Difference between revisions of "Rake tasks"
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'' This is in progress, starred tasks are not recently (re)tested. '' | '' This is in progress, starred tasks are not recently (re)tested. '' | ||
− | |||
=== mx:matrix:load === | === mx:matrix:load === | ||
− | Loads | + | Loads one or more Nexus formatted matrices. In addition to the matrix file a YAML metadata file is required that looks like: |
<div style="padding: 4px; font-family:courier;"> | <div style="padding: 4px; font-family:courier;"> | ||
− | Full_file_name_of_matrix.nex: | + | Full_file_name_of_matrix.nex: # the name of the file, not indented |
− | :data_source_ref_id: 12 | + | :data_source_ref_id: 12 # a mx Ref#id, referenced everywhere a ref_id is needed |
− | :title: "some title" | + | :title: "some title" # the matrix title |
− | :data_source_name: "some datasource name" | + | :data_source_name: "some datasource name" # the datasource tile (essentially the same thing in this case) |
− | :notes: "Some note here." | + | :notes: "Some note here." # <i>not yet implemented</i> |
− | :generate_short_chr_name: true | + | :generate_short_chr_name: true # creates a truncated character name |
− | :generate_otu_name_with_ds_id: | + | :generate_otu_name_with_ds_id: 2 # false or DataSource#id, adds the data source ID to the Otu#name |
− | :generate_chr_name_with_ds_id: | + | :generate_chr_name_with_ds_id: 4 # false or DataSource#id, adds the data source ID to the Chr#name |
− | :match_otu_to_db_using_name: false | + | :match_otu_to_db_using_name: false # attempts to match incoming Otus to Otu#name |
:match_otu_to_db_using_matrix_name: false # attempts to match incoming Otus to Otu#matrix_name | :match_otu_to_db_using_matrix_name: false # attempts to match incoming Otus to Otu#matrix_name | ||
− | :match_chr_to_db_using_name: false | + | :match_chr_to_db_using_name: false # attempts to match incoming Chrs to Chr#name |
− | :generate_chr_with_ds_ref_id: false | + | :generate_chr_with_ds_ref_id: false # needs a valid Ref#id (not tested) |
− | :generate_otu_with_ds_ref_id: false | + | :generate_otu_with_ds_ref_id: false # needs a valid Ref#id (not tested) |
</div> | </div> | ||
+ | |||
+ | You can repeat the above for all the matrices you have to add many matrices at once. | ||
=== mx:clean_author_initials * === | === mx:clean_author_initials * === | ||
− | Removes all characters other than A- | + | Removes all characters other than A-Z |
=== mx:db:dump_data === | === mx:db:dump_data === |
Latest revision as of 12:52, 31 August 2009
[edit] Setting the environment
Some of the most important tasks for an mx developer are those that move data in and out of the database (tasks starting with "mx:db:"). Since RAILS_ENV defaults to 'production' in our current environment.rb, you have to specify if you want to operate on the development database, for example:
rake mx:db:restore_last RAILS_ENV=development
You can see more about a specific task (if there is more to see) with --describe
rake --describe mx:db:restore_last
[edit] Available mx tasks
This is in progress, starred tasks are not recently (re)tested.
[edit] mx:matrix:load
Loads one or more Nexus formatted matrices. In addition to the matrix file a YAML metadata file is required that looks like:
Full_file_name_of_matrix.nex: # the name of the file, not indented :data_source_ref_id: 12 # a mx Ref#id, referenced everywhere a ref_id is needed :title: "some title" # the matrix title :data_source_name: "some datasource name" # the datasource tile (essentially the same thing in this case) :notes: "Some note here." # not yet implemented :generate_short_chr_name: true # creates a truncated character name :generate_otu_name_with_ds_id: 2 # false or DataSource#id, adds the data source ID to the Otu#name :generate_chr_name_with_ds_id: 4 # false or DataSource#id, adds the data source ID to the Chr#name :match_otu_to_db_using_name: false # attempts to match incoming Otus to Otu#name :match_otu_to_db_using_matrix_name: false # attempts to match incoming Otus to Otu#matrix_name :match_chr_to_db_using_name: false # attempts to match incoming Chrs to Chr#name :generate_chr_with_ds_ref_id: false # needs a valid Ref#id (not tested) :generate_otu_with_ds_ref_id: false # needs a valid Ref#id (not tested)
You can repeat the above for all the matrices you have to add many matrices at once.
[edit] mx:clean_author_initials *
Removes all characters other than A-Z
[edit] mx:db:dump_data
Dumps a copy of the database to /dumps.
[edit] mx:db:reload
Dump the data, recreate the tables a...
[edit] mx:db:restore
Dump the data as a backup, then rest...
[edit] mx:db:restore_last
Dumps the current data to /dumps, then restores the data from the (next) youngest dump file (like "2008_07_03_224250.sql") in /dumps.
[edit] mx:db:setup*
(not working yet)
[edit] mx:fk_schema*
deprecated with upcoming migrations Generate the foreign key statements ...
[edit] mx:load_images
Call like: "rake mx:load_images img_...
[edit] mx:load_languages
should deprecate with migration, a one-time use Loads the language table. Call like: "rake mx:load_languages f...
[edit] mx:matrix:debug
Debug a nexus file against the parser.
[edit] mx:matrix:load
Load one or more matrices.
[edit] mx:prepare_release
Export a copy of the mx source code ...
[edit] mx:setup_directories*
Creates the directories mx uses for ...
[edit] mx:update_ref_display_names*
Update all Ref display_name fields.