Feature/hcatoscea_test_data_ami_update #59
Conversation
amnonkhen
changed the base branch from
master
to
feature/hca-to-scea-test-data
| @@ -0,0 +1,30 @@ | |||
|
|
|||
There was a problem hiding this comment.
I would like to suggest a differnt naming convention for the test data.
Please name the spreadsheet and the directory containing the idf and sdrf using the accession number.
In this case:
- spreadsheet: SRP274475.xlsx
- idf & sdrf should be in
test/golden/SRP274475
…ts.csv file to reflect this change.
@ami-day I do not understand your comment. |
Hi @amnonkhen I'm not sure what I meant by this. I made the changes you suggested. Can this request be approved now? |
There was a problem hiding this comment.
Thanks for updating the hca to scea test input spreadsheet. I do not, however, see the expected results files, namely the idf/sdrf files for each of the test cases?
Before merging your changes, the tests should run successfully.
At least for your test cases.
You can run the tests on your environment by running python -munittest.
Also, once you push them to the remote branch github runs them for you. Please examine the output, and fix the errors. If you don't undersatnd the error messages, talk to me.
…ich are not supported by the hca2scea tool as it is currently. I will create tickets for relevant enhancements to the code. Removed a .DS_Store file that was causing issues with test validation.
Replaced None values with empty string when a protocol is applied to some samples and not others. Also changed how the protocol columns are ordered on a protocol type basis. These changes preserve the correct protocol id order for each protocol type.
…re-protocol-type-array-lengths
…-to-scea-test-data-ami-update The hca2scea.py script in the feature/hca-to-scea-test-data-ami-update branch incorrectly enters duplicated SRA file names in the sdrf file. The test branch needs to be updated with the corrected code, and corresonding corrected expected test output files.
…ea-test-data-ami-update
…a-to-scea-test-data-ami-update
Thanks @amnonkhen I have done this, the test is returning "OK" now. |
| enrichment_protocol_cols = [] | ||
| library_preparation_protocol_cols = [] | ||
| for col in list(protocols_sdrf_before_sequencing.columns): | ||
| if col.split(".protocol_core.protocol_id")[0] == "collection_protocol": |
There was a problem hiding this comment.
No need to repeat col.split(".protocol_core.protocol_id")[0] 4 times.
Define a variable and use it in the 4 locations.
| @@ -11,10 +11,10 @@ Person Email alison.simmons@imm.ox.ac.uk | |||
| Person Affiliation MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) Target Discovery Institute MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) John Radcliffe Hospital, University of Oxford MRC Weatherall Institute of Molecular Medicine Sir William Dunn School of Pathology, University of Oxford MRC Weatherall Institute of Molecular Medicine MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) MRC Weatherall Institute of Molecular Medicine (WIMM) Target Discovery Institute Target Discovery Institute St Mary's Hospital, Imperial College MRC Weatherall Institute of Molecular Medicine MRC Weatherall Institute of Molecular Medicine (WIMM) EMBL-EBI | |||
There was a problem hiding this comment.
How come we have Test01 output file but now Test01 spreadsheet in the arguments?
This file will not be used anywhere.
|
Closing this branch, it is an older version that is now out of date. |
Fixed input test files (TEST01.xlsx, TEST02.xlsx) which were resulting in incorrect output files. Updated the arguments.csv file to reflect this.