Difference between revisions of "Team H(oo)KD Week 12 Status Report"
From LMU BioDB 2013
(→Coder Status Update: Added some detail about rerunning the import/export process) |
(→Coder Status Update) |
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ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: | ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: | ||
Java heap space | Java heap space | ||
| − | :*Per Dondi's advice, tomorrow (November 15) | + | :*Per Dondi's advice, tomorrow (November 15) I will try to increase the java heap space and rerun the import/export cycle. |
*Created a custom species profile and committed it to SourceForge. However, this profile still needs work. I will need to work with the QA analyst to add to the profile a species-specific URL that returns a web page describing a gene for the species. | *Created a custom species profile and committed it to SourceForge. However, this profile still needs work. I will need to work with the QA analyst to add to the profile a species-specific URL that returns a web page describing a gene for the species. | ||
Revision as of 07:08, 15 November 2013
| Project Manager/Coder: Katrina Sherbina | Quality Assurance: Hilda Delgadillo | GenMAPP User: Dillon Williams |
| Project Guidelines: | Gene Database Project | Report Guidelines | |
| Team Journal Assignments | Week 12 Status Report | Week 13 Status Report | Week 15 Status Report |
| Individual Status Reports: | HDelgadi Project Notebook | dwilliams Project Notebook | Ksherbina Project Notebook |
| Useful Links: | Class Page | Team Home Page |
| Final Product | Project Deliverables |
Refer to the calendar on the team home page to see the milestones for this week.
Coder Status Update
- Began the gene database import export cycle:
- Downloaded the UniProt XML file for Chlamydia trachomatis serovar A strain HAR-13.
- Downloaded the GOA file for Chlamydia trachomatis serovar A.
- Created a PostgreSQl database for the species.
- I was able to import both the UniProt XML file and the GOA file for the C. trachomatis into the PostgreSQL database through gmbuilder-32bit.bat. While I was also able to import the OBO-XML file, I could not finish processing the data. After gmbuilder processed the 81000 term, I received the following error after which gmbuilder ceased the processing of the OBO-XML file:
ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
- Per Dondi's advice, tomorrow (November 15) I will try to increase the java heap space and rerun the import/export cycle.
- Created a custom species profile and committed it to SourceForge. However, this profile still needs work. I will need to work with the QA analyst to add to the profile a species-specific URL that returns a web page describing a gene for the species.
Ksherbina (talk) 23:04, 14 November 2013 (PST)
QA Status Update
- Obtaining the files GOA file, UniProt XML file, and the GO OBO-XML file were essential to obtain this week. With these files we will begin the importing and exporting of the files Friday November 15th, so we may continue with the exporting of files into the GenMAPP Gene Database next week.
HDelgadi (talk) 10:46, 14 November 2013 (PST)
