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Rentrez错误HTTP失败:下载超过1/3条记录时为400

rentrez r
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  • Josh  · 技术社区  · 8 年前

    我有个奇怪的情况。我正在使用 rentrez 是的。当我跑的时候 entrez_search() 然后 entrez_summary() 然后 entrez_fetch() 我收到这个错误的消息(完整的代码在文章的底部): 

    Error: HTTP failure: 400
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eEfetchResult PUBLIC "-//NLM//DTD efetch 20131226//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20131226/efetch.dtd">
<eFetchResult>
    <ERROR>Cannot retrieve history data. query_key: 1, WebEnv: NCID_1_51629226_130.14.18.34_9001_1531773486_1795859931_0MetA0_S_MegaStore, retstart: 0, retmax: 552</ERROR>
    <ERROR>Can't fetch uids from history because of: NCBI C++ Exception:
    Error: UNK_MODULE(CException::eInvalid) "UNK_FILE", line 18446744073709551615: UNK_FUNC --- 
</ERROR>
</eFetchResult>

    在四处寻找之后,我想我已经在 this discussion 查询大小的。当我减少 retmax_set 从500到10,代码起作用了。然后迭代确定最大值。 retmax_集 不会抛出错误并发现在我看来非常怪异行为的值。

    搜索 term_set = "transcription AND enhancer AND promoter AND 2017:2018[PDAT]" 是的552张唱片。当使用不同的值运行我的代码时 retmax 以下内容:

    • 设置 retmax_集 <=183件
    • 设置 retmax_集 >=184给出上述错误

    修改过的搜索 term_set = "transcription AND enhancer AND promoter AND 2018[PDAT]" 是186张唱片。使用不同的值运行此搜索时 雷特麦克斯 以下内容:

    • 设置 retmax_集 <=61件
    • 设置 retmax_集 >=62给出上述错误

    搜索 term_set = "transcription AND enhancer AND promoter AND 2017[PDAT]" Yeilds 395条记录(由于某种原因,PubMed将29条记录标注为在2017年和2018年发布)。使用不同的值运行此搜索项上的代码时 雷特麦克斯 以下内容:

    • 设置 retmax_集 <=131件
    • 设置 retmax_集 >=132给出上述误差

    有趣的是,当 雷特麦克斯 值大于记录总数的三分之一(552/3=184186/3=62395/3=131.67)。我要修改我的代码来计算 retmax_集 基于返回的结果数 entrez_search ,但我不知道为什么 伦特雷斯 或者NCBI正在这么做。有什么想法吗? 

    > ##  set search term 
> term_set = "transcription AND enhancer AND promoter AND 2017:2018[PDAT]"
> ##  load package
> library(rentrez)
> ##  set maximum records batch
> retmax_set = 182
> ##  search pubmed using web history
> search <- entrez_search(
+   db = "pubmed", 
+   term = term_set, 
+   use_history = T
+ )
> ##  get summaries of search hits 
> summary <- list(); for (seq_start in seq(0, search$count - 1, retmax_set)) {
+     summary1 <- entrez_summary(
+         db = "pubmed", 
+         web_history = search$web_history, 
+         retmax = retmax_set, 
+         retstart = seq_start
+     )
+     summary <- c(summary, summary1)
+ }
> ##  download full XML refs for hits
> XML_refs <- entrez_fetch(
+     db = "pubmed", 
+     web_history = search$web_history, 
+     rettype = "xml", 
+     parsed = TRUE
+ )
> 
> 
> ##  set search term 
> term_set = "transcription AND enhancer AND promoter AND 2017:2018[PDAT]"
> ##  load package
> library(rentrez)
> ##  set maximum records batch
> retmax_set = 183
> ##  search pubmed using web history
> search <- entrez_search(
+   db = "pubmed", 
+   term = term_set, 
+   use_history = T
+ )
> ##  get summaries of search hits 
> summary <- list(); for (seq_start in seq(0, search$count - 1, retmax_set)) {
+     summary1 <- entrez_summary(
+         db = "pubmed", 
+         web_history = search$web_history, 
+         retmax = retmax_set, 
+         retstart = seq_start
+     )
+     summary <- c(summary, summary1)
+ }
> ##  download full XML refs for hits
> XML_refs <- entrez_fetch(
+     db = "pubmed", 
+     web_history = search$web_history, 
+     rettype = "xml", 
+     parsed = TRUE
+ )
> 
> 
> ##  set search term 
> term_set = "transcription AND enhancer AND promoter AND 2017:2018[PDAT]"
> ##  load package
> library(rentrez)
> ##  set maximum records batch
> retmax_set = 184
> ##  search pubmed using web history
> search <- entrez_search(
+   db = "pubmed", 
+   term = term_set, 
+   use_history = T
+ )
> ##  get summaries of search hits 
> summary <- list(); for (seq_start in seq(0, search$count - 1, retmax_set)) {
+     summary1 <- entrez_summary(
+         db = "pubmed", 
+         web_history = search$web_history, 
+         retmax = retmax_set, 
+         retstart = seq_start
+     )
+     summary <- c(summary, summary1)
+ }
> ##  download full XML refs for hits
> XML_refs <- entrez_fetch(
+     db = "pubmed", 
+     web_history = search$web_history, 
+     rettype = "xml", 
+     parsed = TRUE
+ )
Error: HTTP failure: 400
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eEfetchResult PUBLIC "-//NLM//DTD efetch 20131226//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20131226/efetch.dtd">
<eFetchResult>
    <ERROR>Cannot retrieve history data. query_key: 1, WebEnv: NCID_1_51629226_130.14.18.34_9001_1531773486_1795859931_0MetA0_S_MegaStore, retstart: 0, retmax: 552</ERROR>
    <ERROR>Can't fetch uids from history because of: NCBI C++ Exception:
    Error: UNK_MODULE(CException::eInvalid) "UNK_FILE", line 18446744073709551615: UNK_FUNC --- 
</ERROR>
</eFetchResult>
> 
> 
> ##  set search term 
> term_set = "transcription AND enhancer AND promoter AND 2017:2018[PDAT]"
> ##  load package
> library(rentrez)
> ##  set maximum records batch
> retmax_set = 185
> ##  search pubmed using web history
> search <- entrez_search(
+   db = "pubmed", 
+   term = term_set, 
+   use_history = T
+ )
> ##  get summaries of search hits 
> summary <- list(); for (seq_start in seq(0, search$count - 1, retmax_set)) {
+     summary1 <- entrez_summary(
+         db = "pubmed", 
+         web_history = search$web_history, 
+         retmax = retmax_set, 
+         retstart = seq_start
+     )
+     summary <- c(summary, summary1)
+ }
> ##  download full XML refs for hits
> XML_refs <- entrez_fetch(
+     db = "pubmed", 
+     web_history = search$web_history, 
+     rettype = "xml", 
+     parsed = TRUE
+ )
Error: HTTP failure: 400
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eEfetchResult PUBLIC "-//NLM//DTD efetch 20131226//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20131226/efetch.dtd">
<eFetchResult>
    <ERROR>Cannot retrieve history data. query_key: 1, WebEnv: NCID_1_52654089_130.14.22.215_9001_1531773493_484860305_0MetA0_S_MegaStore, retstart: 0, retmax: 552</ERROR>
    <ERROR>Can't fetch uids from history because of: NCBI C++ Exception:
    Error: UNK_MODULE(CException::eInvalid) "UNK_FILE", line 18446744073709551615: UNK_FUNC --- 
</ERROR>
</eFetchResult>
    1 回复  |  直到 8 年前
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  •   Josh    7 年前

    结果是Rentrez使用0进制计数。所以552条记录对应于 retstart 值为0到551。因为我的代码正在寻找值1到552,所以它错过了第一个记录(0),然后在寻找不存在的记录552时抛出了一个错误。

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