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Bexis2 introduction for spp2089
- 2. BEXIS Community Development Partner Project Instances nafiseh.navabpour@ufz.de SPP2089.ufz.de 2
- 3. BEXIS2 Team • Open Source Software Licence: GNU LGPL 3.0 • Website: http://bexis2.uni-jena.de • Demo: http://bexis2.vmguest.uni-jena.de/ • Code: https://github.com/BEXIS2 • Annual User and Developer Conference (since 2015) nafiseh.navabpour@ufz.de SPP2089.ufz.de 3
- 5. BEXIS2 Potencials • designed for collaborative projects • focus on active data (i.e. project life-time) • focus on tabular data, but not limited to • focus on data integration and re-use the structures • Worldwide, modular, free and open source nafiseh.navabpour@ufz.de SPP2089.ufz.de 5
- 6. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 6
- 8. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 8
- 10. Registration nafiseh.navabpour@ufz.de SPP2089.ufz.de 10 Receive an email from: support-spp2089@ufz.de
- 11. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 11
- 13. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 13
- 14. nafiseh.navabpour@ufz.de SPP2089.ufz.de 14 Creating a data structure
- 15. nafiseh.navabpour@ufz.de SPP2089.ufz.de 15 Creating a data structure
- 16. nafiseh.navabpour@ufz.de SPP2089.ufz.de 16 Creating a data structure
- 20. Creating a data structure Restrictions • Free to choose a column name (e.g. [„-%&}) • Choose the common names • Free to design a data table • Design a re-usable structure • Think about empty cells • Not measured or No result • Specify the data type in each column • String: free text format • Integer: …, -3, -2, -1, 0, 1, 2, 3, … • Double: 16 digits (e.g. 2.455433, -0.00006) • Decimal: 29 digits • Date/Time: yyyy-MM-dd, MM/dd/yy, hh:mm, hh:mm:ss nafiseh.navabpour@ufz.de SPP2089.ufz.de 20
- 22. Creating a Data Structure nafiseh.navabpour@ufz.de SPP2089.ufz.de 22
- 23. Creating a Data Structure nafiseh.navabpour@ufz.de SPP2089.ufz.de 23
- 24. Creating a Data Structure nafiseh.navabpour@ufz.de SPP2089.ufz.de 24
- 25. Looking for a Variable template In data structure editor nafiseh.navabpour@ufz.de SPP2089.ufz.de 25
- 26. Looking for a Variable template In variable template manager nafiseh.navabpour@ufz.de SPP2089.ufz.de 26
- 27. Create Variable Template nafiseh.navabpour@ufz.de SPP2089.ufz.de 27
- 30. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 30
- 31. Downloading an Excel template nafiseh.navabpour@ufz.de SPP2089.ufz.de 31
- 32. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 32
- 33. Working with the Excel template nafiseh.navabpour@ufz.de SPP2089.ufz.de 33
- 34. Working with the Excel template nafiseh.navabpour@ufz.de SPP2089.ufz.de 34
- 35. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 35
- 36. Creating a Dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 36
- 37. Creating a Dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 37
- 38. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 38
- 44. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 44
- 45. Uploading the dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 45
- 46. Uploading the dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 46
- 47. Uploading the dataset Select File nafiseh.navabpour@ufz.de SPP2089.ufz.de 47
- 48. Uploading the dataset Specify Dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 48
- 49. Uploading the dataset Validation nafiseh.navabpour@ufz.de SPP2089.ufz.de 49
- 50. Uploading the dataset Finish! nafiseh.navabpour@ufz.de SPP2089.ufz.de 50
- 51. Uploading the dataset Upload text file nafiseh.navabpour@ufz.de SPP2089.ufz.de 51
- 52. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 52
- 53. Seeing a Dataset Metadata nafiseh.navabpour@ufz.de SPP2089.ufz.de 53
- 54. Seeing a Dataset Primary Data nafiseh.navabpour@ufz.de SPP2089.ufz.de 54
- 55. Seeing a Dataset Data Structure nafiseh.navabpour@ufz.de SPP2089.ufz.de 55
- 56. Seeing Dataset Dataset Permission nafiseh.navabpour@ufz.de SPP2089.ufz.de 56
- 59. The Workflow • Registration • Login • Creating a data structure • Downloading an Excel template • Working with the Excel template • Creating a Dataset • Providing metadata • Uploading the dataset • Seeing a Dataset • Searching nafiseh.navabpour@ufz.de SPP2089.ufz.de 59
- 62. Push Big File nafiseh.navabpour@ufz.de SPP2089.ufz.de 62
- 63. Push Big File nafiseh.navabpour@ufz.de SPP2089.ufz.de 63
- 64. Push Big File nafiseh.navabpour@ufz.de SPP2089.ufz.de 64
- 67. Import Data Select File nafiseh.navabpour@ufz.de SPP2089.ufz.de 67
- 68. Import Data Select metadata schema nafiseh.navabpour@ufz.de SPP2089.ufz.de 68
- 69. Import Data Sheet structure and Areas nafiseh.navabpour@ufz.de SPP2089.ufz.de 69
- 72. Access to a dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 72
- 73. Access to a dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 73
- 74. Access to a dataset Send a request to see a dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 74
- 75. Access to a dataset Make a decision nafiseh.navabpour@ufz.de Note: It is a one-time decision! SPP2089.ufz.de 75
- 76. Access to a dataset rBExIS nafiseh.navabpour@ufz.de SPP2089.ufz.de 76
- 77. Access to a dataset rBExIS • Exchange data between R and BExIS2 • Get single and multiple datasets • Upload new or update existing datasets • Install devtools • install.packages("devtools") • Install rBExIS package from github • library(devtools) • install_github("cpfaff/rBExIS", subdir = "rBExIS") nafiseh.navabpour@ufz.de SPP2089.ufz.de 77
- 78. Access to a dataset rBExIS - Web API Data Access Sample REST API calls: Data • http://spp2089.ufz.de/api/data/6 – /api/data/6?header=id,name – /api/data/6?filter=(Grade>50 AND Grade <90) – /api/data/6?header=id,name&filter=(Grade>50) Sample REST API calls: Metadata • http://spp2089.ufz.de/api/metadata/6 nafiseh.navabpour@ufz.de SPP2089.ufz.de 78
- 79. Access to a dataset Download Dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 79
- 80. Access to a dataset Download Dataset nafiseh.navabpour@ufz.de SPP2089.ufz.de 80
- 81. Access to a dataset Download Excel nafiseh.navabpour@ufz.de SPP2089.ufz.de 81
- 82. Access to a dataset Download Excel Template nafiseh.navabpour@ufz.de SPP2089.ufz.de 82
- 83. Access to a dataset Download Excel nafiseh.navabpour@ufz.de SPP2089.ufz.de 83
- 84. Access to a dataset Download Text nafiseh.navabpour@ufz.de SPP2089.ufz.de 84
- 85. Access to a dataset Download Text nafiseh.navabpour@ufz.de SPP2089.ufz.de 85
- 89. Help Guides Data Planning and Data Collection nafiseh.navabpour@ufz.de SPP2089.ufz.de 89
- 99. Error Data is not available nafiseh.navabpour@ufz.de SPP2089.ufz.de 99
- 101. Thank you for your attention! nafiseh.navabpour@ufz.de SPP2089.ufz.de 101
Editor's Notes
- BEXIS 2 is a software that needs individual instances, so ist NOT a portal Designed for large collaborative projects as a central data management and exchange platform, best operated with a dedicated Data Manager It is designed for active data, meaning, that data can evolve and be dynamic, the scope is the project-life-time, For long-term preservation data should be published to dedicated repositories, BEXIS 2 provides mechanisms/workfows for that Focus on tabular data, since this is the main data type in the domains we work with, more details in a minute Focus on data integration and re-use means: a) modelling the data structure, variables, units of each dataset and make those accessible to others, b) re-use of any information in the system to relief users from re-entering things
- What do you think? Could we upload this table exactly with this format? What is the problem?
- You need transform your table to a form with only one line of header
- PLEASE check at first the list of variables.
- You can save the data structure and come back later to edit it.
- Enable macros Quality check
- Open the box of the information about OWNER Open the OWNER 1 Open the box of the information about PERSON