Interpret Errors in the .log File

First, view the .log file.  If your specimen archive does not upload correctly, you will see "ERROR" as the final status for the pipeline task on the "Data Pipeline" page.  To view the error log, click on the word "ERROR" to reach the "Job Status" page. 

Next, identify the error.  To determine which file in the .specimens archive caused problems during import, look at the lines immediately preceding the first mention of an "ERROR."  You will see the type of data (e.g., "Specimens" or "Site") that was not imported properly. Note that the name of the uploaded file (e.g., "labs.tsv") does not necessarily have a 1-to-1 mapping to the type of data imported (e.g., "labs.tsv" provides "Site" data).  

Example.   Consider the log file produced by failed import of a specimen archive that included a labs.tsv file with bad data (unacceptably long site names).  In the .log file excerpted below, you can see that the data type mentioned just above the "ERROR" line is "Site."  Since "labs.tsv" contains "Site" data, you can conclude that the labs.tsv file caused the error.  Note that earlier lines in the .log file mention "Specimens," indicating that the specimens.tsv file was imported successfully before an error was hit while importing the labs.tsv file.

Excerpt from this log file, with highlighting added: 

06 Mar 2008 23:27:39,515 INFO : Specimen: Parsing data file for table...



06 Mar 2008 23:27:39,515 INFO : Specimen: Parsing complete.



06 Mar 2008 23:27:39,890 INFO : Populating temp table...



06 Mar 2008 23:27:40,828 INFO : Temp table populated.



06 Mar 2008 23:27:40,828 INFO : Site: Parsing data file for table...



06 Mar 2008 23:27:40,828 INFO : Site: Parsing complete.



06 Mar 2008 23:27:40,828 INFO : Site: Starting merge of data...



06 Mar 2008 23:27:40,828 ERROR: Unexpected processing specimen archive