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johnmayegonw
johnmay
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egonw
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Cleanup of dependencies in CDK storage/io modules
1 parent 869bfce commit d1dfe3a

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11 files changed

+67
-227
lines changed

11 files changed

+67
-227
lines changed

‎storage/ctab/pom.xml‎

Lines changed: 25 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
<?xml version="1.0" encoding="UTF-8"?>
22
<project xmlns="http://maven.apache.org/POM/4.0.0"
3-
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
4-
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
3+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
4+
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
55
<parent>
66
<artifactId>cdk-storage</artifactId>
77
<groupId>org.openscience.cdk</groupId>
@@ -42,6 +42,29 @@
4242
<type>test-jar</type>
4343
<scope>test</scope>
4444
</dependency>
45+
<dependency>
46+
<groupId>javax.vecmath</groupId>
47+
<artifactId>vecmath</artifactId>
48+
</dependency>
49+
<dependency>
50+
<groupId>com.google.guava</groupId>
51+
<artifactId>guava</artifactId>
52+
</dependency>
53+
<dependency>
54+
<groupId>junit</groupId>
55+
<artifactId>junit</artifactId>
56+
<scope>test</scope>
57+
</dependency>
58+
<dependency>
59+
<groupId>org.openscience.cdk</groupId>
60+
<artifactId>cdk-core</artifactId>
61+
<version>2.7-SNAPSHOT</version>
62+
</dependency>
63+
<dependency>
64+
<groupId>org.openscience.cdk</groupId>
65+
<artifactId>cdk-standard</artifactId>
66+
<version>2.7-SNAPSHOT</version>
67+
</dependency>
4568
<dependency>
4669
<groupId>org.hamcrest</groupId>
4770
<artifactId>hamcrest</artifactId>

‎storage/inchi/pom.xml‎

Lines changed: 11 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -12,16 +12,25 @@
1212

1313
<artifactId>cdk-inchi</artifactId>
1414

15+
<properties>
16+
<jna-inchi.version>1.0.1</jna-inchi.version>
17+
</properties>
18+
1519
<name>cdk-inchi</name>
1620
<dependencies>
1721
<dependency>
1822
<groupId>javax.vecmath</groupId>
1923
<artifactId>vecmath</artifactId>
2024
</dependency>
25+
<dependency>
26+
<groupId>io.github.dan2097</groupId>
27+
<artifactId>jna-inchi-api</artifactId>
28+
<version>${jna-inchi.version}</version>
29+
</dependency>
2130
<dependency>
2231
<groupId>io.github.dan2097</groupId>
2332
<artifactId>jna-inchi-core</artifactId>
24-
<version>1.0.1</version>
33+
<version>${jna-inchi.version}</version>
2534
</dependency>
2635
<dependency>
2736
<groupId>org.apache.logging.log4j</groupId>
@@ -60,7 +69,7 @@
6069
</dependency>
6170
<dependency>
6271
<groupId>${project.groupId}</groupId>
63-
<artifactId>cdk-io</artifactId>
72+
<artifactId>cdk-atomtype</artifactId>
6473
<version>${project.parent.version}</version>
6574
<scope>test</scope>
6675
</dependency>
@@ -88,12 +97,6 @@
8897
<type>test-jar</type>
8998
<scope>test</scope>
9099
</dependency>
91-
<dependency>
92-
<groupId>${project.groupId}</groupId>
93-
<artifactId>cdk-render</artifactId>
94-
<version>${project.parent.version}</version>
95-
<scope>test</scope>
96-
</dependency>
97100
<dependency>
98101
<groupId>${project.groupId}</groupId>
99102
<artifactId>cdk-test</artifactId>

‎storage/io/pom.xml‎

Lines changed: 8 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -38,25 +38,18 @@
3838
<scope>test</scope>
3939
</dependency>
4040
<dependency>
41-
<groupId>org.blueobelisk</groupId>
42-
<artifactId>cmlxom</artifactId>
43-
<version>3.3</version>
44-
<exclusions>
45-
<exclusion>
46-
<groupId>org.apache.logging.log4j</groupId>
47-
<artifactId>log4j</artifactId>
48-
</exclusion>
49-
</exclusions>
50-
<scope>test</scope>
41+
<groupId>xerces</groupId>
42+
<artifactId>xercesImpl</artifactId>
43+
<version>2.8.0</version>
5144
</dependency>
5245
<dependency>
53-
<groupId>org.apache.logging.log4j</groupId>
54-
<artifactId>log4j-core</artifactId>
55-
<scope>test</scope>
46+
<groupId>xml-apis</groupId>
47+
<artifactId>xml-apis</artifactId>
48+
<version>1.3.03</version>
5649
</dependency>
5750
<dependency>
58-
<groupId>xom</groupId>
59-
<artifactId>xom</artifactId>
51+
<groupId>org.apache.logging.log4j</groupId>
52+
<artifactId>log4j-core</artifactId>
6053
<scope>test</scope>
6154
</dependency>
6255
<dependency>

‎storage/ioformats/pom.xml‎

Lines changed: 1 addition & 83 deletions
Original file line numberDiff line numberDiff line change
@@ -28,39 +28,11 @@
2828
<artifactId>junit</artifactId>
2929
<scope>test</scope>
3030
</dependency>
31-
<dependency>
32-
<groupId>org.blueobelisk</groupId>
33-
<artifactId>cmlxom</artifactId>
34-
<version>3.3</version>
35-
<exclusions>
36-
<exclusion>
37-
<groupId>org.apache.logging.log4j</groupId>
38-
<artifactId>log4j</artifactId>
39-
</exclusion>
40-
</exclusions>
41-
<scope>test</scope>
42-
</dependency>
4331
<dependency>
4432
<groupId>org.apache.logging.log4j</groupId>
4533
<artifactId>log4j-core</artifactId>
4634
<scope>test</scope>
4735
</dependency>
48-
<dependency>
49-
<groupId>javax.vecmath</groupId>
50-
<artifactId>vecmath</artifactId>
51-
<scope>test</scope>
52-
</dependency>
53-
<dependency>
54-
<groupId>xom</groupId>
55-
<artifactId>xom</artifactId>
56-
<scope>test</scope>
57-
</dependency>
58-
<dependency>
59-
<groupId>xpp3</groupId>
60-
<artifactId>xpp3</artifactId>
61-
<version>1.1.4c</version>
62-
<scope>test</scope>
63-
</dependency>
6436
<dependency>
6537
<groupId>org.openscience.cdk</groupId>
6638
<artifactId>cdk-interfaces</artifactId>
@@ -72,60 +44,6 @@
7244
<version>${project.parent.version}</version>
7345
<scope>test</scope>
7446
</dependency>
75-
<dependency>
76-
<groupId>${project.groupId}</groupId>
77-
<artifactId>cdk-core</artifactId>
78-
<version>${project.parent.version}</version>
79-
<scope>test</scope>
80-
</dependency>
81-
<dependency>
82-
<groupId>${project.groupId}</groupId>
83-
<artifactId>cdk-standard</artifactId>
84-
<version>${project.parent.version}</version>
85-
<scope>test</scope>
86-
</dependency>
87-
<!--<dependency>
88-
<groupId>${project.groupId}</groupId>
89-
<artifactId>cdk-io</artifactId>
90-
<version>${project.parent.version}</version>
91-
<scope>test</scope>
92-
</dependency>
93-
<dependency>
94-
<groupId>${project.groupId}</groupId>
95-
<artifactId>cdk-iordf</artifactId>
96-
<version>${project.parent.version}</version>
97-
<scope>test</scope>
98-
</dependency>
99-
<dependency>
100-
<groupId>${project.groupId}</groupId>
101-
<artifactId>cdk-smiles</artifactId>
102-
<version>${project.parent.version}</version>
103-
<scope>test</scope>
104-
</dependency>
105-
<dependency>
106-
<groupId>${project.groupId}</groupId>
107-
<artifactId>cdk-pdb</artifactId>
108-
<version>${project.parent.version}</version>
109-
<scope>test</scope>
110-
</dependency>
111-
<dependency>
112-
<groupId>${project.groupId}</groupId>
113-
<artifactId>cdk-libiocml</artifactId>
114-
<version>${project.parent.version}</version>
115-
<scope>test</scope>
116-
</dependency>
117-
<dependency>
118-
<groupId>${project.groupId}</groupId>
119-
<artifactId>cdk-extra</artifactId>
120-
<version>${project.parent.version}</version>
121-
<scope>test</scope>
122-
</dependency>-->
123-
<dependency>
124-
<groupId>${project.groupId}</groupId>
125-
<artifactId>cdk-data</artifactId>
126-
<version>${project.parent.version}</version>
127-
<scope>test</scope>
128-
</dependency>
12947
<dependency>
13048
<groupId>${project.groupId}</groupId>
13149
<artifactId>cdk-test</artifactId>
@@ -138,7 +56,7 @@
13856
<artifactId>cdk-testdata</artifactId>
13957
<version>${project.parent.version}</version>
14058
<type>test-jar</type>
141-
<scope>test</scope>
59+
<scope>test</scope>
14260
</dependency>
14361
</dependencies>
14462

‎storage/iordf/pom.xml‎

Lines changed: 6 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -14,10 +14,6 @@
1414

1515
<name>cdk-iordf</name>
1616
<dependencies>
17-
<dependency>
18-
<groupId>javax.vecmath</groupId>
19-
<artifactId>vecmath</artifactId>
20-
</dependency>
2117
<dependency>
2218
<groupId>org.apache.jena</groupId>
2319
<artifactId>jena-core</artifactId>
@@ -80,21 +76,6 @@
8076
<artifactId>cdk-core</artifactId>
8177
<version>${project.parent.version}</version>
8278
</dependency>
83-
<dependency>
84-
<groupId>${project.groupId}</groupId>
85-
<artifactId>cdk-standard</artifactId>
86-
<version>${project.parent.version}</version>
87-
</dependency>
88-
<dependency>
89-
<groupId>${project.groupId}</groupId>
90-
<artifactId>cdk-atomtype</artifactId>
91-
<version>${project.parent.version}</version>
92-
</dependency>
93-
<dependency>
94-
<groupId>${project.groupId}</groupId>
95-
<artifactId>cdk-io</artifactId>
96-
<version>${project.parent.version}</version>
97-
</dependency>
9879
<dependency>
9980
<groupId>${project.groupId}</groupId>
10081
<artifactId>cdk-diff</artifactId>
@@ -115,36 +96,30 @@
11596
</dependency>
11697
<dependency>
11798
<groupId>${project.groupId}</groupId>
118-
<artifactId>cdk-test</artifactId>
99+
<artifactId>cdk-datadebug</artifactId>
119100
<version>${project.parent.version}</version>
120-
<type>test-jar</type>
121-
<scope>test</scope>
101+
<scope>test</scope>
122102
</dependency>
123103
<dependency>
124104
<groupId>${project.groupId}</groupId>
125105
<artifactId>cdk-io</artifactId>
126106
<version>${project.parent.version}</version>
127107
<type>test-jar</type>
128-
<scope>test</scope>
129-
</dependency>
130-
<dependency>
131-
<groupId>${project.groupId}</groupId>
132-
<artifactId>cdk-datadebug</artifactId>
133-
<version>${project.parent.version}</version>
134108
<scope>test</scope>
135109
</dependency>
136110
<dependency>
137111
<groupId>${project.groupId}</groupId>
138-
<artifactId>cdk-testdata</artifactId>
112+
<artifactId>cdk-test</artifactId>
139113
<version>${project.parent.version}</version>
140114
<type>test-jar</type>
141115
<scope>test</scope>
142116
</dependency>
143117
<dependency>
144118
<groupId>${project.groupId}</groupId>
145-
<artifactId>cdk-isomorphism</artifactId>
119+
<artifactId>cdk-testdata</artifactId>
146120
<version>${project.parent.version}</version>
147-
<scope>test</scope>
121+
<type>test-jar</type>
122+
<scope>test</scope>
148123
</dependency>
149124
</dependencies>
150125

‎storage/libiocml/pom.xml‎

Lines changed: 0 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -120,24 +120,12 @@
120120
<type>test-jar</type>
121121
<scope>test</scope>
122122
</dependency>
123-
<dependency>
124-
<groupId>${project.groupId}</groupId>
125-
<artifactId>cdk-atomtype</artifactId>
126-
<version>${project.parent.version}</version>
127-
<scope>test</scope>
128-
</dependency>
129123
<dependency>
130124
<groupId>${project.groupId}</groupId>
131125
<artifactId>cdk-silent</artifactId>
132126
<version>${project.parent.version}</version>
133127
<scope>test</scope>
134128
</dependency>
135-
<dependency>
136-
<groupId>${project.groupId}</groupId>
137-
<artifactId>cdk-pdb</artifactId>
138-
<version>${project.parent.version}</version>
139-
<scope>test</scope>
140-
</dependency>
141129
<dependency>
142130
<groupId>${project.groupId}</groupId>
143131
<artifactId>cdk-testdata</artifactId>

‎storage/libiomd/pom.xml‎

Lines changed: 5 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -41,14 +41,13 @@
4141
<scope>test</scope>
4242
</dependency>
4343
<dependency>
44-
<groupId>javax.vecmath</groupId>
45-
<artifactId>vecmath</artifactId>
46-
<scope>test</scope>
44+
<groupId>xom</groupId>
45+
<artifactId>xom</artifactId>
4746
</dependency>
4847
<dependency>
49-
<groupId>${project.groupId}</groupId>
50-
<artifactId>cdk-core</artifactId>
51-
<version>${project.parent.version}</version>
48+
<groupId>xml-apis</groupId>
49+
<artifactId>xml-apis</artifactId>
50+
<version>1.3.03</version>
5251
</dependency>
5352
<dependency>
5453
<groupId>${project.groupId}</groupId>
@@ -82,12 +81,6 @@
8281
<type>test-jar</type>
8382
<scope>test</scope>
8483
</dependency>
85-
<dependency>
86-
<groupId>${project.groupId}</groupId>
87-
<artifactId>cdk-formula</artifactId>
88-
<version>${project.parent.version}</version>
89-
<scope>test</scope>
90-
</dependency>
9184
</dependencies>
9285

9386
</project>

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