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5
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1 ---
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6
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2 title: 'Tripal database explorer: search results'
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5
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3 output:
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4 html_document:
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5 theme: cosmo
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6 highlight: tango
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7 ---
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8
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9 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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10 knitr::opts_chunk$set(
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6
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11 echo = FALSE,
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5
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12 error = TRUE
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13 )
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14 ```
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15
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16
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6
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17 ```{r}
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18 # get member ids after implementing search filtering
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19 content_type_url = opt$X_u
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20 path = "organism,genus=Fagus&name=ABall;contains"
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21 path = sub('\\|', '&', opt$X_s)
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22 search_url = paste0(content_type_url, '?', path)
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23 search_members = fromJSON(search_url)
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24 # search_url_rebuild = paste0(search_url, '&limit=', search_members$totalItems)
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25 total_records = as.integer(opt$X_l)
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26 if (total_records == 0) {
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27 total_records = search_members$totalItems
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28 }
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29 search_url_rebuild = paste0(search_url, '&limit=', total_records)
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30 re_search_members = fromJSON(search_url_rebuild)
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5
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31 ```
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32
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33
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6
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34 ```{r}
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35 # get requested field values from search results
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36 request_paths = sub(',', '\\.', strsplit(opt$X_e, '\\|')[[1]])
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37 res = data.frame()
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38 for (id in re_search_members$member$`@id`) {
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39 member = as.data.frame(fromJSON(id))
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40 res = rbind(res, member[, request_paths])
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41 }
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42 colnames(res) = request_paths
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43 ```
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44
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45 ```{r}
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46 if (nrow(res) < 1) {
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47 cat('No records found.')
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48 } else {
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49 DT::datatable(res)
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50 }
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51 ```
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52
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53 ```{r}
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54 # save results to file
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55 write.table(res, file = opt$X_r, quote = FALSE, col.names = FALSE)
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56 ```
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57
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