parasite-static

Keeping static contents for ParaSite website

Structure

Nearly all species:

• species
  • Ancylostoma ceylanicum
    • Ancylostoma ceylanicum.about.md
    • PRJNA231479
      • Ancylostoma_ceylanicum_PRJNA231479.summary.md
      • Ancylostoma_ceylanicum_PRJNA231479.assembly.md
      • Ancylostoma_ceylanicum_PRJNA231479.annotation.md
      • Ancylostoma_ceylanicum_PRJNA231479.resources.md
      • Ancylostoma_ceylanicum_PRJNA231479.publication.md
    • PRJNA72583
      • Ancylostoma_ceylanicum_PRJNA72583.summary.md
      • Ancylostoma_ceylanicum_PRJNA72583.assembly.md
      • Ancylostoma_ceylanicum_PRJNA72583.annotation.md
      • Ancylostoma_ceylanicum_PRJNA72583.resources.md
      • Ancylostoma_ceylanicum_PRJNA72583.publication.md
  • ...etc

Alternative case:

A species may have a separate "about" file for each bioproject:

• species
  • Trichinella_pseudospiralis
    • ISS13PRJNA257433
      • Trichinella_pseudospiralis_ISS13PRJNA257433.about.md
      • Trichinella_pseudospiralis_ISS13PRJNA257433.summary.html
      • Trichinella_pseudospiralis_ISS13PRJNA257433.assembly.html
      • Trichinella_pseudospiralis_ISS13PRJNA257433.annotation.html
      • Trichinella_pseudospiralis_ISS13PRJNA257433.resources.html
      • Trichinella_pseudospiralis_ISS13PRJNA257433.publication.html
    • ISS141PRJNA257433
      • Trichinella_pseudospiralis_ISS141PRJNA257433.about.md
      • Trichinella_pseudospiralis_ISS141PRJNA257433.summary.html
      • Trichinella_pseudospiralis_ISS141PRJNA257433.assembly.html
      • Trichinella_pseudospiralis_ISS141PRJNA257433.annotation.html
      • Trichinella_pseudospiralis_ISS141PRJNA257433.resources.html
      • Trichinella_pseudospiralis_ISS141PRJNA257433.publication.html
    • ...etc
  • ...etc

Note that manage_files.pl (see below) will cope with this alternative case when creating files from the old static content database (--create-missing) and when creating markdown files from HTML (--md2mthml).

Managing files

The script ./bin/manage_files.pl helps manage the files.

Creating files from the static content in the database

The static content in the database cannot be maintained any longer, so the content needs to be placed into Markdown files. This is hopefully be a one-off operation.

To create files for the content that is currently in the database ensembl_production_parasite:

./bin/manage_files.pl --create-missing [--root-dir ./my_dir]

Output: a list of all files that have been created.

This creates only the missing files, i.e. where a Markdown or HTML file is not already present on disk and has non-zero size. The --root-dir option can be used to create a structure (with a complete set of new files) under a different subdirectory.

The HTML files contain the database content. The species' .about.html file containms the description field from the table static_species. The other HTML files are the contents of fields from the table static_genome; the file names match field names (e.g. .summary.html is the content of the summary field).

The Markdown files are created automatically from the HTML files.

Creating files for new species or genomes that are not in the database

Genomes added from WBPS15 will not have static content in the database; the species will also have no existing static content, unless there was already another assembly.

To find all the files that need to be added:

./bin/manage_files.pl --placeholders [--root-dir ./my_dir]

Output: a list of all palceholder files that have been created.

This creates a "placeholder" for every Markdown file that needs to be created. These have the name of the file that is required with .placeholder as a suffix.

Find all missing files

To find all files that, for any reason, are missing from the structure:

./bin/manage_files.pl --find-missing [--root-dir ./my_dir]

Output: a list of all missing files.

Creating HTML files from Markdown

The Markdown files are used to make authoring easier, but the web site requires HTML.

To create HTML files from all Markdown files:

./bin/manage_files.pl --md2html [--root-dir ./my_dir]

Output: a list of all HTML files that have been created.

This creates only the missing files, i.e. where a Markdown file exists but there is no corresponding HTML file that has non-zero size.

If you want to create new HTML files, delete existing HTML files before running this command. e.g. for a complete set of new HTML files (ensuring each one is up-to-date with the current state of the Markdown), first run find ./species -name '*.html' -type f -exec rm {} \;; or to renew all HTML files for Ancylostoma ceylanicum run find ./species/Ancylostoma_ceylanicum -name '*.html' -type f -exec rm {} \;.