twalsh-ebi / ensembl-static

Stores all static contents for Non-vertebrates divisions and species.

This repository replaces the Drupal backend for non-vertebrate static content used on the five divisional websites:

• bacteria.ensembl.org
• fungi.ensembl.org
• metazoa.ensembl.org
• plants.ensembl.org
• protists.ensembl.org

Site homepage content is stored for all divisions, and for all except bacteria, descriptions and annotation information for all species.

Species related file naming

Each "leaf" file for the species data should be prefixed with the species.url from the core's meta table (not a species.production_name).

I.e. for bemisia_tabaci_sweetpotug_core_53_106_1 we have

st3 -D bemisia_tabaci_sweetpotug_core_53_106_1 -e 'select meta_key, meta_value from meta where meta_key in ("species.url", "species.production_name")'
meta_key	meta_value

species.production_name	bemisia_tabaci_sweetpotug
species.url	Bemisia_tabaci_uganda1

And we should use Bemisia_tabaci_uganda1_ as a prefix for the species specific files (see below).

Referencing images

TODO

Referencing PMC publication

TODO

Paths for the species related text(md) files

We suppose files to be put into the directory with the name of this form <division>/species/<species_first_name>/<species_first_and_second_names>/<prefix>_<part>

Part is one of the following:

• acknowledgement.html
• about.md
• annotation.md
• assembly.md
• references.md

N.B. Same directory can be shared by the entities with the different trinomial (production) prefices.

I.e.

metazoa/species/Bemisia/Bemisia_tabaci/Bemisia_tabaci_uganda1_about.md
metazoa/species/Bemisia/Bemisia_tabaci/Bemisia_tabaci_uganda1_acknowledgement.html
metazoa/species/Bemisia/Bemisia_tabaci/Bemisia_tabaci_uganda1_annotation.md
metazoa/species/Bemisia/Bemisia_tabaci/Bemisia_tabaci_uganda1_assembly.md
metazoa/species/Bemisia/Bemisia_tabaci/Bemisia_tabaci_uganda1_references.md

Path to the species specific images

Similar to the md files should be in the form: <division>/images/species/<species_first_name>/<prefix>.png

I.e.

metazoa/images/species/Bemisia/Bemisia_tabaci_uganda1.png

N.B.

1. Only *.png format is supported
2. No <species_first_and_second_names> used.

Hint for cropping (see ImageMagick for details):

convert -crop 500x500+100+100  organism_ch_1.png Clytia_hemisphaerica.png
convert -crop 216x216+0+8 +repage -gravity center Varroa_Mite.jpg Varroa_destructor.png
convert +repage -background black -gravity center -extent 610x610  Clytia-ENSEMBL-2.jpeg Clytia_hemisphaerica.png
convert -crop 385x120+1+10 +repage -background black -gravity center -extent 385x385 hmia_stripes_hor-0.png hmia_stripes_moved.png
convert -crop 1500x850+00+0 -background black -gravity center +repage -extent 1500x1500 -resize 512x512 ensembl_gigas_black.jpg Crassostrea_gigas.png

Path to the general devision specific images

Put it into <division>/images.

Not sure if formats matter here.

I.e.

metazoa/images/European_Commission.png
metazoa/images/wikipedia_logo_v2_en.png

How to merge.

1. Fork.
2. Clone from the master branch.
3. Edit, add, commit to your copy. Push to your copy.
4. Create a PR from your fork to the master branch of the source.