BIMS: Importing Data

To import data into BIMS, the data need to be in BIMS templates. Phenotype data either needs to be files exported from Field Book or data entered into the BIMS templates.  To download the BIMS templates, click on the "Data Import" section of the left-hand accordion menu and then click on "Template List" (Fig. 18A).  You will then see the "Data Templates" tab that has information about each template and links to download the template (Fig. 18B).  You can also download all the templates as a single Excel file by clicking below (Fig. 18C).

Figure 18.  Downloading BIMS data templates

 

To upload data files, click on the "Upload data" link (Fig. 19A) under the "Data Import" section and the "Upload Data" tab will open.  Then, under the "Upload data by Excel template" section on the right side, select the data file and click "Upload" (Fig. 19B).  Enter a file description if desired, and once the file has uploaded, click "Submit".  The file name will then appear in the "Uploaded Files" section (Fig. 19C).

Figure 19.  Upload Data tab in BIMS

 

To view the progress of an upload job, click on the file name under "Uploaded files" (Fig. 20A).  Summary information about the file will appear below and then click the "View" button (Fig. 20B).  The "Upload Job" tab appears and will show the "Job Details" table (Fig. 20C).  On the table you can see the job progress.  If the job is still running, you can click the "Refresh" button to update the job progress.

Figure 20.  How to view upload job progress

 

BIMS also provides links to log files on the "Upload Job" tab.  When a job successfully loads, there are three types of logs: New Data Logs, Warning Logs, and Duplicate Logs.  To view the logs, first expand the log type section you want to view and then click on "view" (Fig. 21A) to see the log messages (Fig. 21B).  New Data Logs describe the new data that was loaded.  Warning Logs indicate if any data was skipped due to incorrect column headers or typos, but this data was not critical for BIMS to load data so the job still completed.  It is recommended that you look at the Warning Logs to make sure data was not omitted accidently.  The Duplicate Logs display what data was a duplication of data already present in BIMS.

Figure 21.  BIMS upload job logs

 

If there is an error in the data that causes the upload job to fail, you will see "FAILED" under the job progress (Fig. 22A).   An Error Log section will also be available on the "Uploading Job" tab.  Expand the Error Log section and click on "view" (Fig. 22B) to see the error messages (Fig. 22C).  Use the Error Log information to correct the original file.

Figure 22.  Failed jobs and the Error Logs

 

To re-run a failed job, use the "Re-Run Job" section on the "Uploading Job" tab.  Select and upload the revised file (Fig. 23A) and then click the "Re-Run the Job" button (Fig. 23B).  To monitor the re-run progress, click on the "Refresh" button (Fig. 23C). If the error was something that you did online, not in the template, for example you had a typo in the configuration setting, it is best not to use Re-Run Job, but go back and start the loading process again.

Figure 23.  Re-running a job