ncbi_blast_results_parser 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.gitignore +17 -0
- data/Gemfile +3 -0
- data/LICENCE +20 -0
- data/README.md +30 -0
- data/Rakefile +8 -0
- data/lib/ncbi_blast_results_parser.rb +39 -0
- data/lib/ncbi_blast_results_parser/rid_parser.rb +22 -0
- data/lib/ncbi_blast_results_parser/status_parser.rb +15 -0
- data/lib/ncbi_blast_results_parser/version.rb +3 -0
- data/ncbi_blast_results_parser.gemspec +25 -0
- data/spec/fixtures/ready_response.html +135 -0
- data/spec/fixtures/rid_response.html +553 -0
- data/spec/fixtures/unknown_response.html +135 -0
- data/spec/fixtures/waiting_response.html +135 -0
- data/spec/lib/ncbi_blast_results_parser/rid_parser_spec.rb +22 -0
- data/spec/lib/ncbi_blast_results_parser/status_parser_spec.rb +29 -0
- data/spec/lib/ncbi_blast_results_parser_spec.rb +24 -0
- data/spec/spec_helper.rb +8 -0
- metadata +115 -0
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<div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span id="trdm"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
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// --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
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bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td
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bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
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src="http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif" alt="My NCBI help" /></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a
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href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to sign in"
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onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Sign In]</a> <a
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href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to register for an account"
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onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Register]</a></td></tr></table></div>
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<li class="first "><a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
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<li class="recent "><a href="Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
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<li class="saved "><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
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<a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
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<a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/
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<a href="Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=">blastn suite</a>/
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<strong>Formatting Results - HZMF5DEN015</strong>
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<div class="inlineDiv resHeader">
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<a id="frmPage" class="WAITING" href="#" submitForm="reformat">[Formatting options] </a>
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</div>
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<h3 id="jtitle" >Job Title: </h3>
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<!--<ul id="msg" class="msg"><li class=""><p class=""></p><p class=""></p><p class=""></p></ul> -->
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<p><!--
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QBlastInfoBegin
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Status=UNKNOWN
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QBlastInfoEnd
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--></p>
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//--></SCRIPT>
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<table id="statInfo" class="WAITING">
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<tr><td>Request ID</td><td> <b>HZMF5DEN015</b></td></tr>
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<tr class="odd"><td>Status</td><td>Searching</td></tr>
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<tr><td>Submitted at</td><td>Sat Feb 16 13:37:25 2013</td></tr>
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<tr class="odd"><td>Current time</td><td>Sat Feb 16 13:37:26 2013</td></tr>
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<tr><td>Time since submission</td><td>00:00:01</td></tr>
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<p class="WAITING">This page will be automatically updated in <b>2</b> seconds</p>
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<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
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<input name="ALIGNMENTS" type="hidden" value="200"><input name="ALIGNMENT_TYPE" type="hidden" value="Pairwise"><input name="DESCRIPTIONS" type="hidden" value="100"><input name="FORMAT_OBJECT" type="hidden" value="Alignment"><input name="FORMAT_TYPE" type="hidden" value="XML"><input name="OLD_BLAST" type="hidden" value="false"><input name="OVERVIEW" type="hidden" value="yes"><input name="RID" type="hidden" value="HZMF5DEN015"><input name="SEARCH_DB_STATUS" type="hidden" value="31"><input name="USER_TYPE" type="hidden" value="2"><input name="_PGR" type="hidden" value="0">
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<!-- TO DO: test all of those changes -->
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<a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
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<a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
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<a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
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title='NCBI intellectual property statement'>Copyright</a> |
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<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer'
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title='About liability, endorsements, external links, pop-up advertisements'>Disclaimer</a> |
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title='NLM privacy policy'>Privacy</a> |
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title='About using NCBI resources with assistive technology'>Accessibility</a> |
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title='How to get help, submit data, or provide feedback'>Contact</a> |
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title='How to get help, submit data, or provide feedback'>Send feedback</a>
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<div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span id="trdm"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
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// --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
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bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td
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bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
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src="http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif" alt="My NCBI help" /></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a
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href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to sign in"
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onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Sign In]</a> <a
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href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to register for an account"
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onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Register]</a></td></tr></table></div>
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</div>
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<a class="skp" href="#content-wrap">Jump to Page Content</a>
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<ul id="nav">
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<li class="first "><a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
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<li class="recent "><a href="Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
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<li class="saved "><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
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<a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/
|
|
51
|
+
<a href="Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=">blastn suite</a>/
|
|
52
|
+
<strong>Formatting Results - HZMF5DEN015</strong>
|
|
53
|
+
</div>
|
|
54
|
+
<div class="inlineDiv resHeader">
|
|
55
|
+
<a id="frmPage" class="WAITING" href="#" submitForm="reformat">[Formatting options] </a>
|
|
56
|
+
</div>
|
|
57
|
+
<h3 id="jtitle" >Job Title: </h3>
|
|
58
|
+
|
|
59
|
+
<div id="content">
|
|
60
|
+
<!--<ul id="msg" class="msg"><li class=""><p class=""></p><p class=""></p><p class=""></p></ul> -->
|
|
61
|
+
<ul id="msg" class="msg"><li class=""></li></ul>
|
|
62
|
+
<p><!--
|
|
63
|
+
QBlastInfoBegin
|
|
64
|
+
Status=WAITING
|
|
65
|
+
QBlastInfoEnd
|
|
66
|
+
--></p>
|
|
67
|
+
|
|
68
|
+
<SCRIPT LANGUAGE="JavaScript"><!--
|
|
69
|
+
var tm = "2000";
|
|
70
|
+
if (tm != "") {
|
|
71
|
+
setTimeout('document.forms[0].submit();',tm);
|
|
72
|
+
}
|
|
73
|
+
//--></SCRIPT>
|
|
74
|
+
<table id="statInfo" class="WAITING">
|
|
75
|
+
<tr><td>Request ID</td><td> <b>HZMF5DEN015</b></td></tr>
|
|
76
|
+
<tr class="odd"><td>Status</td><td>Searching</td></tr>
|
|
77
|
+
<tr><td>Submitted at</td><td>Sat Feb 16 13:37:25 2013</td></tr>
|
|
78
|
+
<tr class="odd"><td>Current time</td><td>Sat Feb 16 13:37:26 2013</td></tr>
|
|
79
|
+
<tr><td>Time since submission</td><td>00:00:01</td></tr>
|
|
80
|
+
</table>
|
|
81
|
+
<p class="WAITING">This page will be automatically updated in <b>2</b> seconds</p>
|
|
82
|
+
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
|
|
83
|
+
<input name="ALIGNMENTS" type="hidden" value="200"><input name="ALIGNMENT_TYPE" type="hidden" value="Pairwise"><input name="DESCRIPTIONS" type="hidden" value="100"><input name="FORMAT_OBJECT" type="hidden" value="Alignment"><input name="FORMAT_TYPE" type="hidden" value="XML"><input name="OLD_BLAST" type="hidden" value="false"><input name="OVERVIEW" type="hidden" value="yes"><input name="RID" type="hidden" value="HZMF5DEN015"><input name="SEARCH_DB_STATUS" type="hidden" value="31"><input name="USER_TYPE" type="hidden" value="2"><input name="_PGR" type="hidden" value="0">
|
|
84
|
+
<input name="_PGR" type="hidden" value="0" >
|
|
85
|
+
<input name="CMD" type="hidden" value="Get">
|
|
86
|
+
|
|
87
|
+
</form>
|
|
88
|
+
|
|
89
|
+
</div><!-- /#content -->
|
|
90
|
+
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="reformat" id="reformat">
|
|
91
|
+
<input name="QUERY_INFO" type="hidden" value="" />
|
|
92
|
+
<input name="ENTREZ_QUERY" type="hidden" value="" />
|
|
93
|
+
<input name="CDD_RID" type="hidden" value="" />
|
|
94
|
+
<input name="CDD_SEARCH_STATE" type="hidden" value="" />
|
|
95
|
+
<input name="RID" type="hidden" value="HZMF5DEN015" />
|
|
96
|
+
<input name="STEP_NUMBER" type="hidden" value="" />
|
|
97
|
+
<input name="CMD" type="hidden" value="Web"/>
|
|
98
|
+
<input NAME="PAGE_TYPE" type="hidden" value="BlastFormatting"/>
|
|
99
|
+
|
|
100
|
+
<!-- TO DO: test all of those changes -->
|
|
101
|
+
<!-- Psi blast params PSI_BLAST_PARAMS - commented- using forms[0] from fromatter> -->
|
|
102
|
+
<!-- Current Formatting options FORMATTING_OPTIONS- commented- using forms[0] from fromatter> -->
|
|
103
|
+
<!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
|
|
104
|
+
</form>
|
|
105
|
+
</div><!-- /#content-wrap -->
|
|
106
|
+
|
|
107
|
+
|
|
108
|
+
<div id="footer">
|
|
109
|
+
<div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div>
|
|
110
|
+
<p id="orgns">
|
|
111
|
+
<a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
|
|
112
|
+
<a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
|
|
113
|
+
<a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
|
|
114
|
+
<a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
|
|
115
|
+
</p>
|
|
116
|
+
|
|
117
|
+
<p>
|
|
118
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html'
|
|
119
|
+
title='NCBI intellectual property statement'>Copyright</a> |
|
|
120
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer'
|
|
121
|
+
title='About liability, endorsements, external links, pop-up advertisements'>Disclaimer</a> |
|
|
122
|
+
<a href='http://www.nlm.nih.gov/privacy.html'
|
|
123
|
+
title='NLM privacy policy'>Privacy</a> |
|
|
124
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/accessibility.html'
|
|
125
|
+
title='About using NCBI resources with assistive technology'>Accessibility</a> |
|
|
126
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html'
|
|
127
|
+
title='How to get help, submit data, or provide feedback'>Contact</a> |
|
|
128
|
+
<a href='mailto:blast-help@ncbi.nlm.nih.gov'
|
|
129
|
+
title='How to get help, submit data, or provide feedback'>Send feedback</a>
|
|
130
|
+
</p>
|
|
131
|
+
</div>
|
|
132
|
+
</div><!--/#wrap-->
|
|
133
|
+
</body>
|
|
134
|
+
|
|
135
|
+
</html>
|
|
@@ -0,0 +1,22 @@
|
|
|
1
|
+
require_relative '../../spec_helper'
|
|
2
|
+
|
|
3
|
+
describe NCBIBlastResultsParser::RIDParser do
|
|
4
|
+
|
|
5
|
+
# Parser Setup
|
|
6
|
+
let(:rid_parser) { NCBIBlastResultsParser::RIDParser.new }
|
|
7
|
+
let(:parser) { Nokogiri::HTML::SAX::Parser.new(rid_parser) }
|
|
8
|
+
|
|
9
|
+
# RID Response
|
|
10
|
+
let(:response) { File.read(File.expand_path('../../fixtures/rid_response.html', File.dirname(__FILE__))) }
|
|
11
|
+
|
|
12
|
+
it 'parses an RID response' do
|
|
13
|
+
parser.parse(response)
|
|
14
|
+
rid_parser.rid.must_equal 'BUCSAKD101R'
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
it 'parses the suggested wait time' do
|
|
18
|
+
parser.parse(response)
|
|
19
|
+
rid_parser.wait.must_equal 17
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
end
|
|
@@ -0,0 +1,29 @@
|
|
|
1
|
+
require_relative '../../spec_helper'
|
|
2
|
+
|
|
3
|
+
describe NCBIBlastResultsParser::StatusParser do
|
|
4
|
+
|
|
5
|
+
# Parser Setup
|
|
6
|
+
let(:status_parser) { NCBIBlastResultsParser::StatusParser.new }
|
|
7
|
+
let(:parser) { Nokogiri::HTML::SAX::Parser.new(status_parser) }
|
|
8
|
+
|
|
9
|
+
# Status Responses
|
|
10
|
+
let(:ready) { File.read(File.expand_path('../../fixtures/ready_response.html', File.dirname(__FILE__))) }
|
|
11
|
+
let(:waiting) { File.read(File.expand_path('../../fixtures/waiting_response.html', File.dirname(__FILE__))) }
|
|
12
|
+
let(:unknown) { File.read(File.expand_path('../../fixtures/unknown_response.html', File.dirname(__FILE__))) }
|
|
13
|
+
|
|
14
|
+
it 'parses a ready response' do
|
|
15
|
+
parser.parse(ready)
|
|
16
|
+
status_parser.status.must_equal 'READY'
|
|
17
|
+
end
|
|
18
|
+
|
|
19
|
+
it 'parses a waiting response' do
|
|
20
|
+
parser.parse(waiting)
|
|
21
|
+
status_parser.status.must_equal 'WAITING'
|
|
22
|
+
end
|
|
23
|
+
|
|
24
|
+
it 'parses an unknown response' do
|
|
25
|
+
parser.parse(unknown)
|
|
26
|
+
status_parser.status.must_equal 'UNKNOWN'
|
|
27
|
+
end
|
|
28
|
+
|
|
29
|
+
end
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
require_relative '../spec_helper'
|
|
2
|
+
|
|
3
|
+
describe NCBIBlastResultsParser do
|
|
4
|
+
|
|
5
|
+
# Parser Setup
|
|
6
|
+
let(:parser) { NCBIBlastResultsParser }
|
|
7
|
+
|
|
8
|
+
# Responses
|
|
9
|
+
let(:rid_response) { File.read(File.expand_path('../fixtures/rid_response.html', File.dirname(__FILE__))) }
|
|
10
|
+
let(:ready_response) { File.read(File.expand_path('../fixtures/ready_response.html', File.dirname(__FILE__))) }
|
|
11
|
+
|
|
12
|
+
it 'parses a request id' do
|
|
13
|
+
parser.rid(rid_response).must_equal 'BUCSAKD101R'
|
|
14
|
+
end
|
|
15
|
+
|
|
16
|
+
it 'parses a suggested wait time' do
|
|
17
|
+
parser.wait(rid_response).must_equal 17
|
|
18
|
+
end
|
|
19
|
+
|
|
20
|
+
it 'parses a status' do
|
|
21
|
+
parser.status(ready_response).must_equal 'READY'
|
|
22
|
+
end
|
|
23
|
+
|
|
24
|
+
end
|
data/spec/spec_helper.rb
ADDED
metadata
ADDED
|
@@ -0,0 +1,115 @@
|
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
|
2
|
+
name: ncbi_blast_results_parser
|
|
3
|
+
version: !ruby/object:Gem::Version
|
|
4
|
+
version: 0.1.0
|
|
5
|
+
prerelease:
|
|
6
|
+
platform: ruby
|
|
7
|
+
authors:
|
|
8
|
+
- Gareth Rees
|
|
9
|
+
autorequire:
|
|
10
|
+
bindir: bin
|
|
11
|
+
cert_chain: []
|
|
12
|
+
date: 2013-02-17 00:00:00.000000000 Z
|
|
13
|
+
dependencies:
|
|
14
|
+
- !ruby/object:Gem::Dependency
|
|
15
|
+
name: nokogiri
|
|
16
|
+
requirement: &70334262957880 !ruby/object:Gem::Requirement
|
|
17
|
+
none: false
|
|
18
|
+
requirements:
|
|
19
|
+
- - ! '>='
|
|
20
|
+
- !ruby/object:Gem::Version
|
|
21
|
+
version: '0'
|
|
22
|
+
type: :runtime
|
|
23
|
+
prerelease: false
|
|
24
|
+
version_requirements: *70334262957880
|
|
25
|
+
- !ruby/object:Gem::Dependency
|
|
26
|
+
name: minitest
|
|
27
|
+
requirement: &70334259121780 !ruby/object:Gem::Requirement
|
|
28
|
+
none: false
|
|
29
|
+
requirements:
|
|
30
|
+
- - ! '>='
|
|
31
|
+
- !ruby/object:Gem::Version
|
|
32
|
+
version: '0'
|
|
33
|
+
type: :development
|
|
34
|
+
prerelease: false
|
|
35
|
+
version_requirements: *70334259121780
|
|
36
|
+
- !ruby/object:Gem::Dependency
|
|
37
|
+
name: turn
|
|
38
|
+
requirement: &70334264495440 !ruby/object:Gem::Requirement
|
|
39
|
+
none: false
|
|
40
|
+
requirements:
|
|
41
|
+
- - ! '>='
|
|
42
|
+
- !ruby/object:Gem::Version
|
|
43
|
+
version: '0'
|
|
44
|
+
type: :development
|
|
45
|
+
prerelease: false
|
|
46
|
+
version_requirements: *70334264495440
|
|
47
|
+
- !ruby/object:Gem::Dependency
|
|
48
|
+
name: rake
|
|
49
|
+
requirement: &70334264471540 !ruby/object:Gem::Requirement
|
|
50
|
+
none: false
|
|
51
|
+
requirements:
|
|
52
|
+
- - ! '>='
|
|
53
|
+
- !ruby/object:Gem::Version
|
|
54
|
+
version: '0'
|
|
55
|
+
type: :development
|
|
56
|
+
prerelease: false
|
|
57
|
+
version_requirements: *70334264471540
|
|
58
|
+
description: Parses useful information from the HTML response of an NCBI Blast
|
|
59
|
+
email:
|
|
60
|
+
- gareth@garethrees.co.uk
|
|
61
|
+
executables: []
|
|
62
|
+
extensions: []
|
|
63
|
+
extra_rdoc_files: []
|
|
64
|
+
files:
|
|
65
|
+
- .gitignore
|
|
66
|
+
- Gemfile
|
|
67
|
+
- LICENCE
|
|
68
|
+
- README.md
|
|
69
|
+
- Rakefile
|
|
70
|
+
- lib/ncbi_blast_results_parser.rb
|
|
71
|
+
- lib/ncbi_blast_results_parser/rid_parser.rb
|
|
72
|
+
- lib/ncbi_blast_results_parser/status_parser.rb
|
|
73
|
+
- lib/ncbi_blast_results_parser/version.rb
|
|
74
|
+
- ncbi_blast_results_parser.gemspec
|
|
75
|
+
- spec/fixtures/ready_response.html
|
|
76
|
+
- spec/fixtures/rid_response.html
|
|
77
|
+
- spec/fixtures/unknown_response.html
|
|
78
|
+
- spec/fixtures/waiting_response.html
|
|
79
|
+
- spec/lib/ncbi_blast_results_parser/rid_parser_spec.rb
|
|
80
|
+
- spec/lib/ncbi_blast_results_parser/status_parser_spec.rb
|
|
81
|
+
- spec/lib/ncbi_blast_results_parser_spec.rb
|
|
82
|
+
- spec/spec_helper.rb
|
|
83
|
+
homepage: ''
|
|
84
|
+
licenses: []
|
|
85
|
+
post_install_message:
|
|
86
|
+
rdoc_options: []
|
|
87
|
+
require_paths:
|
|
88
|
+
- lib
|
|
89
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
|
90
|
+
none: false
|
|
91
|
+
requirements:
|
|
92
|
+
- - ! '>='
|
|
93
|
+
- !ruby/object:Gem::Version
|
|
94
|
+
version: '0'
|
|
95
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
96
|
+
none: false
|
|
97
|
+
requirements:
|
|
98
|
+
- - ! '>='
|
|
99
|
+
- !ruby/object:Gem::Version
|
|
100
|
+
version: '0'
|
|
101
|
+
requirements: []
|
|
102
|
+
rubyforge_project:
|
|
103
|
+
rubygems_version: 1.8.15
|
|
104
|
+
signing_key:
|
|
105
|
+
specification_version: 3
|
|
106
|
+
summary: Parses useful information from the HTML response of an NCBI Blast
|
|
107
|
+
test_files:
|
|
108
|
+
- spec/fixtures/ready_response.html
|
|
109
|
+
- spec/fixtures/rid_response.html
|
|
110
|
+
- spec/fixtures/unknown_response.html
|
|
111
|
+
- spec/fixtures/waiting_response.html
|
|
112
|
+
- spec/lib/ncbi_blast_results_parser/rid_parser_spec.rb
|
|
113
|
+
- spec/lib/ncbi_blast_results_parser/status_parser_spec.rb
|
|
114
|
+
- spec/lib/ncbi_blast_results_parser_spec.rb
|
|
115
|
+
- spec/spec_helper.rb
|