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wendel
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git migration cleanup
git-svn-id: svn://svn.microbio.me/QIIME-webdev/trunk/qiime_web_app@2426 aa835298-08e1-4b45-9256-153aff0879ff
1 parent 2c4556d commit b4c33ac

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+3363
-2889
lines changed

‎python_code/data_access/qiime_data_access.py

+2,906-2,886
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‎python_code/ebi_output_parser.py

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#!/usr/bin/env python
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__author__ = "Doug Wendel"
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__copyright__ = "Copyright 2010, The QIIME project"
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__credits__ = ["Doug Wendel"]
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__license__ = "GPL"
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__version__ = "1.2.0-dev"
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__maintainer__ = "Doug Wendel"
9+
__email__ = "[email protected]"
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__status__ = "Development"
11+
12+
from xml.dom.minidom import parse
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class EBIOutputParser(object):
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def __init__(self, file_path):
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self.file_path = file_path
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self.dom = parse(file_path)
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def __del__(self):
20+
pass
21+
22+
def parse_samples(self):
23+
samples = {}
24+
for node in self.dom.getElementsByTagName('SAMPLE'):
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samples[node.getAttribute('alias')] = note.getAttribute('accession')
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return samples

‎python_code/load_analysis_seqs_through_otu_table.py

+1-1
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@@ -297,7 +297,7 @@ def load_split_lib_sequences(data_access,input_dir,analysis_id, seq_run_id,
297297

298298
end = time.time()
299299
print 'Total processor time elapsed: %s' % str(end - start)
300-
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301301
print 'Finished loading split_library FNA file.'
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303303
try:

‎python_code/tests/support_files/ebi_results.xml

+3
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‎python_code/tests/support_files/qiime_test_datasets/illumina_test_set/Archive.zip

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‎python_code/tests/support_files/qiime_test_datasets/illumina_test_set/metadata.zip

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‎python_code/tests/support_files/qiime_test_datasets/illumina_test_set/metadata_short.zip

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‎python_code/tests/support_files/qiime_test_datasets/illumina_test_set/metadata_short/Archive.zip

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‎python_code/tests/support_files/qiime_test_datasets/illumina_test_set/metadata_short/prep_template_2012-04-27 14:10:12.785153.txt

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sample_name BARCODE EXPERIMENT_CENTER EXPERIMENT_DESIGN_DESCRIPTION EXPERIMENT_TITLE KEY_SEQ LIBRARY_CONSTRUCTION_PROTOCOL LINKER PLATFORM primer region RUN_CENTER RUN_DATE run_prefix SAMPLE_CENTER STUDY_CENTER samp_size sequencing_meth target_geneHKH07June07 CTAGCGTGCGTT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH23July07 CATCGACGAGTT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE01Aug07 GTACGCACAGTT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE08Aug07 TCGACATCTCTT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH15June07 CGACTGCAGCTT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH08Aug07 ACGAGACTGATT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE20June07 CGAGTCACGATT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH20June07 GCCATAGTGTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE26June07 GTAGACATGTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH26June07 TGTGGCTCGTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE28June07 TAGACACCGTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH28June07 CGGATCTAGTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE04July07 CATGAACAGTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH04July07 TGAGTGGTCTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE06July07 AGCCGACTCTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH06July07 GACCACTGCTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE09July07 CAAGCTAGCTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKH09July07 ATGAAGCACTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNAHKE12July07 TCGCGCAACTGT CCME 11 Temperate Bog Lakes unknown 11 Illumina CCGGACTACHVGGGTWTCTAAT CCME 6/7/07 S_1_1_sequences CCME CCME "1,mL" pyrosequencing 16S rRNA

‎python_code/tests/support_files/qiime_test_datasets/illumina_test_set/metadata_short/sample_template_2012-04-27 14:10:12.785153.txt

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sample_name ANONYMIZED_NAME DESCRIPTION TAXON_ID TITLE altitude assigned_from_geo collection_date country depth elevation env_biome env_feature env_matter latitude longitude publicHKH07June07 HKH07June07 HKH07June07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH23July07 HKH23July07 HKH23July07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE01Aug07 HKE01Aug07 HKE01Aug07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE08Aug07 HKE08Aug07 HKE08Aug07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH15June07 HKH15June07 HKH15June07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH08Aug07 HKH08Aug07 HKH08Aug07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE20June07 HKE20June07 HKE20June07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH20June07 HKH20June07 HKH20June07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE26June07 HKE26June07 HKE26June07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH26June07 HKH26June07 HKH26June07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE28June07 HKE28June07 HKE28June07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH28June07 HKH28June07 HKH28June07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE04July07 HKE04July07 HKE04July07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH04July07 HKH04July07 HKH04July07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE06July07 HKE06July07 HKE06July07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH06July07 HKH06July07 HKH06July07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE09July07 HKE09July07 HKE09July07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKH09July07 HKH09July07 HKH09July07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 nHKE12July07 HKE12July07 HKE12July07 449393 soil metagenome 0 n 6/7/07 GAZ:United States of America 11.5 304.11 ENVO:freshwater biome ENVO:freshwater habitat ENVO:water 46.250683 -89.900328 n

‎python_code/tests/support_files/qiime_test_datasets/illumina_test_set/s_1_1_sequences.fastq.gz

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‎python_code/tests/support_files/qiime_test_datasets/illumina_test_set/s_1_1_sequences_barcodes.fastq.gz

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‎python_code/tests/test_ebi_output_parser.py

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#!/usr/bin/env python
2+
# File created on 19 Apr 2011
3+
from __future__ import division
4+
5+
__author__ = "Doug Wendel"
6+
__copyright__ = "Copyright 2011, The QIIME-webdev project"
7+
__credits__ = ["Doug Wendel"]
8+
__license__ = "GPL"
9+
__version__ = "1.2.1-dev"
10+
__maintainer__ = "Doug Wendel"
11+
__email__ = "[email protected]"
12+
__status__ = "Development"
13+
14+
from ebi_output_parser import *
15+
from cogent.util.unit_test import TestCase, main
16+
17+
class Tests(TestCase):
18+
19+
def setUp(self):
20+
""" Setup
21+
"""
22+
self.parser = ebi_output_parser('support_files/ebi_results.xml')
23+
pass
24+
25+
def tearDown(self):
26+
""" Clean up
27+
"""
28+
pass
29+
30+
def test_parse_samples(self):
31+
""" Test instantiation of base services
32+
"""
33+
samples = self.parser.parse_samples()
34+
self.assertIsNotNone(samples)
35+
36+
if __name__ == "__main__":
37+
main()

‎support_files/populate_sequence_counts.py

+2
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@@ -51,6 +51,8 @@
5151
for sequence_prep_id, seq_count in results:
5252
seq_prep_counts.append((sequence_prep_id, seq_count))
5353

54+
print '{0}: {1}'.format(sequence_prep_id, seq_count)
55+
5456
query_string_2 = """
5557
update sequence_prep
5658
set num_sequences = {0}

‎www/accordian.psp

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1+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml2/DTD/xhtml1-strict.dtd">
2+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
3+
4+
<head>
5+
6+
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script>
7+
<script type="text/javascript" src="js/ddaccordion.js">
8+
9+
/***********************************************
10+
* Accordion Content script- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)
11+
* Visit http://www.dynamicDrive.com for hundreds of DHTML scripts
12+
* This notice must stay intact for legal use
13+
***********************************************/
14+
15+
</script>
16+
17+
18+
<script type="text/javascript">
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20+
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ddaccordion.init({
22+
headerclass: "silverheader", //Shared CSS class name of headers group
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contentclass: "submenu", //Shared CSS class name of contents group
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revealtype: "click", //Reveal content when user clicks or onmouseover the header? Valid value: "click", "clickgo", or "mouseover"
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mouseoverdelay: 200, //if revealtype="mouseover", set delay in milliseconds before header expands onMouseover
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collapseprev: true, //Collapse previous content (so only one open at any time)? true/false
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defaultexpanded: [0], //index of content(s) open by default [index1, index2, etc] [] denotes no content
28+
onemustopen: true, //Specify whether at least one header should be open always (so never all headers closed)
29+
animatedefault: false, //Should contents open by default be animated into view?
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persiststate: true, //persist state of opened contents within browser session?
31+
toggleclass: ["", "selected"], //Two CSS classes to be applied to the header when it's collapsed and expanded, respectively ["class1", "class2"]
32+
togglehtml: ["", "", ""], //Additional HTML added to the header when it's collapsed and expanded, respectively ["position", "html1", "html2"] (see docs)
33+
animatespeed: "fast", //speed of animation: integer in milliseconds (ie: 200), or keywords "fast", "normal", or "slow"
34+
oninit:function(headers, expandedindices){ //custom code to run when headers have initalized
35+
//do nothing
36+
},
37+
onopenclose:function(header, index, state, isuseractivated){ //custom code to run whenever a header is opened or closed
38+
//do nothing
39+
}
40+
})
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</script>
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<style type="text/css">
47+
48+
.applemenu{
49+
margin: 5px 0;
50+
padding: 0;
51+
width: 170px; /*width of menu*/
52+
border: 1px solid #9A9A9A;
53+
}
54+
55+
.applemenu div.silverheader a{
56+
background: black url(img/silvergradient.gif) repeat-x center left;
57+
font: normal 12px Tahoma, "Lucida Grande", "Trebuchet MS", Helvetica, sans-serif;
58+
color: white;
59+
display: block;
60+
position: relative; /*To help in the anchoring of the ".statusicon" icon image*/
61+
width: auto;
62+
padding: 5px 0;
63+
padding-left: 8px;
64+
text-decoration: none;
65+
}
66+
67+
68+
.applemenu div.silverheader a:visited, .applemenu div.silverheader a:active{
69+
color: white;
70+
}
71+
72+
73+
.applemenu div.selected a, .applemenu div.silverheader a:hover{
74+
background-image: url(img/silvergradientover.gif);
75+
color: white;
76+
}
77+
78+
.applemenu div.submenu{ /*DIV that contains each sub menu*/
79+
background: white;
80+
padding: 5px;
81+
height: 600px; /*Height that applies to all sub menu DIVs. A good idea when headers are toggled via "mouseover" instead of "click"*/
82+
}
83+
84+
</style>
85+
86+
</head>
87+
88+
<body>
89+
90+
<div class="applemenu">
91+
<div class="silverheader"><a href="http://www.dynamicdrive.com">Dynamic Drive</a></div>
92+
<div class="submenu">
93+
Some random content here<br />
94+
</div>
95+
<div class="silverheader"><a href="http://www.dynamicdrive.com/style/" >CSS Examples</a></div>
96+
<div class="submenu">
97+
Some random content here<br />
98+
</div>
99+
<div class="silverheader"><a href="http://www.javascriptkit.com">JavaScript Kit</a></div>
100+
<div class="submenu">
101+
Some random content here<br />
102+
</div>
103+
<div class="silverheader"><a href="http://www.cssdrive.com">CSS Drive</a></div>
104+
<div class="submenu">
105+
Some random content here<br />
106+
<img src="http://i27.tinypic.com/sy7295.gif" />
107+
</div>
108+
<div class="silverheader"><a href="http://www.codingforums.com">Coding Forums</a></div>
109+
<div class="submenu">
110+
Some random content here<br />
111+
</div>
112+
</div>
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<p>Assuming the current page is named "current.htm", the below links when navigated to expands a particular header on that page:</p>
115+
<p>
116+
- <a href="current.htm?silverheader=0">Expand 1st header within "submenuheader" header group</a><br />
117+
</p>
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<p>Helpful links: </p>
120+
<p>
121+
- <a href="http://www.dynamicdrive.com/dynamicindex17/ddaccordion_suppliment.htm">Adding arbitrary links hat expand/ collapse the contents</a><br />
122+
- <a href="http://www.dynamicdrive.com/dynamicindex17/ddaccordion_suppliment2.htm">Taking advantage of the oninit() and onopenclose() event handlers</a><br />
123+
</p>
124+
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</body>
126+
</html>

‎www/data/router.psp

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../r/router.psp

‎www/new_study.psp

+3-2
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@@ -252,10 +252,11 @@ for item in sorted(list):
252252
</div>
253253
</td>
254254
<td>*
255-
<select class="input required" name="environmental_package" name="environmental_package" multiple>
255+
<select class="input required" name="environmental_package" name="environmental_package" multiple size="19">
256256
<%
257257
list = qda.getListValues('Package Type')
258-
for item in sorted(list):
258+
list.sort(key=lambda x: x[1])
259+
for item in list:
259260
if item[0] > 0:
260261
if item[0] in environmental_packages:
261262
req.write('<option value=\"%s\" selected>%s</option>\n' % (item[0], item[1]))

‎www/r/.htaccess_orig

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RewriteEngine On
2+
RewriteRule ^(.*$) router.psp?query=$1 [QSA]

‎www/test/bioportal_widgets.psp

+139
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<html>
2+
<head>
3+
4+
<script type="text/javascript" src="./js/quick_jump.js"></script>
5+
</head>
6+
7+
<body>
8+
9+
<h1>BioPortal Widgets</h1>
10+
11+
12+
<form>
13+
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<h3>Input Widget</h3>
15+
GAZ<br/>
16+
<input type="text" name="a" class="bp_form_complete-1397-ontprefix_name" size="100"/><br/>
17+
ENVO Biome with ID_Name<br/>
18+
<input type="text" name="a" class="bp_form_complete-1069-shortid_name" data-bp_search_branch="ENVO:00000428" size="100"/><br/>
19+
ENVO Search - Replace with ID<br/>
20+
<input type="text" name="a" class="bp_form_complete-1069-shortid" size="100"/><br/>
21+
ENVO Search - Replace with name<br/>
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<input type="text" name="a" class="bp_form_complete-1069-name" size="100"/><br/>
23+
ENVO Search - Replace with URI<br/>
24+
<input type="text" name="a" class="bp_form_complete-1069-uri" size="100"/><br/>
25+
<br/>
26+
27+
<h3>Ontology Search Widget</h3>
28+
<div id="bp_quick_jump"></div>
29+
<script type="text/javascript">
30+
var BP_ontology_id = "1069";
31+
</script>
32+
33+
<br/>
34+
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<h3>Feed Widget</h3>
36+
<script type="text/javascript">
37+
var BP_ontology_id = "1032"
38+
</script>
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<script src="http://bioportal.bioontology.org/javascripts/widgets/feed_widget.js" type="text/javascript" charset="utf-8"></script>
40+
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<br/>
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<h3>Ontology Visualization Widget</h3>
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<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
46+
id="FlexoViz" width="100%" height="100%"
47+
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab">
48+
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" />
49+
<param name="quality" value="high" />
50+
<param name="bgcolor" value="#ffffff" />
51+
<param name="allowScriptAccess" value="always" />
52+
<embed src="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" bgcolor="#ffffff"
53+
width="100%" height="100%" name="FlexoViz" align="middle"
54+
play="true"
55+
loop="false"
56+
quality="high"
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allowScriptAccess="always"
58+
type="application/x-shockwave-flash"
59+
flashVars="widget=true&ontology=1069&server=http://rest.bioontology.org/bioportal/"
60+
pluginspage="http://www.adobe.com/go/getflashplayer">
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</embed>
62+
</object>
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<br/>
64+
65+
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<h3>Ontology Tree Widget</h3>
68+
<script src="http://keg.cs.uvic.ca/ncbo/ontologytree/AC_OETags.js" language="javascript"></script>
69+
<script>
70+
// -----------------------------------------------------------------------------
71+
// Globals
72+
// Major version of Flash required
73+
var requiredMajorVersion = 9;
74+
// Minor version of Flash required
75+
var requiredMinorVersion = 0;
76+
// Minor version of Flash required
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var requiredRevision = 124;
78+
// -----------------------------------------------------------------------------
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// Version check for the Flash Player that has the ability to start Player Product Install (6.0r65)
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var hasProductInstall = DetectFlashVer(6, 0, 65);
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// Version check based upon the values defined in globals
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var hasRequestedVersion = DetectFlashVer(requiredMajorVersion, requiredMinorVersion, requiredRevision);
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if (hasProductInstall && !hasRequestedVersion) {
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// DO NOT MODIFY THE FOLLOWING FOUR LINES
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// Location visited after installation is complete if installation is required
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var MMPlayerType = (isIE == true) ? "ActiveX": "PlugIn";
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var MMredirectURL = window.location;
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document.title = document.title.slice(0, 47) + " - Flash Player Installation";
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var MMdoctitle = document.title;
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AC_FL_RunContent(
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"src", "playerProductInstall",
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"FlashVars", "MMredirectURL=" + MMredirectURL + '&MMplayerType=' + MMPlayerType + '&MMdoctitle=' + MMdoctitle + "",
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"width", "300",
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"height", "100%",
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"align", "middle",
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"id", "OntologyTree",
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"quality", "high",
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"bgcolor", "#ffffff",
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"name", "OntologyTree",
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"allowScriptAccess", "always",
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"type", "application/x-shockwave-flash",
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"pluginspage", "http://www.adobe.com/go/getflashplayer"
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);
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} else if (hasRequestedVersion) {
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// if we've detected an acceptable version
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// embed the Flash Content SWF when all tests are passed
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AC_FL_RunContent(
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"src", "http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf",
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"width", "300",
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"height", "500",
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"align", "middle",
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"id", "OntologyTree",
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"quality", "high",
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"bgcolor", "#ffffff",
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"name", "OntologyTree",
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"allowScriptAccess", "always",
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"flashVars", "ontology=1069&virtual=false&alerterrors=true&canchangeontology=false&rootconceptid=ENVO:00000428",
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"type", "application/x-shockwave-flash",
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"pluginspage", "http://www.adobe.com/go/getflashplayer"
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);
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} else {
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// flash is too old or we can't detect the plugin
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var alternateContent = 'Alternate HTML content should be placed here. '
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+ 'This content requires the Adobe Flash Player. '
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+ '<a href=http://www.adobe.com/go/getflash/>Get Flash</a>';
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document.write(alternateContent);
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// insert non-flash content
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}
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</script>
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</form>
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</body>
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</html>

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