Repository housekeeping

lmu-bioinformatics / xmlpipedb

XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources.

http://xmlpipedb.cs.lmu.edu

GNU Lesser General Public License v3.0

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Repository housekeeping #33

Open kdahlquist opened 7 years ago

kdahlquist commented 7 years ago

[x] It looks like we need to add the LICENSE file at the top level of the repository.
[x] We need to put a README at the top level of the repository.
[x] I'll go ahead and add the Code of Conduct when I do GRNmap and GRNsight.
[x] If I get around to it, I might rearrange some folders, creating a single "documents" folder with subfolders for manuscripts, posters, abstracts, and manual. It looks like the "xmlpipedb" folder should be removed and its contents moved to one of these other folders.

kdahlquist commented 7 years ago

Create a documents folder on the top level with the following sub-directories:

posters
manual
manuscripts (which is a re-naming of the papers folder).

kdahlquist commented 7 years ago

Rearrange files in GenMAPP Gene Databases folder as follows:

in the V. cholerae folder move the README.md file from the V. cholerae 20101022 folder into the #current folder.
The #current folder should then have the following structure:
- "source_files" directory: this contains the UniProt XML, GO OBO-XML, and goa files with their original filenames.
- there should be a README.md file in this directory that gives the filenames and the versions for these three files (simple, like in the Gene Database Testing Report).
- the current gdb, zipped together with the PDF version of the readme
- "README.md" file which is the markdown version of the readme for the gdb; this gets converted into a PDF for inclusion with the zipped gdb
- the PDF version of the readme to stand alone as well.

kdahlquist commented 7 years ago

Readme content is waiting for content to be restored on the XMLPipeDB website #39.

Vibrio stuff is waiting on getting a functional export first.

NAnguiano commented 7 years ago

Everything except the readme at the top level is complete, still awaiting completion of #39.

kdahlquist commented 7 years ago

We found the About content here:

https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/site/src/site/resources/html/briefsketch.html

and here:

https://github.com/lmu-bioinformatics/xmlpipedb/blob/master/site/src/site/resources/html/abstract.html

so we can build a ReadMe from that.

We'll ask @dondi to comment on #39 at the GRNsight meeting today.

kdahlquist commented 7 years ago

@NAnguiano completed all tasks assigned to her. I'm keeping this one open, though, so that when @kdahlquist and @dondi next meet, they can do a quick review of all the directories and move anything that needs to be moved. I note that there is a different version of the manual in the xmlpipedb directory that should be moved or deleted.