synapser update caused data frame function to fail

PNNL-CompBio · Jun 19, 2024 · 7b837c6 · 7b837c6
1 parent 1e2fabc
commit 7b837c6
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Showing 4 changed files with 6 additions and 1 deletion.
diff --git 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
@@ -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
@@ -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
@@ -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