Extend the 'roles' test case with some sequence-related tests

[Nicklas Nordborg]

This is subticket related to #1153. The test case also need to be fixed due to the changes in extract -> raw bioassay areas.

[Nicklas Nordborg]

(In [5699]) References #1613: Extend the 'roles' test case with some sequence-related tests

Fixed in the manual test instructions and the hard-coded programmatic tests. The exception is that we do not yet have a defined raw data type + test data files for sequence data (using GenePix as a temporary solution). The overview tests can't be completed until the item overview has been fixed by #1153.

The batch importer tests (instructions + programmatic tests) have not been fixed yet.

[Nicklas Nordborg]

(In [5700]) References #1613: Extend the 'roles' test case with some sequence-related tests

Fixed batch importer tests. Beware that the tab-separated text files are a bit different than those used by BASE 2.17 and before.

[Nicklas Nordborg]

(In [5751]) References #1613: Extend the 'roles' test case with some sequence-related tests

Created a "RefSeq" array design which is used by the sequence raw bioassays. Preparations for associating data files once we have defined them and have some test data files. Preparations for importing features and raw data once we have importer plug-ins (or configurations to the existing importers) in place.

[Nicklas Nordborg]

(In [5765]) References #1613: Extend the 'roles' test case with some sequence-related tests

• Added GTF reporter importer test (in admin test)
• Added GTF file and GTF feature importer test (in power user test)

[Nicklas Nordborg]

(In [5778]) References #1613: Extend the 'roles' test case with some sequence-related tests

• Fixed reporter and array design test to use the same GTF file that the fpkm_tracking files use.
• Raw bioassays and experiment now use the sequencing platform
• Added isoforms.fpkm_tracking files and import data from them with the raw data importer.
• Create a root bioassay set using the fpkm values and a filtered bioassay set were both data sets have a value (seems like the .2 data set has very few values).

[Nicklas Nordborg]

(In [5779]) References #1613: Extend the 'roles' test case with some sequence-related tests

Should now work with batch importers also.

[Nicklas Nordborg]

(In [5788]) References #1613: Extend the 'roles' test case with some sequence-related tests

Updated and synchronized the test instructions with the test code. Fixed a few issues with the test code.

The "Item overview" and analysis sections remains.

[Nicklas Nordborg]

(In [5813]) References #1613: Extend the 'roles' test case with some sequence-related tests

• Final changes for item overview tests
• Could not save platform variant as default item
• All validation options are collapsed to begin with

[Nicklas Nordborg]

(In [5866]) References #1648 and #1613. Added a duplicate image reference to a single file to the test program.