diff --git a/app/views/homes/documentation.html.erb b/app/views/homes/documentation.html.erb index 51f66f2c..f3e58291 100644 --- a/app/views/homes/documentation.html.erb +++ b/app/views/homes/documentation.html.erb @@ -142,7 +142,8 @@

After uploading a read, the app will automatically try to assign it to a contig and a primer. Multiple reads generated from the same isolate will automatically be assigned to the same contig.

For this to work it is very important that all file names follow the pattern <isolate_identifier>_<primer_name>.scf/ab1! - It is also important that a record for the used primer was added to the app before uploading the read file.

+ It is also important that a record for the used primer was added to the app before uploading the read file. + Isolate names may only contain letters, numbers or underscores. Primer names may only contain letters, numbers or hyphens.

The app will attempt to trim the reads based on some preset parameters (the default settings are that in a window of 10 bases, at least 8 have to have a quality score above 30). You can change these parameters before attempting to trim the read again. diff --git a/config/environments/test.rb b/config/environments/test.rb index fe83d71d..79c4cb30 100644 --- a/config/environments/test.rb +++ b/config/environments/test.rb @@ -5,7 +5,7 @@ # test suite. You never need to work with it otherwise. Remember that # your test database is "scratch space" for the test suite and is wiped # and recreated between test runs. Don't rely on the data there! - config.cache_classes = true + config.cache_classes = false # Do not eager load code on boot. This avoids loading your whole application # just for the purpose of running a single test. If you are using a tool that diff --git a/db/schema.rb b/db/schema.rb index 9d2e9f71..88099b3e 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -210,6 +210,7 @@ t.text "locality" t.string "latitude_original", limit: 255 t.string "longitude_original", limit: 255 + t.string "elevation_orig", limit: 255 t.string "exposition", limit: 255 t.text "habitat" t.string "substrate", limit: 255 @@ -226,7 +227,6 @@ t.integer "collection_id" t.integer "tissue_id" t.bigint "taxon_id" - t.string "elevation_orig" t.decimal "elevation" t.index ["collection_id"], name: "index_individuals_on_collection_id" t.index ["taxon_id"], name: "index_individuals_on_taxon_id"