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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.dbdefs-module.html">Package dbdefs</a> ::
Module medline
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<h1 class="epydoc">Source Code for <a href="Bio.dbdefs.medline-module.html">Module Bio.dbdefs.medline</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Database definitions for retrieval of Medline information.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-1', 'config', 'link-1');">config</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.config.DBRegistry=Bio.config.DBRegistry-module.html,Class Bio.config.DBRegistry.DBRegistry=Bio.config.DBRegistry.DBRegistry-class.html"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-2', 'DBRegistry', 'link-2');">DBRegistry</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.config.DBRegistry.DBGroup=Bio.config.DBRegistry.DBGroup-class.html"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-3', 'DBGroup', 'link-3');">DBGroup</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.config.DBRegistry.EUtilsDB=Bio.config.DBRegistry.EUtilsDB-class.html"><a title="Bio.config.DBRegistry.EUtilsDB" class="py-name" href="#" onclick="return doclink('link-4', 'EUtilsDB', 'link-4');">EUtilsDB</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name" targets="Module Bio.config._support=Bio.config._support-module.html,Module Bio.dbdefs._support=Bio.dbdefs._support-module.html"><a title="Bio.config._support
Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-5', '_support', 'link-5');">_support</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-6', 'Martel', 'link-6');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt id="link-7" class="py-name" targets="Variable Bio.dbdefs.fasta.proxy_error_expr=Bio.dbdefs.fasta-module.html#proxy_error_expr,Variable Bio.dbdefs.genbank.proxy_error_expr=Bio.dbdefs.genbank-module.html#proxy_error_expr,Variable Bio.dbdefs.medline.proxy_error_expr=Bio.dbdefs.medline-module.html#proxy_error_expr"><a title="Bio.dbdefs.fasta.proxy_error_expr
Bio.dbdefs.genbank.proxy_error_expr
Bio.dbdefs.medline.proxy_error_expr" class="py-name" href="#" onclick="return doclink('link-7', 'proxy_error_expr', 'link-7');">proxy_error_expr</a></tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Function Bio.dbdefs._support.has_expr()=Bio.dbdefs._support-module.html#has_expr"><a title="Bio.dbdefs._support.has_expr" class="py-name" href="#" onclick="return doclink('link-8', 'has_expr', 'link-8');">has_expr</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name" targets="Function Martel.Alt()=Martel-module.html#Alt,Class Martel.Expression.Alt=Martel.Expression.Alt-class.html"><a title="Martel.Alt
Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-9', 'Alt', 'link-9');">Alt</a></tt><tt class="py-op">(</tt><tt id="link-10" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-10', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"500"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-11', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"502"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-12" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-12', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" Proxy Error"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt id="link-13" class="py-name" targets="Variable Bio.dbdefs.fasta.diagnostic_error_expr=Bio.dbdefs.fasta-module.html#diagnostic_error_expr,Variable Bio.dbdefs.genbank.diagnostic_error_expr=Bio.dbdefs.genbank-module.html#diagnostic_error_expr,Variable Bio.dbdefs.medline.diagnostic_error_expr=Bio.dbdefs.medline-module.html#diagnostic_error_expr"><a title="Bio.dbdefs.fasta.diagnostic_error_expr
Bio.dbdefs.genbank.diagnostic_error_expr
Bio.dbdefs.medline.diagnostic_error_expr" class="py-name" href="#" onclick="return doclink('link-13', 'diagnostic_error_expr', 'link-13');">diagnostic_error_expr</a></tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name" targets="Function Bio.dbdefs._support.has_str()=Bio.dbdefs._support-module.html#has_str"><a title="Bio.dbdefs._support.has_str" class="py-name" href="#" onclick="return doclink('link-14', 'has_str', 'link-14');">has_str</a></tt><tt class="py-op">(</tt><tt class="py-string">"WWW Error 500 Diagnostic"</tt><tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt id="link-15" class="py-name" targets="Variable Bio.dbdefs.fasta.error_expr=Bio.dbdefs.fasta-module.html#error_expr,Variable Bio.dbdefs.genbank.error_expr=Bio.dbdefs.genbank-module.html#error_expr,Variable Bio.dbdefs.medline.error_expr=Bio.dbdefs.medline-module.html#error_expr"><a title="Bio.dbdefs.fasta.error_expr
Bio.dbdefs.genbank.error_expr
Bio.dbdefs.medline.error_expr" class="py-name" href="#" onclick="return doclink('link-15', 'error_expr', 'link-15');">error_expr</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-16', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"ERROR"</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt id="link-17" class="py-name" targets="Variable Bio.dbdefs.fasta.ncbi_failures=Bio.dbdefs.fasta-module.html#ncbi_failures,Variable Bio.dbdefs.genbank.ncbi_failures=Bio.dbdefs.genbank-module.html#ncbi_failures,Variable Bio.dbdefs.medline.ncbi_failures=Bio.dbdefs.medline-module.html#ncbi_failures"><a title="Bio.dbdefs.fasta.ncbi_failures
Bio.dbdefs.genbank.ncbi_failures
Bio.dbdefs.medline.ncbi_failures" class="py-name" href="#" onclick="return doclink('link-17', 'ncbi_failures', 'link-17');">ncbi_failures</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.dbdefs.fasta.proxy_error_expr
Bio.dbdefs.genbank.proxy_error_expr
Bio.dbdefs.medline.proxy_error_expr" class="py-name" href="#" onclick="return doclink('link-18', 'proxy_error_expr', 'link-7');">proxy_error_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"proxy error"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.dbdefs.fasta.diagnostic_error_expr
Bio.dbdefs.genbank.diagnostic_error_expr
Bio.dbdefs.medline.diagnostic_error_expr" class="py-name" href="#" onclick="return doclink('link-19', 'diagnostic_error_expr', 'link-13');">diagnostic_error_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"diagnostic error"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.dbdefs.fasta.error_expr
Bio.dbdefs.genbank.error_expr
Bio.dbdefs.medline.error_expr" class="py-name" href="#" onclick="return doclink('link-20', 'error_expr', 'link-15');">error_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"ERROR"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-21" class="py-name" targets="Variable Bio.dbdefs._support.html_expr=Bio.dbdefs._support-module.html#html_expr"><a title="Bio.dbdefs._support.html_expr" class="py-name" href="#" onclick="return doclink('link-21', 'html_expr', 'link-21');">html_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"I got HTML and shouldn't have"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-22', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Please try again later"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Please try again later"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-23', 'Str', 'link-10');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"The sequence has been intentionally withdrawn"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-string">"Sequence withdrawn"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-24" class="py-name" targets="Variable Bio.dbdefs._support.blank_expr=Bio.dbdefs._support-module.html#blank_expr"><a title="Bio.dbdefs._support.blank_expr" class="py-name" href="#" onclick="return doclink('link-24', 'blank_expr', 'link-24');">blank_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"No data returned"</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-op">]</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt id="link-25" class="py-name" targets="Variable Bio.dbdefs.medline.medline_eutils=Bio.dbdefs.medline-module.html#medline_eutils"><a title="Bio.dbdefs.medline.medline_eutils" class="py-name" href="#" onclick="return doclink('link-25', 'medline_eutils', 'link-25');">medline_eutils</a></tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name"><a title="Bio.config.DBRegistry.EUtilsDB" class="py-name" href="#" onclick="return doclink('link-26', 'EUtilsDB', 'link-4');">EUtilsDB</a></tt><tt class="py-op">(</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt id="link-27" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-27', 'name', 'link-27');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"medline-eutils"</tt><tt class="py-op">,</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-string">"Retrieve Medline data from NCBI using EUtils"</tt><tt class="py-op">,</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-name">delay</tt> <tt class="py-op">=</tt> <tt class="py-number">5.0</tt><tt class="py-op">,</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt id="link-28" class="py-name" targets="Variable Bio.LocusLink.locus_format.db=Bio.LocusLink.locus_format-module.html#db,Variable Bio.config.DBRegistry.db=Bio.config.DBRegistry-module.html#db"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-28', 'db', 'link-28');">db</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">rettype</tt> <tt class="py-op">=</tt> <tt class="py-string">"medline"</tt><tt class="py-op">,</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-name">failure_cases</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.dbdefs.fasta.ncbi_failures
Bio.dbdefs.genbank.ncbi_failures
Bio.dbdefs.medline.ncbi_failures" class="py-name" href="#" onclick="return doclink('link-29', 'ncbi_failures', 'link-17');">ncbi_failures</a></tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt id="link-30" class="py-name" targets="Module Bio.dbdefs.medline=Bio.dbdefs.medline-module.html,Variable Bio.dbdefs.medline.medline=Bio.dbdefs.medline-module.html#medline"><a title="Bio.dbdefs.medline
Bio.dbdefs.medline.medline" class="py-name" href="#" onclick="return doclink('link-30', 'medline', 'link-30');">medline</a></tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-31', 'DBGroup', 'link-3');">DBGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt id="link-32" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-32', 'name', 'link-27');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"medline"</tt><tt class="py-op">,</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-name">behavior</tt> <tt class="py-op">=</tt> <tt class="py-string">"serial"</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt id="link-33" class="py-name"><a title="Bio.dbdefs.medline
Bio.dbdefs.medline.medline" class="py-name" href="#" onclick="return doclink('link-33', 'medline', 'link-30');">medline</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-34', 'add', 'link-34');">add</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.dbdefs.medline.medline_eutils" class="py-name" href="#" onclick="return doclink('link-35', 'medline_eutils', 'link-25');">medline_eutils</a></tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt><script type="text/javascript">
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// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
