project's root folder or subfolder, where an item with the same name already exists. The list below illustrates the possible cases of naming conflicts and the way they are resolved depending on which option is selected in the **Resolve naming conflicts** dropdown:\n1. Importing a **file** that has the same name as an existing **file** at the destination path:\n    * **Skip** (default): The file won't be imported. This is the default behavior.\n    * **Auto-rename**: The imported file will be automatically renamed by adding a prefix (underscore and serial number).\n    * **Overwrite**: The existing file will be overwritten by the file imported from the server.\n2. Importing a **file** that has the same name as an existing **folder** at the destination path:\n    * **Skip** (default): The file won't be imported.\n    * **Auto-rename**: The imported file will be automatically renamed by adding a prefix (underscore and serial number).\n    * **Overwrite**: The file won't be imported.\n\nThe following table illustrates the entire naming conflict resolution mechanism:\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/faa7761-ae02f2e-conflict-resolution-matrix2.png\",\n        \"ae02f2e-conflict-resolution-matrix2.png\",\n        471,\n        224,\n        \"#333\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n## TROUBLESHOOTING\n\nIf the import feature fails to upload all the files whose links you provided, please retry by providing shorter lists of links.","updates":[],"order":7,"isReference":false,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"606c0b6333afba02cd87ef69","createdAt":"2021-04-06T07:18:59.092Z","user":"566590c83889610d0008a253","category":{"sync":{"isSync":false,"url":""},"pages":[],"title":"Bring data to CAVATICA","slug":"bring-your-data","order":6,"from_sync":false,"reference":false,"_id":"5a3a574a2be213002675c6d2","project":"5773dcfc255e820e00e1cd4d","version":"5773dcfc255e820e00e1cd50","createdAt":"2017-12-20T12:27:54.317Z","__v":1},"version":{"version":"1.0","version_clean":"1.0.0","codename":"","is_stable":true,"is_beta":false,"is_hidden":false,"is_deprecated":false,"categories":["5773dcfc255e820e00e1cd51","5773df36904b0c0e00ef05ff","577baf92451b1e0e006075ac","577bb183b7ee4a0e007c4e8d","577ce77a1cf3cb0e0048e5ea","577d11865fd4de0e00cc3dab","578e62792c3c790e00937597","578f4fd98335ca0e006d5c84","578f5e5c3d04570e00976ebb","57bc35f7531e000e0075d118","57f801b3760f3a1700219ebb","5804d55d1642890f00803623","581c8d55c0dc651900aa9350","589dcf8ba8c63b3b00c3704f","594cebadd8a2f7001b0b53b2","59a562f46a5d8c00238e309a","5a2aa096e25025003c582b58","5a2e79566c771d003ca0acd4","5a3a5166142db90026f24007","5a3a52b5bcc254001c4bf152","5a3a574a2be213002675c6d2","5a3a66bb2be213002675cb73","5a3a6e4854faf60030b63159","5c8a68278e883901341de571","5cb9971e57bf020024523c7b","5cbf1683e2a36d01d5012ecd","5dc15666a4f788004c5fd7d7","5eaff69e844d67003642a020","5eb00899b36ba5002d35b0c1","5eb0172be179b70073dc936e","5eb01b42b36ba5002d35ebba","5eb01f202654a20136813093","5eb918ef149186021c9a76c8","5f0839d3f4b24e005ebbbc29","5f893e508c9862002d0614a9","6024033e2b2f6f004dfe994c","60a7a12f9a06c70052b7c4db","60a7ab97266a4700161507c4","60b0c84babba720010a8b0b5"],"_id":"5773dcfc255e820e00e1cd50","__v":39,"createdAt":"2016-06-29T14:36:44.812Z","releaseDate":"2016-06-29T14:36:44.812Z","project":"5773dcfc255e820e00e1cd4d"},"project":"5773dcfc255e820e00e1cd4d","__v":0,"parentDoc":null}

Import from a DRS server


## OVERVIEW CAVATICA Powered by Seven Bridges allows you to import DRS files from either open external sources or known ones such as the following compatible Seven Bridges environments: * [CGC Powered by Seven Bridges](https://cgc.sbgenomics.com) * [BioData Catalyst Powered by Seven Bridges](https://platform.sb.biodatacatalyst.nhlbi.nih.gov/) After importing the files, you can then use them as any other file on CAVATICA. Please note that files imported via DRS are only linked, meaning that they're not physically transferred to CAVATICA, but instead they remain hosted on the source platform. However, after importing the files, you can then use them as any other file on CAVATICA. ## PREREQUISITE In order to be able to import a DRS file, your account on CAVATICA has to be connected to the DRS server of the environment you are importing data from. [Learn more](doc:connect-to-biodata-catalyst-drs-server) about this procedure. ## PROCEDURE 1. [Open](doc:view-a-project) the project to which you're importing files. 2. Select the **Files** tab and then click **+ Add Files**. 3. Click **Add Files** > **GA4GH Data Repository Service (DRS)**. [block:image] { "images": [ { "image": [ "https://files.readme.io/418c2b3-cavatica-import-from-a-drs-server-1.png", "cavatica-import-from-a-drs-server-1.png", 447, 543, "#333" ] } ] } [/block] 4. Enter DRS URIs into the text area (see [Form a DRS URI](#section-form-a-drs-uri-on-a-compatible-seven-bridges-environment) below) or click **Browse file** to navigate to a text file on your computer containing DRS URIs. [block:callout] { "type": "info", "body": "The maximum number of links you can put inside the text area is 500. To import again, you will have to wait for 5 minutes. In addition, please bear in mind that all other API calls you make within this time frame will also count toward this limit. URLs should be entered one per row.", "title": "Important notes:" } [/block] 5. _Optional:_ Enter tags in the **Tag files** box. This makes it easier to visually identify and organize files. Separate tags with commas or hit the return key. All tags which are already in the selected project are autosuggested in the drop-down menu. Learn more about [tagging your files](doc:tag-your-files).  6. **Resolve naming conflicts**-  Select the action to be taken if a naming conflict occurs. Available actions are **Skip**(default option), **Auto-rename**and **Overwrite**. Read more about naming conflicts resolution [below](#section-resolving-naming-conflicts). [block:callout] { "type": "info", "body": "Allowed characters in **file names** are all alphanumerics and special characters except slash (/). File names can’t be longer than 255 characters.Allowed characters in **folder names** are a-z, A-Z, 0-9, and special characters (_), (-), and (.). Folder names can’t be longer than 255 characters." } [/block] 7. Give your consent regarding importing sensitive data by checking the related option. 8. Click **Import** to start the upload. ### Form a DRS URI on a compatible Seven Bridges environment _This step takes place on [CGC Powered by Seven Bridges](https://cgc.sbgenomics.com) or [BioData Catalyst Powered by Seven Bridges](https://platform.sb.biodatacatalyst.nhlbi.nih.gov/)_. A DRS URI is formed by appending the ID of the file you want to import, to the DRS endpoint of the environment you are importing the files from. To form a DRS URI for importing a file: 1. Use the DRS endpoint for the environment you are importing the file from: * CGC Powered by Seven Bridges: `drs://cgc-ga4gh-api.sbgenomics.com` * BioData Catalyst Powered by Seven Bridges: `drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov` You can also find the endpoint when logged in to the chosen environment, in the **Account Settings** page under **Dataset Access**. 2. Get the ID of the file from the URL, once you have clicked on a file to see its details. [block:image] { "images": [ { "image": [ "https://files.readme.io/81d7bbf-cavatica-import-from-a-drs-server-2.png", "cavatica-import-from-a-drs-server-2.png", 878, 296, "#333" ] } ] } [/block] 3. Form the DRS URI by following the `<drs-endpoint>/<file-id>` pattern. For example, a full DRS URI for a file you want to import from BioData Catalyst Powered by Seven Bridges would be: `drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5cd573bce4b0359df2c239ae`. 4. (Optional) In the **Add tags** field add the keywords (tags) that describe the imported items. 5. **Resolve naming conflicts** - Select the action to be taken if a naming conflict occurs. Available actions are **Skip** (default option), **Auto-rename** and **Overwrite**. Read more about [naming conflicts resolution](#section-resolving-naming-conflicts). 6. Click the checkbox to confirm that you understand the terms of use. 7. Click **Import**. The file import process starts. ## DURING UPLOAD Track the import progress under the import status icon on the right-hand side of the main menu. When the upload completes, review your files in the **Files** tab of your project. ## RESOLVING NAMING CONFLICTS Naming conflicts happen when you try to import an item (file or folder) from a DRS server to a project's root folder or subfolder, where an item with the same name already exists. The list below illustrates the possible cases of naming conflicts and the way they are resolved depending on which option is selected in the **Resolve naming conflicts** dropdown: 1. Importing a **file** that has the same name as an existing **file** at the destination path: * **Skip** (default): The file won't be imported. This is the default behavior. * **Auto-rename**: The imported file will be automatically renamed by adding a prefix (underscore and serial number). * **Overwrite**: The existing file will be overwritten by the file imported from the server. 2. Importing a **file** that has the same name as an existing **folder** at the destination path: * **Skip** (default): The file won't be imported. * **Auto-rename**: The imported file will be automatically renamed by adding a prefix (underscore and serial number). * **Overwrite**: The file won't be imported. The following table illustrates the entire naming conflict resolution mechanism: [block:image] { "images": [ { "image": [ "https://files.readme.io/faa7761-ae02f2e-conflict-resolution-matrix2.png", "ae02f2e-conflict-resolution-matrix2.png", 471, 224, "#333" ], "border": true } ] } [/block] ## TROUBLESHOOTING If the import feature fails to upload all the files whose links you provided, please retry by providing shorter lists of links.