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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| library(dplyr) | ||
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| #' Retrieve the details of a PEcAn format, based on format_id | ||
| #' @param format_id Format ID (character) | ||
| #' @return Format details | ||
| #' @author Tezan Sahu | ||
| #* @get /<format_id> | ||
| getFormat <- function(format_id, res){ | ||
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| dbcon <- PEcAn.DB::betyConnect() | ||
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| Format <- tbl(dbcon, "formats") %>% | ||
| select(format_id = id, name, notes, header, mimetype_id) %>% | ||
| filter(format_id == !!format_id) | ||
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| Format <- tbl(dbcon, "mimetypes") %>% | ||
| select(mimetype_id = id, mimetype = type_string) %>% | ||
| inner_join(Format, by = "mimetype_id") %>% | ||
| select(-mimetype_id) | ||
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| qry_res <- Format %>% collect() | ||
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| if (nrow(qry_res) == 0) { | ||
| PEcAn.DB::db.close(dbcon) | ||
| res$status <- 404 | ||
| return(list(error="Format not found")) | ||
| } | ||
| else { | ||
| # Convert the response from tibble to list | ||
| response <- list() | ||
| for(colname in colnames(qry_res)){ | ||
| response[colname] <- qry_res[colname] | ||
| } | ||
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| format_vars <- tbl(dbcon, "formats_variables") %>% | ||
| select(name, unit, format_id, variable_id) %>% | ||
| filter(format_id == !!format_id) | ||
| format_vars <- tbl(dbcon, "variables") %>% | ||
| select(variable_id = id, description, units) %>% | ||
| inner_join(format_vars, by="variable_id") %>% | ||
| mutate(unit = ifelse(unit %in% "", units, unit)) %>% | ||
| select(-variable_id, -format_id, -units) %>% | ||
| collect() | ||
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| PEcAn.DB::db.close(dbcon) | ||
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| response$format_variables <- format_vars | ||
| return(response) | ||
| } | ||
| } | ||
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| ######################################################################### | ||
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| #' Search for PEcAn format(s) containing wildcards for filtering | ||
| #' @param format_name Format name search string (character) | ||
| #' @param mimetype Mime type search string (character) | ||
| #' @param ignore_case Logical. If `TRUE` (default) use case-insensitive search otherwise, use case-sensitive search | ||
| #' @return Formats subset matching the model search string | ||
| #' @author Tezan Sahu | ||
| #* @get / | ||
| searchFormats <- function(format_name="", mimetype="", ignore_case=TRUE, res){ | ||
| format_name <- URLdecode(format_name) | ||
| mimetype <- URLdecode(mimetype) | ||
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| dbcon <- PEcAn.DB::betyConnect() | ||
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| Formats <- tbl(dbcon, "formats") %>% | ||
| select(format_id = id, format_name=name, mimetype_id) %>% | ||
| filter(grepl(!!format_name, format_name, ignore.case=ignore_case)) | ||
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| Formats <- tbl(dbcon, "mimetypes") %>% | ||
| select(mimetype_id = id, mimetype = type_string) %>% | ||
| inner_join(Formats, by = "mimetype_id") %>% | ||
| filter(grepl(!!mimetype, mimetype, ignore.case=ignore_case)) %>% | ||
| select(-mimetype_id) %>% | ||
| arrange(format_id) | ||
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| qry_res <- Formats %>% collect() | ||
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| PEcAn.DB::db.close(dbcon) | ||
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| if (nrow(qry_res) == 0) { | ||
| res$status <- 404 | ||
| return(list(error="Format(s) not found")) | ||
| } | ||
| else { | ||
| return(list(formats=qry_res, count = nrow(qry_res))) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| library(dplyr) | ||
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| get.file <- function(filepath, userid) { | ||
| # Check if the file path is valid | ||
| if(! file.exists(filepath)){ | ||
| return(list(status = "Error", message = "File not found")) | ||
| } | ||
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| # Check if the workflow for run after obtaining absolute path is owned by the user or not | ||
| parent_dir <- normalizePath(dirname(filepath)) | ||
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| run_id <- substr(parent_dir, stringi::stri_locate_last(parent_dir, regex="/")[1] + 1, stringr::str_length(parent_dir)) | ||
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| if(Sys.getenv("AUTH_REQ") == TRUE) { | ||
| dbcon <- PEcAn.DB::betyConnect() | ||
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| Run <- tbl(dbcon, "runs") %>% | ||
| filter(id == !!run_id) | ||
| Run <- tbl(dbcon, "ensembles") %>% | ||
| select(ensemble_id=id, workflow_id) %>% | ||
| full_join(Run, by="ensemble_id") %>% | ||
| filter(id == !!run_id) | ||
| user_id <- tbl(dbcon, "workflows") %>% | ||
| select(workflow_id=id, user_id) %>% full_join(Run, by="workflow_id") %>% | ||
| filter(id == !!run_id) %>% | ||
| pull(user_id) | ||
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| PEcAn.DB::db.close(dbcon) | ||
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| if(! user_id == userid) { | ||
| return(list(status = "Error", message = "Access forbidden")) | ||
| } | ||
| } | ||
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| # Read the data in binary form & return it | ||
| bin <- readBin(filepath,'raw', n = file.info(filepath)$size) | ||
| return(list(file_contents = bin)) | ||
| } |
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