Export ==== ## Export to File ### Export Lab Notebooks & Inventory Spaces All levels of the *Lab Notebook* and *Inventory* can be exported, using the **Export** option in the **More..** drop down, as shown below for a *Space*.   ![image info](img/201012-export-space.png) In each case, the following export options are available:  ![image info](img/new-export-options.png)   - **Make import compatible**. If selected, datasets are exported in a **data** folder and are in a format ready to be uploaded in openBIS using the default eln-lims dropbox; the metadata are exported in a **xlsx** folder which contains information in a format ready to be uploaded via the openBIS admin UI. - **Export metadata as PDF**. Metadata are exported in a **hierarchy** folder that keeps the folder structure of the ELN. At each level, one pdf file for each exported entity is generated. - **Export metadata as XLSX**. Metadata are exported in one **xlsx** folder. The folder contains the metadata of all exported entities and the corresponding masterdata in a **metadata.xlsx** file. If **Make import compatible** is selected, this file is suitable for re-import in openBIS. If not, the file contains some fields which are not compatible with re-imports. These fields are: PermId of entities, registrator, registration date, modifier, modification date. In addition to the metadata.xlsx file, the **xlsx** folder might contain additional folders: - a **scripts** folder, which contains scripts associated with types in the metadata.xlsx file, if these are present; - a **data** folder which holds the content of large text fields that exceed the size of an Excel cell; - a **miscellaneous** folder which contain images embedded in text of exported entries, if present. - **Export data**. The default maximum size of all datasets to be exported is 10GB. This can be configured by a system admin in the [AS service.properties file](../../system-documentation/configuration/optional-application-server-configuration.md). We recommend to use [sftp](../general-users/lab-notebook.md#data-access) to download large datasets. If **Make import compatible** is selected, datasets are exported in a **data** folder in a format ready to be uploaded in openBIS using the default eln-lims dropbox. If not, the datasets are exported in a **hiearchy** folder that matches the ELN hierarchy. - **Include levels below from same space**. If selected, all hierachy levels below the selected entity and belonging to the same *Space* are exported. - **Include Object and Dataset parents from same space**. If selected, Object parents and Dataset parents from the same *Space* are exported. Example: I export Object A, in Experiment A, in Space 1. Object B in Experiment B also in Space 1 is parent of Object A. When this option is selected, Object B is also exported, otherwise it is not. - **Include Objects and Datasets parents and children from different spaces**. This allows to export Object and Dataset parents and children that belong to a different Space than the Space from where Objects and Datasets are being exported. Example: I export Object A in Space 1, which has parents in Space 2. If this option is selected, the parents in Space 2 are also exported, otherwise they are not. - **Wait for download to complete in browser**. This is suitable when exporting only metadata or small datasets. When the dowload is ready, a zip file will be available to download from the browser. _Note: ensure that pop-ups are not disabled in your browser_. - **Receive results by email**. If this option is selected, when the export is ready, you will receive an email notification with a download link. Email notification needs to be configured on *system level* during or after installation, as explained in [Configure Data Store Server](../../system-documentation/configuration/optional-datastore-server-configuration.md) We provide below a couple of examples of the export, to clarify how it works. ### **1. Import-compatible export of a Space selecting all options** We select all options from the export widget, as shown below.  ![image info](img/space-export-all-options-import-compatible.png) We export a *Space* called BARILLAC in the Lab Notebook with all its sublevels (see below). ![image info](img/201012-export-barillac-space.png) One *Object* in this *Space* has a protocol as parent, and this is in the METHODS *Space*. The exported zip file contains 3 folders: **A.** **data** folder This contains the datasets in the correct format to be uploaded via eln-lims dropbox, as shown below. ![image info](img/201012-export-data-folder.png) **B.** **hiearchy** folder This contains folders that match the openBIS hierarchy (*Space, Project, Experiment/Collection, Object*). In this case 2 *Space* folders are present: 1. **BARILLAC**: is the exported space. ![image info](img/201012-export-hierarchy-barillac.png) 2. **METHODS**: contains a protocol which is parent of a measurement in the *Space* BARILLAC. This was exported because the option **Include Objects and Datasets parents and children from different spaces** was selected for export. ![image info](img/201012-export-hierarchy-methods.png) Inside each folder, there is a pdf of the corresponding entity. Example: - in the Space folder **BARILLAC** there is a **BARILLAC.pdf** file that contains the metadata of the *Space*; - in the **Measurement 1 (ENTRY8)** folder there is a **Measurement 1 (ENTRY8).pdf** file that contains the metadata of this *Object*; - in the Project folder **PROJECT_1** there is a **PROJECT_1.pdf** file that contains the metadata of the Project; **C.** **xlsx** folder. This contains: - a **metadata.xlsx** file which has the metadata of the exported entities and the corresponding masterdata (types and properties) in the correct format to be re-imported in another openBIS instance; ![image info](img/201012-export-xlsx-folder-xlsx-file.png) - a **scripts** folder that contains evaluation plugins associated to two types defined in the metadata.xlsx file. This folder is present only if the exported types have plugins associated with them. ![image info](img/201012-export-xlsx-folder-scripts.png) - a **miscellaneous** folder that contains images that are embedded in text fields of the exported entities. This folder is present only if exported entities contain images embedded in text. ![image info](img/201012-export-xlsx-folder-miscellaneous.png) If the entities you are exporting contain very large txt with more than 32,767 characters (Excel limit for cell size), these are exported separately to a **data** folder inside the **xlsx** folder. ### **2. Non import-compatible export of a Space selecting all options** We export the same *Space* as described in Example 1, with all options selected, but the export this time is not import-compatible, as shown below.  ![image info](img/space-export-all-options-non-import-compatible.png) In this case the exported *.zip* file contains only 2 folders: **hierarchy** and **xlsx**. Data are exported inside the **hierachy** folder, instead of being in a separate **data** folder. **A.** **hierarchy** folder This contains the same folder structure as described above. In addition, in this case, if an *Object* or an *Experiment/Collection* contains a dataset, this is exported in a **data** folder inside the entity it belongs to. **B.** **xlsx** folder This contains the same files and folders as described in Example 1. The only difference in this case is that the metadata.xlsx is not import-compatible. It contains some fields which are not compatible with openBIS re-import, as explained above. ## Export to Zenodo openBIS provides an integration with the **Zenodo** data repository ([https://zenodo.org/).](https://zenodo.org/) This enables data direct data transfer from openBIS to Zenodo. First of all the connection to Zenodo needs to be configured on *system level* in the DSS service.properties (see [How to configure the openBIS DSS)](../../system-documentation/standalone/optional-datastore-server-configuration.md) If this is configured, a lab manager, who has admin rights for the **Settings,** needs to enable it in the ELN, as explained in [Enable Transfer to Data Repositories](../general-admin-users/admins-documentation/enable-transfer-to-data-repositories.md)**.** ### Create Zenodo Personal Access Token In order to be able to export data to Zenodo, you need a valid Zenodo account. You also need to create a **personal access token.** This can be done from the **Applications** under **Settings** in Zenodo, as shown below: ![image info](img/generate-zenodo-token-1024x498.png) ### Save Zenodo Personal Access Token in openBIS After creating the personal access token in Zenodo, this needs to be stored in openBIS, with the following procedure: 1. Go to **User Profile** under **Utilities** in the main menu, in the **Tools** tab. 2. Enable editing. 3. Add the Zenodo API Token. 4. **Save.**   ![image info](img/201012-user-profile.png) ### Export data to Zenodo To export data to Zenodo: 1. Go to **Exports** -> **Export to Zenodo** under **Utilities** in the main menu, in the **Tools** tab. 2. Select the Export options you want to use: - **Make import compatible**: export can be imported in openBIS. - **Export metadata as PDF**: metadata of selected entries is exported in pdf files. - **Export metadata as XLSX**: metadata of selected entries is exported in an xlsx file. - **Export data**: export datasets. 3. Select the entities you want to export from the menu. 4. Enter a **Submission** **Title.** 5. Click **Export Selected** on top of the export form. 6. The selected data are transferred as a *.zip* file to Zenodo. You are now redirected to Zenodo, where you should fill in additional metadata information. 7. Publish the entry in Zenodo.   ![image info](img/201012-zenodo-export-builder.png)   After you hit the **Publish** button in Zenodo, a new entry with the details of this submission will be created in the **Publications** folder in the **Inventory**. Please note that this may take a few minutes.   ![image info](img/201012-inventory-publications-collection.png) ## Export data to Zenodo in a multi-group instance If you export data from a multi-group instance where you have access to more than one group, you need to select the group under which the new publication entry should be created. In the example below we see 3 group names: GENERAL, ETHRDH, RDM. ![image info](img/201012-zenodo-export-multigroup.png) If you select GENERAL, the publication entry will be created under the PUBLICATION *Space* (if present). If you select ETHRDH, the publication entry will be created under the ETHRDH_PUBLICATION *Space*. If you select RDM, the publication entry will be created under the RDM_PUBLICATION *Space*. ## Export to ETH Research Collection The [ETH Research Collection](https://www.research-collection.ethz.ch/) is a FAIR repository for publications and research data provided by ETH Zurich to its scientists.   Data can be uploaded to the ETH Research Collection **only by members of ETH Zurich**. This export feature is only available to ETHZ members.   To export data to the ETH Research Collection: 1. Go to **Exports** -> **Export to Research Collection** under **Utilities** in the main menu, in the **Tools** tab. 2. Select the Export options you want to use: - **Make import compatible**: export is compatible with import in openBIS. - **Export metadata as PDF**: metadata of selected entries is exported in pdf files. - **Export metadata as XLSX**: metadata of selected entries is exported in an xlsx file. - **Export data**: export datasets. 3. Select what to export from the tree. 4. Select the **Submission Type** from the available list: *Data collection, Dataset, Image, Model, Sound, Video, Other Research Data*. 5. Select the **Retention Period** that will be used in the ETH Research Collection: *10 years, 15 years, indefinite.* This is time for which the data will be preserved in the Research Collection. 6. Click the **Export Selected** button on top of the page. 7. The selected data are transferred as *.zip* file to the ETH Research Collection. You will be redirected to the ETH Research Collection and will need to complete the submission process there.   ![image info](img/201012-research-collection-export-builder.png) A new entry with the details of this submission will be created in the **Publications** folder in the **Inventory** after the submission process in complete. This may take a few minutes. ![image info](img/201012-inventory-publications-collection.png)   The size limit for one single export to the ETH Research Collection is 10GB. ## Export data to the ETH Research Collection in a multi-group instance   If you export data from a multi-group instance where you have access to more than one group, you need to select the group under which the new publication entry should be created. See explanation in section **Export data to Zenodo in a multi-group instance** above.