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| 2018-08-16 Li Jianfeng <[email protected]> | ||
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| * add pubmed search tool | ||
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| 2018-08-15 Li Jianfeng <[email protected]> | ||
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| * add datasets2tools plugin | ||
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| Package: BioInstaller | ||
| Title: Integrator of Bioinformatics Resources | ||
| Version: 0.3.5.3000 | ||
| Version: 0.3.5.4000 | ||
| Authors@R: person("Jianfeng", "Li", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X")) | ||
| Maintainer: Jianfeng Li <[email protected]> | ||
| Description: | ||
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| all: build | ||
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| build: | ||
| cp *.parameters.toml ~/.BioInstaller/plugins/ && \ | ||
| cp shiny.config.yaml ~/.BioInstaller |
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| [pubmed.ui.sections] | ||
| order = ["pubmed_input_box", "pubmed_output_table"] | ||
| [pubmed.ui.sections.ui_basic] | ||
| pubmed_input_box = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE" | ||
| pubmed_output_table = "title = 'Output of pubmed (Table)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE" | ||
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| [pubmed.paramters.pubmed_input_box] | ||
| # For reading annovarR shiny APP pubmed tool input files | ||
| section_type = "input" | ||
| rcmd_last = """ | ||
| set_entrez_key(pubmed_account_key) | ||
| max_n_items <- as.numeric(max_n_items) | ||
| objs <- NULL | ||
| if (term != "") { | ||
| objs <- entrez_search(db = "pubmed", term = term, retmax = 99999, use_history=TRUE) | ||
| if (objs$count > 99999 && max_n_items > 99999) { | ||
| for( seq_start in seq(99999, objs$count, 99999)){ | ||
| objs_tmp <- entrez_search(db = "pubmed", term = term, | ||
| retstart = seq_start, retmax = 99999) | ||
| objs$id <- c(objs$id, objs_tmp$id) | ||
| } | ||
| } | ||
| if (objs$count < max_n_items) max_n_items <- objs$count | ||
| } | ||
| result <- data.frame() | ||
| if (!is.null(objs) && (max_n_items >= 500)){ | ||
| for(seq_start in seq(1,max_n_items,500)){ | ||
| if ((max_n_items - seq_start) >= 500) { | ||
| fetch.pubmed.tmp <- entrez_fetch(db = "pubmed", web_history = objs$web_history, | ||
| rettype = "xml", parsed = T, retstart = seq_start, retmax = 500) | ||
| } else { | ||
| fetch.pubmed.tmp <- entrez_fetch(db = "pubmed", web_history = objs$web_history, | ||
| rettype = "xml", parsed = T, retstart = seq_start, retmax = max_n_items - seq_start + 1) | ||
| } | ||
| xL <- xmlToList(fetch.pubmed.tmp) | ||
| abstracts.tmp = xpathApply(fetch.pubmed.tmp, '//*//Article|//*//BookDocument', function(x) | ||
| xmlValue(xmlChildren(x)$Abstract)) | ||
| title.tmp = xpathApply(fetch.pubmed.tmp, '//*//Article|//*//BookDocument', function(x) | ||
| xmlValue(xmlChildren(x)$ArticleTitle)) | ||
| journal.name.tmp <- xpathApply(fetch.pubmed.tmp, '//*//Article//Journal|//*//BookDocument//Book', | ||
| function(x) xmlValue(xmlChildren(x)[["Title"]])) | ||
| book.name.tmp <- xpathApply(fetch.pubmed.tmp, '//*//Article//Journal|//*//BookDocument//Book', | ||
| function(x) xmlValue(xmlChildren(x)[["BookTitle"]])) | ||
| publish.year.tmp <- xpathApply(fetch.pubmed.tmp, '//*//Article//Journal//PubDate|//*//BookDocument//Book//PubDate', | ||
| function(x) xmlValue(x)) | ||
| publish.year.tmp <- unlist(publish.year.tmp) | ||
| pmid.tmp <- xpathApply(fetch.pubmed.tmp, '//*/ArticleIdList//ArticleId[@IdType="pubmed"]', function(x) xmlValue(x)) | ||
| pmid.tmp <- unlist(pmid.tmp) | ||
| journal.name.tmp <- unlist(journal.name.tmp) | ||
| book.name.tmp <- unlist(book.name.tmp) | ||
| abstracts.tmp <- unlist(abstracts.tmp) | ||
| abstracts.tmp[is.na(abstracts.tmp)] <- "" | ||
| title.tmp <- unlist(title.tmp) | ||
| title.tmp[is.na(title.tmp)] <- "" | ||
| res <- suppressWarnings(rentrez::parse_pubmed_xml(fetch.pubmed.tmp)) | ||
| doi.tmp <- unlist(lapply(res, function(x) {if (length(x$doi) == 0) return(NA); x$doi})) | ||
| result.tmp <- cbind(pmid.tmp, doi.tmp, title.tmp, abstracts.tmp, publish.year.tmp, journal.name.tmp, book.name.tmp) | ||
| result <- rbind(result, result.tmp) | ||
| } | ||
| result <- result[1:max_n_items,] | ||
| } else if (!is.null(objs)) { | ||
| fetch.pubmed.tmp <- entrez_fetch(db = "pubmed", web_history = objs$web_history, | ||
| rettype = "xml", parsed = T, retmax = max_n_items) | ||
| abstracts.tmp = xpathApply(fetch.pubmed.tmp, '//*//Article|//*//BookDocument', function(x) | ||
| xmlValue(xmlChildren(x)$Abstract)) | ||
| title.tmp = xpathApply(fetch.pubmed.tmp, '//*//Article|//*//BookDocument', function(x) | ||
| xmlValue(xmlChildren(x)$ArticleTitle)) | ||
| pmid.tmp <- xpathApply(fetch.pubmed.tmp, '//*/ArticleIdList//ArticleId[@IdType="pubmed"]', function(x) xmlValue(x)) | ||
| journal.name.tmp <- xpathApply(fetch.pubmed.tmp, '//*//Article//Journal|//*//BookDocument//Book', | ||
| function(x) xmlValue(xmlChildren(x)[["Title"]])) | ||
| book.name.tmp <- xpathApply(fetch.pubmed.tmp, '//*//Article//Journal|//*//BookDocument//Book', | ||
| function(x) xmlValue(xmlChildren(x)[["BookTitle"]])) | ||
| publish.year.tmp <- xpathApply(fetch.pubmed.tmp, '//*//Article//Journal//PubDate|//*//BookDocument//Book//PubDate', | ||
| function(x) xmlValue(x)) | ||
| publish.year.tmp <- unlist(publish.year.tmp) | ||
| journal.name.tmp <- unlist(journal.name.tmp) | ||
| book.name.tmp <- unlist(book.name.tmp) | ||
| abstracts.tmp <- unlist(abstracts.tmp) | ||
| title.tmp <- unlist(title.tmp) | ||
| pmid.tmp <- unlist(pmid.tmp) | ||
| res <- suppressWarnings(rentrez::parse_pubmed_xml(fetch.pubmed.tmp)) | ||
| doi.tmp <- unlist(lapply(res, function(x) {if (length(x$doi) == 0) return(NA); x$doi})) | ||
| result <- cbind(pmid.tmp, doi.tmp, title.tmp, abstracts.tmp, publish.year.tmp, journal.name.tmp, book.name.tmp) | ||
| } | ||
| colnames(result) <- c("PMID", "DOI", "Title", "Abstract", "PublishDate", "JournalName", "BookName") | ||
| """ | ||
| progressbar_message = "Running pubmed functions." | ||
| render_id = "pubmed_pubmed_input_box" | ||
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| #!!!!! input_ui_order required related section | ||
| input_ui_order = ["single_input", "start_analysis"] | ||
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| [pubmed.paramters.pubmed_input_box.input.single_input] | ||
| title = "Parameters:" | ||
| title_control = "class = 'input-section-p'" | ||
| varname = ["term", "max_n_items", "pubmed_account_key"] | ||
| input_id = ["input_pubmed_1", "input_pubmed_2", "input_pubmed_3"] | ||
| type = ["shiny::textInput", "shiny::numericInput", "shiny::textInput"] | ||
| label = ["Term (e.g. 30105797,30105798,B-ALL)", "Counts", "Pubmed Account Key"] | ||
| [pubmed.paramters.pubmed_input_box.input.single_input.value] | ||
| max_n_items = 100 | ||
| pubmed_account_key = "193124979d2e7f360c150dadc5b1e3bfec09" | ||
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| [pubmed.paramters.pubmed_input_box.input.start_analysis] | ||
| input_id = "start_pubmed_analysis" | ||
| type = "shiny::actionButton" | ||
| label = "Run" | ||
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| [pubmed.paramters.pubmed_output_table] | ||
| section_type = "output" | ||
| rcmd_last = """ | ||
| result | ||
| """ | ||
| render_type = "DT::renderDataTable" | ||
| render_id = "pubmed_output_table" | ||
| output_type = "DT::dataTableOutput" | ||
| progressbar_message = "PUBMED search ouput" |
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