From 7b837c6ee9ab25f75c9e3bdf828d9d21c4c6006f Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 19 Jun 2024 11:07:02 -0700 Subject: [PATCH] synapser update caused data frame function to fail --- build/mpnst/00_sample_gen.R | 3 ++- build/mpnst/01_mpnst_get_omics.R | 1 + build/mpnst/02_get_drug_data.R | 1 + build/mpnst/03_get_drug_response_data.R | 2 ++ 4 files changed, 6 insertions(+), 1 deletion(-) diff --git a/build/mpnst/00_sample_gen.R b/build/mpnst/00_sample_gen.R index 7268b57e..ec68b873 100755 --- a/build/mpnst/00_sample_gen.R +++ b/build/mpnst/00_sample_gen.R @@ -15,7 +15,8 @@ if(length(args)!=2){ orig_samples<-fread(args[1]) synapser::synLogin(authToken=args[2]) -manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame() +manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> + as.data.frame() ###sample file has a strict schema diff --git a/build/mpnst/01_mpnst_get_omics.R b/build/mpnst/01_mpnst_get_omics.R index b9950977..ae5f1730 100755 --- a/build/mpnst/01_mpnst_get_omics.R +++ b/build/mpnst/01_mpnst_get_omics.R @@ -37,6 +37,7 @@ tumor_samps<-subset(samples_df,model_type=='tumor') ##now get the manifest from synapse manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> + as.data.frame() dplyr::rename(common_name='Sample') diff --git a/build/mpnst/02_get_drug_data.R b/build/mpnst/02_get_drug_data.R index 5403e8fc..27b238c6 100644 --- a/build/mpnst/02_get_drug_data.R +++ b/build/mpnst/02_get_drug_data.R @@ -27,6 +27,7 @@ synLogin(authToken = PAT) ##now get the manifest from synapse manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> + as.data.frame()|> dplyr::rename(common_name='Sample') diff --git a/build/mpnst/03_get_drug_response_data.R b/build/mpnst/03_get_drug_response_data.R index 49d8b896..4b44720e 100644 --- a/build/mpnst/03_get_drug_response_data.R +++ b/build/mpnst/03_get_drug_response_data.R @@ -31,6 +31,7 @@ org_samps<-subset(samples_df,model_type=='organoid') ##now get the manifest from synapse manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> + as.data.frame()|> dplyr::rename(common_name='Sample') @@ -68,6 +69,7 @@ extract_date_hour <- function(experiment_id) { ##first function to get children from parentId getDrugDataByParent<-function(parid,sampleId){ qtab<-synTableQuery(paste('select id,name,experimentalCondition,parentId from syn21993642 where parentId=\'',parid,'\''))$asDataFrame()|> + as.data.frame()|> subset(!is.na(experimentalCondition))|>dplyr::select(id,name,experimentalCondition) ##now we need to parse the metadatda table get the info