candygene / siga Goto Github PK

Issue by bakhshir
Tuesday Mar 21, 2017 at 21:05 GMT
Originally opened as NLeSC/candYgene#5

The dictionary feature_onto_class representing feature type to SO mappings can be provided from the external input file (currently hardcoded).

Issue by bakhshir
Wednesday Mar 22, 2017 at 12:36 GMT
Originally opened as NLeSC/candYgene#8

These changes are related to the issues #1, #2 and #7.

bakhshir included the following code: https://github.com/NLeSC/candYgene/pull/8/commits

Issue by bakhshir
Tuesday Mar 21, 2017 at 21:07 GMT
Originally opened as NLeSC/candYgene#6

Add namespaces to a config file (currently hardcoded).

Issue by bakhshir
Tuesday Mar 21, 2017 at 21:03 GMT
Originally opened as NLeSC/candYgene#4

Adding usage parameters of SIGA.py to markdown.

Issue by bakhshir
Tuesday Mar 21, 2017 at 20:50 GMT
Originally opened as NLeSC/candYgene#3

We can add an information regarding required version of the python packages and python itself.

• created - overwrites the current date added at runtime
• modified

Check if the repo has everything from the software checklist, in preparation for the release:

Version control

• version control from the beginning of the project
• use git as version control system (vcs)
• choose one branching model
• public vcs repository
• meaningful commit messages need to work on this

Releases

• semantic versioning
• tagged releases
• CHANGELOG.md
• one command install
• package in package manager
• discuss release cycle with coordinator
• release quick-scan by other engineer
• Citeable
• Dissemination

Licensing

• Apache 2 license
• compatible license of all libraries
• NOTICE(.txt|.md)

Communication

• home page
• discussion list
• demo docker image in dockerhub (with Dockerfile)
• an online demo
• screencast

Code Quality

• use editorconfig
• code style applied in automated way

Testing

• unit tests
• continuous integration
• continuous code coverage
• end2end test
• dependencies tracking

Documentation

• README.md
• well defined functionality
• source code documentation
• usage documentation
• documented development setup
• contribution guidelines
• code of conduct
• documented code style
• how to file a bug report
• explained meaning of issue labels
• DOI or PID
• CITATION file
• print software version

Development setup

• dev environment docker images in Dockerhub (with Dockerfile)

Standards

• Exchange formats
• Protocols

pytest preferred

corresponding term in SO is currently missing.

Currently, all features are anchored on{base URI}/genome/{species} - dcmitype:Dataset - regardless of GFF files used (e.g., gene modes or markers).

Issue by bakhshir
Wednesday Mar 22, 2017 at 16:44 GMT
Originally opened as NLeSC/candYgene#11

This addresses issues #3 and #5.

bakhshir included the following code: https://github.com/NLeSC/candYgene/pull/11/commits

Issue by bakhshir
Wednesday Mar 22, 2017 at 13:28 GMT
Originally opened as NLeSC/candYgene#9

add citation information into the markdown

See also https://github.com/yatiml/yatiml

JSON-LD, TriG, N-Quads

Issue by bakhshir
Tuesday Mar 21, 2017 at 20:40 GMT
Originally opened as NLeSC/candYgene#2

The license information is missing in the markdown file.

For example:
http://localhost:8890/genome/Solanum_pennellii/chromosome/11 dcterms:identifier "11"

see the code:

When converting the Araport11 GFF file to RDF, SIGA produces an error (at the write step):
UnicodeEncodeError: 'ascii' codec can't encode character u'\xf3' in position 6267791: ordinal not in range(128)

This is the used GFF file:
http://datacommons.cyverse.org/browse/iplant/home/araport/public_data/Araport11_Release_201606/annotation/Araport11_GFF3_genes_transposons.201606.gff.gz

Replacing this encoded character %C3%B3 with an "o" solves it.

Issue by bakhshir
Tuesday Mar 21, 2017 at 20:39 GMT
Originally opened as NLeSC/candYgene#1

Expand the description of the tool before the key feature part. It would be also helpful to have a diagram depicting the architecture (i.e. SIGA.png).

Issue by bakhshir
Wednesday Mar 22, 2017 at 14:43 GMT
Originally opened as NLeSC/candYgene#10

merge to include citation info. This also addresses the issue #9

bakhshir included the following code: https://github.com/NLeSC/candYgene/pull/10/commits

currently rdflib used with in-memory graph store

Issue by bakhshir
Wednesday Mar 22, 2017 at 11:41 GMT
Originally opened as NLeSC/candYgene#7

The example usage section in the markdown does not refer to the proper examples directory.
For instance, python SIGA.py db -rV ITAG2.4_gene_models.gff3 should be python SIGA.py db -rV ../examples/ITAG2.4_gene_models.gff3