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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.EUtils-module.html">Package EUtils</a> ::
Module HistoryClient
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<h1 class="epydoc">Module HistoryClient</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.EUtils.HistoryClient-pysrc.html">source code</a></span></p>
<p>Search and retreive information using the EUtils history.</p>
<p>EUtils has two major modes. One uses history while the other uses
database identifiers. This is a high-level interface for working with
the history. You should use this module if you expect to work with large
or an unknown number of identifiers.</p>
<p>See DBIdsClient if you want to get information about a set of known
database identifiers.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.EUtils <span class="py-keyword">import</span> HistoryClient
<span class="py-prompt">>>> </span>client = HistoryClient.HistoryClient()
<span class="py-prompt">>>> </span>cancer = client.search(<span class="py-string">"cancer"</span>)
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> len(cancer)
<span class="py-output">1458353</span>
<span class="py-output"></span><span class="py-prompt">>>></span></pre>
<p>That's quite a few hits. Most people would like to see the first few
records then try to refine the search.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> cancer[:5].efetch(retmode = <span class="py-string">"text"</span>, rettype = <span class="py-string">"docsum"</span>).read()</pre>
<p>1: Seow-Choen F. Author's reply: Adjuvant therapy for rectal cancer
cannot be based on the results of other surgeons (Br J Surg 2002; 89:
946-947). Br J Surg. 2003 Jan;90(1):121-122. PMID: 12520589 [PubMed - as
supplied by publisher]</p>
<p>2: Mortensen N, Lindsey I. Adjuvant therapy for rectal cancer cannot
be based on the results of other surgeons (Br J Surg 2002; 89: 946-947).
Br J Surg. 2003 Jan;90(1):121. PMID: 12520588 [PubMed - as supplied by
publisher]</p>
<p>3: Osugi H, Takemura M, Higashino M, Takada N, Lee S, Kinoshita H. A
comparison of video-assisted thoracoscopic oesophagectomy and radical
lymph node dissection for squamous cell cancer of the oesophagus with
open operation. Br J Surg. 2003 Jan;90(1):108-13. PMID: 12520585 [PubMed
- in process]</p>
<p>4: Tanaka M, Kitajima Y, Sato S, Miyazaki K. Combined evaluation of
mucin antigen and E-cadherin expression may help select patients with
gastric cancer suitable for minimally invasive therapy. Br J Surg. 2003
Jan;90(1):95-101. PMID: 12520583 [PubMed - in process]</p>
<p>5: Diaz De Liano A, Oteiza Martinez F, Ciga MA, Aizcorbe M, Cobo F,
Trujillo R. Impact of surgical procedure for gastric cancer on quality of
life. Br J Surg. 2003 Jan;90(1):91-4. PMID: 12520582 [PubMed - in
process]</p>
<p>>>></p>
<p>Now refine the query to publications in the last day</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio <span class="py-keyword">import</span> EUtils
<span class="py-prompt">>>> </span>recent_cancer = client.search(<span class="py-string">"#%s"</span> % (cancer.query_key,),
<span class="py-more">... </span> daterange = EUtils.WithinNDays(1))
<span class="py-prompt">>>> </span>len(recent_cancer)
<span class="py-output">106</span>
<span class="py-output"></span><span class="py-prompt">>>></span></pre>
<p>Still quite a few. What's the last one about? >>> for k, v
in recent_cancer[-1].summary().dataitems.allitems(): ... print k,
"=", v ...</p>
<p>PubDate = 2002/12/01 Source = Nippon Shokakibyo Gakkai Zasshi Authors
= Kuroki T Title = [Strategy against cancer in 21 century, with emphasis
of cancer prevention and refractory cancer] Volume = 99 Pages = 1423-7
EntrezDate = 2003/01/10 PubMedId = 12518389 MedlineId = 22406828 Lang =
Japanese PubType = RecordStatus = PubMed - in process Issue = 12 SO =
2002 Dec;99(12):1423-7 DOI = JTA = KJY ISSN = 0446-6586 PubId = PubStatus
= 4 Status = 6 HasAbstract = 0 ArticleIds = {'MedlineUID': u'22406828',
'PubMedId': u'12518389'} >>></p>
<p>Here's an interesting one. Which articles are related to this one but
are not about cancer? First, get the related articles.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>neighbors = recent_cancer[-1].neighbor_links()
<span class="py-prompt">>>> </span>dbids = neighbors.linksetdbs[<span class="py-string">"pubmed_pubmed"</span>].dbids
<span class="py-prompt">>>> </span>len(dbids)
<span class="py-output">10296</span>
<span class="py-output"></span><span class="py-prompt">>>></span></pre>
<p>Upload that back to the server</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>related_result = client.post(dbids)
<span class="py-prompt">>>></span>
<span class="py-prompt">>>> </span>non_cancer = client.search(<span class="py-string">"#%s NOT #%s"</span> % (related_result.query_key,
<span class="py-more">... </span> cancer.query_key))
<span class="py-prompt">>>> </span>len(non_cancer)
<span class="py-output">4000</span>
<span class="py-output"></span><span class="py-prompt">>>></span></pre>
<p>The HistoryClient instance has an attribute named 'query_history'
which stores the searches done so far, keyed by the query_key value
assigned by the server. The history on the server can expire. If that
is detected during a search then previous results are invalidated and
removed from the query_history. Future requests from invalidated results
will raise an error.</p>
<p>If a request is made from a search which has not been invalidated but
whose history has expired then queries like 'summary' will raise an
error. Some other request (like 'dbids') may return success but contain
undefined information.</p>
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<a href="Bio.EUtils.HistoryClient.HistoryCookie-class.html" class="summary-name">HistoryCookie</a><br />
Data needed to get back to the history
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<a href="Bio.EUtils.HistoryClient.HistoryLookup-class.html" class="summary-name">HistoryLookup</a><br />
Look up information about a search in history
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<a href="Bio.EUtils.HistoryClient.HistoryRecord-class.html" class="summary-name">HistoryRecord</a><br />
Get information about a single record in a history
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<a href="Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin-class.html" class="summary-name">SequenceHistoryFetchMixin</a>
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<a href="Bio.EUtils.HistoryClient.SequenceHistoryRecord-class.html" class="summary-name">SequenceHistoryRecord</a>
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<a href="Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin-class.html" class="summary-name">PublicationHistoryFetchMixin</a>
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<a href="Bio.EUtils.HistoryClient.HistoryClient-class.html" class="summary-name">HistoryClient</a>
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<td><span class="summary-sig"><a name="_get_recordset_constructor"></a><span class="summary-sig-name">_get_recordset_constructor</span>(<span class="summary-sig-arg">db</span>,
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<span class="codelink"><a href="Bio.EUtils.HistoryClient-pysrc.html#_get_recordset_constructor">source code</a></span>
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