## ----包括=假-----------------------------------------------图书馆（生物陶瓷）knitr :: Opts_chunk $ set（eval = false）## ----设置，包括=假-------------------------------------------------------＃knitr :: Opts_chunk $ set（echo = true）## ---- eval = false ----------------------------------------------------＃库（sparql）＃endpoint =“https://opensparql.sbgenomics.com/bigdata/namespace/tcga_metadata_kb/sparql”#query =“#weix rdfs： #weix tcga： ##选择截然不同？案例？示例？file_name？path？xs_label？subtype_label＃{＃？case一个tcga：case。＃？案例tcga：hasdiseasetype？sulties_type。＃？疾病_TYPE RDFS：标签'肺腺癌'。##？案例TCGA：哈希主义学Diagnosis？HD。＃？HD RDFS：标签'肺腺癌混合亚型'。##？案例tcga：hasfollowup？power_up。＃？power_up tcga：hasdaystolastfollowup？days_to_last_follow_up。＃过滤器（？day_to_last_follow_up> 550）##？power_up tcga：hasvitalstatus？vital_status。＃？vital_status rdfs：label？vital_status_label。＃过滤器（？Vital_status_Label ='Alive'）##？案例TCGA：Hasdrugtherapy？Drug_therapy。 # ?drug_therapy tcga:hasPharmaceuticalTherapyType ?pt_type . # ?pt_type rdfs:label ?pt_type_label . # filter(?pt_type_label='Chemotherapy') # # ?case tcga:hasSample ?sample . # ?sample tcga:hasSampleType ?st . # ?st rdfs:label ?st_label # filter(?st_label='Primary Tumor') # # ?sample tcga:hasFile ?file . # ?file rdfs:label ?file_name . # # ?file tcga:hasStoragePath ?path. # # ?file tcga:hasExperimentalStrategy ?xs. # ?xs rdfs:label ?xs_label . # filter(?xs_label='WXS') # # ?file tcga:hasDataSubtype ?subtype . # ?subtype rdfs:label ?subtype_label # # } # # " # qd <- SPARQL(endpoint,query) # df <- qd$results # head(df) ## ------------------------------------------------------------------------ # # ## api(api_url=base,auth_token=auth_token,path='action/files/get_ids', method='POST',query=None,data=filelist) # df.path <- df[,"path"] # df.path ## ------------------------------------------------------------------------ # library(sevenbridges) # a = Auth(platform = "cgc", username = "tengfei") # ## get id (only works for CGC platform) # ids = a$get_id_from_path(df.path) # ## copy file from id to project with controlled access # (p = a$project(id = "tengfei/control-test")) # a$copyFile(ids, p$id)