Bugfix – Inferred cell type field not in SDRF breaks experiment design #69
Conversation
…sent in the SDRF file
|
Hi @alfonsomunozpomer can you please rebase to include this #68 |
There was a problem hiding this comment.
LGTM @alfonsomunozpomer !
I have a small request related to
Replaced the condensed SDRF to test the experiment design load to use a file where a field isn’t present in the SDRF file
New experiment for test is E-CURD-4 (Arabidopsis). Could we still keep the previous one E-MTAB-2983 (human) as a separate test in the .bats file?
| @@ -1,4 +1,4 @@ | |||
| FROM quay.io/ebigxa/atlas-db-scxa-base:0.1.0 | |||
| FROM quay.io/ebigxa/atlas-db-scxa-base:0.15.0.0 | |||
There was a problem hiding this comment.
This tag doesn't have the best naming - but it does exist in quay so let's leave it as it is
There was a problem hiding this comment.
I decided to keep it in sync with major releases of Single Cell Expression Atlas (so that v15 corresponds to 0.15.0.0).
…ll-type-field-not-in-sdrf-breaks-experiment-design # Conflicts: # bin/add_exps_to_collection.sh # bin/create_collection.sh # bin/delete_collection.sh # bin/delete_exp_from_collection.sh # bin/get_experiment_info.sh # bin/load_db_scxa_analytics.sh # bin/load_db_scxa_analytics_pg9.sh # bin/load_db_scxa_cell_clusters.sh # bin/load_db_scxa_dimred.sh # bin/load_db_scxa_marker_genes.sh # bin/load_exp_design.sh # bin/modify_collection.sh
Done. |
alfonsomunozpomer
deleted the
bugfix/inferred-cell-type-field-not-in-sdrf-breaks-experiment-design
branch
If inferred cell type fields are not present in the SDRF file (e.g. E-CURD-4) then the script assigns a null value to the experiment design column ordinal.
In such cases, the inferred cell type column should be placed in the last position (highest ordinal plus one).
Things I did here:
common_routines.shINSERTtopsqlall the statements are written to a file, enclosed in a transaction block and then havepsqlprocess ittestsdirectory (remember: thefixturesdirectory is for the scripts that we use to generate fixtures foratlas-web-single-cell)