Skip to content

Commit 7d594d6

Browse files
author
eoberortner
committed
Merge branch 'GSoC18'
Conflicts: src/main/java/gov/doe/jgi/boost/client/BOOSTClient.java src/main/java/gov/doe/jgi/boost/client/RequestBuilder.java src/main/java/gov/doe/jgi/boost/client/constants/BOOSTConstants.java src/main/java/gov/doe/jgi/boost/client/constants/JSONKeys.java src/test/java/gov/doe/jgi/boost/client/DemoClient.java
2 parents c407df6 + dadac00 commit 7d594d6

39 files changed

Lines changed: 1403 additions & 316 deletions

boost-client.jar

46.7 KB
Binary file not shown.

data/.gitignore

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
/bugs/

data/codon_juggle.sbol.xml

Lines changed: 123 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,123 @@
1+
<?xml version="1.0" ?>
2+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:sbol="http://sbols.org/v2#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#">
3+
<sbol:ComponentDefinition rdf:about="http://www.async.ece.utah.edu/BBa_C0062">
4+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_C0062"/>
5+
<sbol:displayId>BBa_C0062</sbol:displayId>
6+
<prov:wasDerivedFrom rdf:resource="http://partsregistry.org/Part:BBa_C0062"/>
7+
<dcterms:title>luxR</dcterms:title>
8+
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
9+
<sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
10+
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
11+
</sbol:ComponentDefinition>
12+
<sbol:ComponentDefinition rdf:about="http://www.async.ece.utah.edu/BBa_I0462">
13+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462"/>
14+
<sbol:displayId>BBa_I0462</sbol:displayId>
15+
<prov:wasDerivedFrom rdf:resource="http://partsregistry.org/Part:BBa_I0462"/>
16+
<dcterms:title>I0462</dcterms:title>
17+
<dcterms:description>LuxR protein generator</dcterms:description>
18+
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
19+
<sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
20+
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000804"/>
21+
<sbol:component>
22+
<sbol:Component rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034">
23+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034"/>
24+
<sbol:displayId>BBa_B0034</sbol:displayId>
25+
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
26+
<sbol:definition rdf:resource="http://www.async.ece.utah.edu/BBa_B0034"/>
27+
</sbol:Component>
28+
</sbol:component>
29+
<sbol:component>
30+
<sbol:Component rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015">
31+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015"/>
32+
<sbol:displayId>BBa_B0015</sbol:displayId>
33+
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
34+
<sbol:definition rdf:resource="http://www.async.ece.utah.edu/BBa_B0015"/>
35+
</sbol:Component>
36+
</sbol:component>
37+
<sbol:component>
38+
<sbol:Component rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062">
39+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062"/>
40+
<sbol:displayId>BBa_C0062</sbol:displayId>
41+
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
42+
<sbol:definition rdf:resource="http://www.async.ece.utah.edu/BBa_C0062"/>
43+
</sbol:Component>
44+
</sbol:component>
45+
<sbol:sequenceAnnotation>
46+
<sbol:SequenceAnnotation rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation">
47+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation"/>
48+
<sbol:displayId>BBa_C0062_annotation</sbol:displayId>
49+
<prov:wasDerivedFrom rdf:resource="http://sbols.org/anot#2345678"/>
50+
<sbol:location>
51+
<sbol:Range rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range">
52+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062_annotation/range"/>
53+
<sbol:displayId>range</sbol:displayId>
54+
<sbol:start>19</sbol:start>
55+
<sbol:end>774</sbol:end>
56+
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
57+
</sbol:Range>
58+
</sbol:location>
59+
<sbol:component rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062"/>
60+
</sbol:SequenceAnnotation>
61+
</sbol:sequenceAnnotation>
62+
<sbol:sequenceAnnotation>
63+
<sbol:SequenceAnnotation rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation">
64+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation"/>
65+
<sbol:displayId>BBa_B0015_annotation</sbol:displayId>
66+
<prov:wasDerivedFrom rdf:resource="http://sbols.org/anot#3456789"/>
67+
<sbol:location>
68+
<sbol:Range rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range">
69+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation/range"/>
70+
<sbol:displayId>range</sbol:displayId>
71+
<sbol:start>808</sbol:start>
72+
<sbol:end>936</sbol:end>
73+
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
74+
</sbol:Range>
75+
</sbol:location>
76+
<sbol:component rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015"/>
77+
</sbol:SequenceAnnotation>
78+
</sbol:sequenceAnnotation>
79+
<sbol:sequenceAnnotation>
80+
<sbol:SequenceAnnotation rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation">
81+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation"/>
82+
<sbol:displayId>BBa_B0034_annotation</sbol:displayId>
83+
<prov:wasDerivedFrom rdf:resource="http://sbols.org/anot#1234567"/>
84+
<sbol:location>
85+
<sbol:Range rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range">
86+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range"/>
87+
<sbol:displayId>range</sbol:displayId>
88+
<sbol:start>1</sbol:start>
89+
<sbol:end>12</sbol:end>
90+
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
91+
</sbol:Range>
92+
</sbol:location>
93+
<sbol:component rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034"/>
94+
</sbol:SequenceAnnotation>
95+
</sbol:sequenceAnnotation>
96+
<sbol:sequence rdf:resource="http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973"/>
97+
</sbol:ComponentDefinition>
98+
<sbol:ComponentDefinition rdf:about="http://www.async.ece.utah.edu/BBa_B0015">
99+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_B0015"/>
100+
<sbol:displayId>BBa_B0015</sbol:displayId>
101+
<prov:wasDerivedFrom rdf:resource="http://partsregistry.org/Part:BBa_B0015"/>
102+
<dcterms:title>B0015</dcterms:title>
103+
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
104+
<sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
105+
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000141"/>
106+
</sbol:ComponentDefinition>
107+
<sbol:ComponentDefinition rdf:about="http://www.async.ece.utah.edu/BBa_B0034">
108+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_B0034"/>
109+
<sbol:displayId>BBa_B0034</sbol:displayId>
110+
<prov:wasDerivedFrom rdf:resource="http://partsregistry.org/Part:BBa_B0034"/>
111+
<dcterms:title>B0034</dcterms:title>
112+
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
113+
<sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
114+
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
115+
</sbol:ComponentDefinition>
116+
<sbol:Sequence rdf:about="http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973">
117+
<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973"/>
118+
<sbol:displayId>seq_d23749adb3a7e0e2f09168cb7267a6113b238973</sbol:displayId>
119+
<prov:wasDerivedFrom rdf:resource="http://sbols.org/seq#d23749adb3a7e0e2f09168cb7267a6113b238973"/>
120+
<sbol:elements>aaagaggagaaatactagatgaaaaacataaatgccgacgacacatacagaataattaataaaattaaagcttgtagaagcaataatgatattaatcaatgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcactactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata</sbol:elements>
121+
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
122+
</sbol:Sequence>
123+
</rdf:RDF>
Binary file not shown.
Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
9cf0cf991adcaee84fa51c500718e920
Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
dda3e13c6db8fc6b35ae6a636e2436c736cb70b3
Lines changed: 9 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,9 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
3+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
4+
<modelVersion>4.0.0</modelVersion>
5+
<groupId>gov.doe.jgi</groupId>
6+
<artifactId>boost-client</artifactId>
7+
<version>1.0.0-SNAPSHOT</version>
8+
<description>POM was created from install:install-file</description>
9+
</project>
Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
4b71192f199c21b7ee05dbb0b1144e57
Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
c686da6f83821bdd0a83803fb8f0e3220c6667aa
Lines changed: 24 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
<metadata modelVersion="1.1.0">
3+
<groupId>gov.doe.jgi</groupId>
4+
<artifactId>boost-client</artifactId>
5+
<version>1.0.0-SNAPSHOT</version>
6+
<versioning>
7+
<snapshot>
8+
<localCopy>true</localCopy>
9+
</snapshot>
10+
<lastUpdated>20180710020401</lastUpdated>
11+
<snapshotVersions>
12+
<snapshotVersion>
13+
<extension>jar</extension>
14+
<value>1.0.0-SNAPSHOT</value>
15+
<updated>20180710020401</updated>
16+
</snapshotVersion>
17+
<snapshotVersion>
18+
<extension>pom</extension>
19+
<value>1.0.0-SNAPSHOT</value>
20+
<updated>20180710020401</updated>
21+
</snapshotVersion>
22+
</snapshotVersions>
23+
</versioning>
24+
</metadata>

0 commit comments

Comments
 (0)