Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

#1613 closed task (fixed)

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

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: BASE 3.0
Component: test Version:
Keywords: Cc:

Description

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

Change History (11)

comment:1 Changed 10 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

comment:2 Changed 10 years ago by 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.

comment:3 Changed 10 years ago by 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.

comment:4 Changed 10 years ago by 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.

comment:5 Changed 10 years ago by 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)

comment:6 Changed 10 years ago by 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).

comment:7 Changed 10 years ago by Nicklas Nordborg

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

Should now work with batch importers also.

comment:8 Changed 10 years ago by 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.

comment:9 Changed 10 years ago by 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

comment:10 Changed 10 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

comment:11 Changed 10 years ago by Nicklas Nordborg

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

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