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Revision as of 12:30, 21 December 2016

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<!-- ADD REPORT LINK -->

=== Statement of Work ===

=== Statement of Work ===

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On my project, I completed a successful export of [https://github.com/lmu-bioinformatics/xmlpipedb/tree/master/GenMAPP%20Gene%20Databases/V.%20cholerae/%23current V. cholerae] which solved the problems I had faced in the [[Nanguiano_Week_9|initial export I had attempted]]. To perform the export, I modified an existing [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/godb/xsd/go_daily-obo-xml-manual.dtd GO OBO-XML DTD schema] to work with [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/GenMAPP%20Gene%20Databases/V.%20cholerae/%23current/source_files/go_daily-termdb.obo-xml a new OBO-XML file] that used a schema that no longer worked with GenMAPP Builder. I ran [https://github.com/lmu-bioinformatics/xmlpipedb/tree/master/xsd2db xsd2db] on the manually edited DTD file to obtain files that could be used in GenMAPP Builder. I ran [https://github.com/lmu-bioinformatics/xmlpipedb/tree/master/godb/tools GODB Post Processor] on the specified [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/godb/hbm/To.hbm.xml HBM] and [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/godb/sql/schema.sql SQL] files to allow them to be properly added to GenMAPP Builder. I replaced the old files in GenMAPP Builder with the new files generated by xsd2db and GODBPostProcessor, and overwrote [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/gmbuilder/sql/gmbuilder.sql GMBuilder.sql] with the contents of the schema.sql file that was edited by GODB Post Processor so that it could build the proper table initially. I wrote [https://github.com/lmu-bioinformatics/xmlpipedb/wiki/Updating-GMBuilder-to-work-GO's-OBO-XML-Files documentation on how to perform updates to GMBuilder] in the event of an OBO-XML schema change in the future. Following all of this, I performed an export of V. cholerae, which completed successfully. Then I performed quality assurance on the export, the details of which can be found in the  

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On my project, I completed a successful export of [https://github.com/lmu-bioinformatics/xmlpipedb/tree/master/GenMAPP%20Gene%20Databases/V.%20cholerae/%23current V. cholerae] which solved the problems I had faced in the [[Nanguiano_Week_9|initial export I had attempted]]. To perform the export, I modified an existing [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/godb/xsd/go_daily-obo-xml-manual.dtd GO OBO-XML DTD schema] to work with [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/GenMAPP%20Gene%20Databases/V.%20cholerae/%23current/source_files/go_daily-termdb.obo-xml a new OBO-XML file] that used a schema that no longer worked with GenMAPP Builder. I ran [https://github.com/lmu-bioinformatics/xmlpipedb/tree/master/xsd2db xsd2db] on the manually edited DTD file to obtain files that could be used in GenMAPP Builder. I ran [https://github.com/lmu-bioinformatics/xmlpipedb/tree/master/godb/tools GODB Post Processor] on the specified [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/godb/hbm/To.hbm.xml HBM] and [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/godb/sql/schema.sql SQL] files to allow them to be properly added to GenMAPP Builder. I replaced the old files in GenMAPP Builder with the new files generated by xsd2db and GODBPostProcessor, and overwrote [https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/gmbuilder/sql/gmbuilder.sql GMBuilder.sql] with the contents of the schema.sql file that was edited by GODB Post Processor so that it could build the proper table initially. I wrote [https://github.com/lmu-bioinformatics/xmlpipedb/wiki/Updating-GMBuilder-to-work-GO's-OBO-XML-Files documentation on how to perform updates to GMBuilder] in the event of an OBO-XML schema change in the future. Following all of this, I performed an export of V. cholerae, which completed successfully. Then I performed quality assurance on the export, the details of which can be found in the [[Media:NA_Final_Report.docx|report]]. Following this, I converted the [https://xmlpipedb.cs.lmu.edu XMLPipeDB website] to Jekyll, and moved it to a [https://github.com/lmu-bioinformatics/xmlpipedb/tree/gh-pages gh-pages branch] on github, giving it a new [http://lmu-bioinformatics.github.io/xmlpipedb/ github domain]. The primary website was redirected to the github site link. Following this, I ran [http://schemaspy.sourceforge.net/ SchemaSpy] on the database, the results of which can be found [http://lmu-bioinformatics.github.io/xmlpipedb/assets/schemaspy/uniprotdb/ here for uniprotdb], [http://lmu-bioinformatics.github.io/xmlpipedb/assets/schemaspy/godb/ here for godb], and [http://lmu-bioinformatics.github.io/xmlpipedb/assets/schemaspy/gmbuilderdb/ here for gmbuilder]. I also wrote up [https://github.com/lmu-bioinformatics/xmlpipedb/wiki/Using-SchemaSpy documentation on how to use SchemaSpy] for future reference.

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Report  <!-- ADD LINK HEREEEE -->

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. Following this, I converted the [https://xmlpipedb.cs.lmu.edu XMLPipeDB website] to Jekyll, and moved it to a [https://github.com/lmu-bioinformatics/xmlpipedb/tree/gh-pages gh-pages branch] on github, giving it a new [http://lmu-bioinformatics.github.io/xmlpipedb/ github domain]. The primary website was redirected to the github site link. Following this, I ran [http://schemaspy.sourceforge.net/ SchemaSpy] on the database, the results of which can be found [http://lmu-bioinformatics.github.io/xmlpipedb/assets/schemaspy/uniprotdb/ here for uniprotdb], [http://lmu-bioinformatics.github.io/xmlpipedb/assets/schemaspy/godb/ here for godb], and [http://lmu-bioinformatics.github.io/xmlpipedb/assets/schemaspy/gmbuilderdb/ here for gmbuilder]. I also wrote up [https://github.com/lmu-bioinformatics/xmlpipedb/wiki/Using-SchemaSpy documentation on how to use SchemaSpy] for future reference.

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=== Assessment of Project ===

=== Assessment of Project ===

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 I am very pleased with the results of my work on the V. cholera export (and corresponding edits to GMBuilder), the XMLPipeDB site, and the SchemaSpy documentation. The export and quality assurance performed seemed to indicate that the edits to GMBuilder will allow for future GO OBO-XML files to run smoothly without error, provided another DTD schema change does not occur. However, should one occur in the future, the documentation written should make the process much smoother for future developers. Due to the use of Github, I would say the project was very organized. Tasks and accomplishments were clearly marked, and questions and concerns were generally kept in their relevant threads. The entire process from beginning to end is documented fully on [https://github.com/lmu-bioinformatics/xmlpipedb/issues github's issues], in issues both opened and closed as of the time of this writing. Additionally, all code written and changed can be found in the [https://github.com/lmu-bioinformatics/xmlpipedb github repository] for XMLPipeDB. It is my belief that Github allowed for this project to run very smoothly and for all correspondences to be recorded without confusion.
-I did find the creation of the report to be very difficult due to the nature of the class this semester. However, for the most part, I feel as though it was fully complete. The only sections not completed were those using GenMAPP (as GenMAPP crashes upon running on my computer), and the database schema diagram (though the SchemaSpy results on the website may be a substitute for this).
+I did find the creation of the report to be very difficult due to the nature of the class this semester, at least within the scope of the existing report guidelines. However, for the most part, I feel as though it was fully complete. The only sections not completed were those using GenMAPP (as GenMAPP crashes upon running on my computer), and the database schema diagram (though the SchemaSpy results on the website may be a substitute for this).
 === Reflection on the Process ===

Nanguiano Individual Assessement - Revision history

Nanguiano: added report link

Nanguiano: added a bit more