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rdms:metadata:metadatawebportal [2023/09/11 09:50]
pascal [Import metadata] |
rdms:metadata:metadatawebportal [2023/09/13 10:36] (current)
pascal [Import Metadata] |
| {{ :rdms:webapp:meta_crud_0.png?800 |}} | {{ :rdms:webapp:meta_crud_0.png?800 |}} |
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| ==== Create Metadata ==== | ==== Create Metadata in the Web Portal==== |
| | <hidden> |
| When you first upload a file to the RDMS, all the metadata attached to it will be related to system information, such as upload time and file size, as shown above. You can easily attach new metadata to your data by right-clicking the object or collection you wish to add metadata to and then selecting ''Add Metadata''. If you click any of the {{:rdms:webapp:interface_info_button.png?20|}} icons highlighted in the screenshot below, the web portal will open a side menu containing all information about the selected data. There you can easily check what metadata is already attached to the data you selected, as described in the [[https://wiki.hpc.rug.nl/rdms/metadata/metadatawebportal#read_metadata|Read Metadata section]]. | When you first upload a file to the RDMS, all the metadata attached to it will be related to system information, such as upload time and file size, as shown above. You can easily attach new metadata to your data by right-clicking the object or collection you wish to add metadata to and then selecting ''Add Metadata''. If you click any of the {{:rdms:webapp:interface_info_button.png?20|}} icons highlighted in the screenshot below, the web portal will open a side menu containing all information about the selected data. There you can easily check what metadata is already attached to the data you selected, as described in the [[https://wiki.hpc.rug.nl/rdms/metadata/metadatawebportal#read_metadata|Read Metadata section]]. |
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| {{ :rdms:webapp:meta_crud_3.png?800 |}} | {{ :rdms:webapp:meta_crud_3.png?800 |}} |
| | </hidden> |
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| ==== Read Metadata ==== | |
| | ==== Read Metadata in the Web Portal ==== |
| | <hidden> |
| Once you created metadata related to your data, you will always be able to display that information by clicking on the {{:rdms:webapp:interface_info_button.png?20|}} icon next to the respective entry in the web portal. In the screenshot below, clicking on the icon in the red box will display the metadata for the selected object, while clicking on the icon in the blue box will display the information of the current collection, in this case the user's home collection. | Once you created metadata related to your data, you will always be able to display that information by clicking on the {{:rdms:webapp:interface_info_button.png?20|}} icon next to the respective entry in the web portal. In the screenshot below, clicking on the icon in the red box will display the metadata for the selected object, while clicking on the icon in the blue box will display the information of the current collection, in this case the user's home collection. |
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| {{ :rdms:webapp:meta_crud_4.png?800 |}} | {{ :rdms:webapp:meta_crud_4.png?800 |}} |
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| When the {{:rdms:webapp:interface_info_button.png?20|}} icon was clicked, a menu will appear on the right side of the portal. The first tab contains the metadata information of the object or collection you selected. Depending on the amount of metadata you recorded for this object, you might need to scroll down to find the entry you are interested in. | When the {{:rdms:webapp:interface_info_button.png?20|}} icon is clicked, a menu will appear on the right side of the portal. The first tab contains the metadata information of the object or collection you selected. Depending on the amount of metadata you recorded for this object, you might need to scroll down to find the entry you are interested in. |
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| **Note**:\\ | **Note**:\\ |
| The metadata entries are ordered based on the time they where created. If you enter ''Test_meta_0'' after ''Test_meta_1'', as is shown in the figure, the system **will not** reorder them numerically. | The metadata entries are ordered based on the time they were created. If you enter ''Test_meta_0'' after ''Test_meta_1'', as is shown in the figure, the system **will not** reorder them numerically. |
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| {{ :rdms:webapp:meta_crud_5.png?800 |}} | {{ :rdms:webapp:meta_crud_5.png?800 |}} |
| | </hidden> |
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| ==== Update Metadata ==== | ==== Update Metadata in the Web Portal ==== |
| | <hidden> |
| Whether it be because you do not always have all the details related to certain data at the time of its storage in the RDMS or because you spot an error, you can change or update metadata you attached to an object or collection in the way described below. | Whether it be because you do not always have all the details related to certain data at the time of its storage in the RDMS or because you spot an error, you can change or update metadata you attached to an object or collection in the way described below. |
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| {{ :rdms:webapp:meta_crud_7.png?800 |}} | {{ :rdms:webapp:meta_crud_7.png?800 |}} |
| ==== Delete Metadata ==== | </hidden> |
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| | ==== Delete Metadata in the Web Portal ==== |
| | <hidden> |
| During your data's life cycle, errors can occur or metadata tags can become irrelevant. For those cases, you can easily delete a metadata tag by selecting the {{:rdms:webapp:interface_info_button.png?20|}} icon once again and clicking on the {{:rdms:webapp:delete_icon.png?30|}} button next to a metadata entry in the metadata tab in the right-side window. | During your data's life cycle, errors can occur or metadata tags can become irrelevant. For those cases, you can easily delete a metadata tag by selecting the {{:rdms:webapp:interface_info_button.png?20|}} icon once again and clicking on the {{:rdms:webapp:delete_icon.png?30|}} button next to a metadata entry in the metadata tab in the right-side window. |
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| {{ :rdms:webapp:meta_crud_9.png?800 |}} | {{ :rdms:webapp:meta_crud_9.png?800 |}} |
| | </hidden> |
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| | ===== Automatic Extraction of Metadata ===== |
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| | What we described above is the functionality of the web portal to let the user add metadata entries by hand. However, there are files which require a large amount of metadata to be properly described. Such data often has the information needed to describe stored as metadata in their file header. The web portal offers the user the possibility to extract and import the metadata contained in the file header directly into the RDMS. |
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| | To access this functionality, right-click the file you wish to extract metadata from, then scroll down the menu to ''Extract metadata''. |
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| | {{ :rdms:webapp:meta_extract_1.png?800 |}} |
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| | Once you click on the menu item, the system will display the message below to inform you of the formats that are currently supported for automatic metadata extraction. To check if the extraction was successful, follow the same steps as in [[https://wiki.hpc.rug.nl/rdms/metadata/metadatawebportal#read_metadata|Read Metadata]] and verify that the header in your file and the metadata in the RDMS overlap. |
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| | {{ :rdms:webapp:meta_extract_2.png?800 |}} |
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| | **Note**: The extract function of the web portal extracts information contained in the file header. If your file does not have a header, no information will be extracted, even when the system reports successfully finishing the extraction. |
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| | ==== Supported File Formats for automated Metadata Extraction ==== |
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| ====== Automatic extraction of metadata ====== | Below you can find the list of file extension for which automatic extraction is supported: |
| |
| What we described above is the functionality of the web portal to let the user add metadata entries by hand. There are data objects or collections, however, which require a large amount of metadata to be properly described. Such data objects often have the information needed to describe them stored in their file header. The web portal offers the user the possibility to extract and import the metadata contained in the file header directly into the RDMS system. Contrary to the manual input, this action generates a single metadata entry for multiple values, similarly to what you would get by inputting values into a template. | * ''.dcm'' , ''.dcm30'': DICOM (Digital Imaging and Communications in Medicine) images (dicomstandard.org) |
| | * ''.doc'', ''.docx'': Microsoft Word documents (microsoft.com) |
| | * ''.fits'', ''.fit'': FITS (Flexible Image Transport System) images (fits.gsfc.nasa.gov) |
| | * ''.hdr'', ''.nii'': NIfTI (Neuroimaging Informatics Technology Initiative) headers (nifti.nimh.nih.gov) |
| | * ''.jpeg'', ''.jpg'' : Exif (Exchangeable image file format) (en.wikipedia.org/wiki/Exif) |
| | * ''.pdf'': -'description': PDF (Portable Document Format) files (adobe.com/acrobat/about-adobe-pdf.html) |
| | * ''.ppt'', ''.pptx'': Microsoft Powerpoint documents (microsoft.com) |
| | * ''.tif'', ''.tiff'': Exif (Exchangeable image file format) (en.wikipedia.org/wiki/Exif) |
| | * ''.txt'': ASCII text files containing key=value pairs |
| | * ''.xls'', ''.xlsx'': Microsoft Excel documents (microsoft.com) |
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| {{ :rdms:webapp:meta_extract_1.png?800 |}} | If the file type you wish to extract metadata from has a readable file structure and is not present in the list above, we can probably add that file type to the list of supported extensions. Please send an e-mail to [[rdms-support@rug.nl|RDMS support]] to let us know that you wish for a file type to be added to the list. |
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| To access this functionality, right-click the file you wish to extract metadata from, then scroll down the menu to ''Extract metadata''. Once you click on the menu item, the system will display the message below to inform you of the formats that are currently supported for automatic metadata extraction. To check if the extraction was successful, follow the same steps as in [[https://wiki.hpc.rug.nl/rdms/metadata/metadatawebportal#read_metadata|Read Metadata]] and verify that the header in your file and the metadata in the RDMS overlap. | |
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| **N.B.**: The extract function of the web portal extracts information contained in the file header. If your file does not have a header, no information will be extracted, even when the system reports successfully finishing the extraction. | ===== Import Metadata ===== |
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| {{ :rdms:webapp:meta_extract_2.png?800 |}} | Metadata can also be imported from a local file using the web portal. The ''Name'', ''Value'', and ''Extra Value'' are called AVUs for Attribute, Value, Unit combinations in this context. AVUs are defined in a so-called JSON structure as a ''.txt'' file or a ''.json'' file. Multiple AVUs can be added at once with this approach. |
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| Below you can find the list of file extension for which automatic extraction is supported: | The structure of the file should be as followed: |
| | <code> |
| | [ |
| | {"Attribute" : "Author", |
| | "Value": "Tester_1", |
| | "Unit": "" |
| | }, |
| | {"Attribute" : "Distance", |
| | "Value": "100", |
| | "Unit": "km" |
| | }, |
| | {"Attribute" : "Location", |
| | "Value": "Groningen", |
| | "Unit": "" |
| | } |
| | ] |
| | </code> |
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| * 'dcm' , 'dcm30': 'description': 'DICOM (Digital Imaging and Communications in Medicine) image','reference': 'dicomstandard.org', | Metadata from a local file can be added to both collections and objects by right clicking the target of interest and selecting the ''Load metadata'' option. |
| * 'doc', 'docx': 'description': 'Microsoft Word document', -'reference': 'microsoft.com', | |
| * 'fits', 'fit': 'description': 'FITS (Flexible Image Transport System) image', -'reference': 'fits.gsfc.nasa.gov', | |
| * 'hdr', 'nii': 'description': 'NIfTI (Neuroimaging Informatics Technology Initiative) header', -'reference': 'nifti.nimh.nih.gov', | |
| * 'jpeg', 'jpg' : 'description': 'Exif (Exchangeable image file format)', -'reference': 'en.wikipedia.org/wiki/Exif', | |
| * 'pdf': -'description': 'PDF (Portable Document Format) file', -'reference': 'adobe.com/acrobat/about-adobe-pdf.html', | |
| * 'ppt', 'pptx' -'description': 'Microsoft Powerpoint document', -'reference': 'microsoft.com', | |
| * 'tif', 'tiff': -'description': 'Exif (Exchangeable image file format)', -'reference': 'en.wikipedia.org/wiki/Exif', | |
| * 'txt': -'description': 'ASCII text file containing key=value pairs', -'reference': '', | |
| * 'xls', 'xlsx' -'description': 'Microsoft Excel document', -'reference': 'microsoft.com', | |
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| If the file type you wish to extract metadata from has a readable file structure and is not present in the list above, we can probably add that file type to the list of supported extensions. Please send an e-mail to [[rdms-support@rug.nl|RDMS support]] to let us know that you wish for a file type to be added to the list. | {{ :rdms:metadata:import_1_new.png?800 |}} |
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| | Upon selecting a file with AVUs in a JSON structure as indicated above, the metadata is automatically recognized and can be added by selecting the ''Load metadata'' button. In this example a .txt file was used. **Please note that multiple AVUs can be added at once.** |
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| ====== Import metadata ====== | {{ :rdms:metadata:import_2_new.png?800 |}} |
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| Metadata can also be imported from a local file using the web portal. | Upon loading the AVU file the metadata is displayed for the selected data. |
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| | {{ :rdms:metadata:import_3_new.png?800 |}} |