Skip to content

Commit 4d0614f

Browse files
committed
update GPML2021 tests
Visible changes in the GPML2021 test files: Element "InfoBox" has been removed. Infobox is always at coordinates 0,0 in the top left corner. Attribute "rotation" is optional and is not written out if it is equal to 0. Other changes which are not covered in these tests (more tests will need to be created eventually): DataNode "elementRef" was renamed to "aliasRef." All shaped pathway elements (DataNode, State, Label, Shape, Group) can have attribute "rotation." We do not yet have tests covering Annotation/AnnotationRef, Citation/CitationRef, and Evidence/EvidenceRef.
1 parent e6a9077 commit 4d0614f

File tree

97 files changed

+2298
-2395
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

97 files changed

+2298
-2395
lines changed

GPML2021/tests/WP1243_69897.gpml

Lines changed: 62 additions & 63 deletions
Large diffs are not rendered by default.

GPML2021/tests/WP1818.gpml

Lines changed: 636 additions & 637 deletions
Large diffs are not rendered by default.

GPML2021/tests/WP1_73346.gpml

Lines changed: 68 additions & 69 deletions
Large diffs are not rendered by default.

GPML2021/tests/WP2211_71653.gpml

Lines changed: 43 additions & 44 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,16 @@
22
<Pathway xmlns="http://pathvisio.org/GPML/2021" title="Geranylgeranyldiphosphate biosynthesis II (plastidic)" organism="Oryza sativa" source="RiceCyc" version="20110915">
33
<Description>In plants the geranyl-geranyl diphosphate (GGPP) as a precursor molecule that feeds in the biosynthesis of essential compounds such as chlorophylls, carotenoids, plastoquinones, growth hormone gibberellin and other secondary metabolites. Occurs in plastids.</Description>
44
<Comment source="WikiPathways-category">Metabolic Process</Comment>
5-
<AnnotationRef elementRef="b2f1c" />
6-
<AnnotationRef elementRef="b1d73" />
5+
<AnnotationRef elementRef="ddc43" />
6+
<AnnotationRef elementRef="fcfa8" />
77
<CitationRef elementRef="b1a" />
88
<CitationRef elementRef="a22" />
99
<CitationRef elementRef="f44" />
1010
<CitationRef elementRef="bdb" />
1111
<CitationRef elementRef="acd" />
1212
<CitationRef elementRef="d3e" />
1313
<CitationRef elementRef="d01" />
14-
<Graphics boardWidth="1021.5571635209417" boardHeight="965.4425607010502" />
15-
<InfoBox centerX="0.0" centerY="0.0" />
14+
<Graphics boardWidth="1029.5571635209417" boardHeight="965.4425607010502" />
1615
<DataNodes>
1716
<DataNode elementId="d120d" textLabel="Delta3-isopentenyl-PP" type="Metabolite">
1817
<Xref identifier="C00129" dataSource="kegg.compound" />
@@ -140,122 +139,122 @@
140139
<Interactions>
141140
<Interaction elementId="idb3e022e0">
142141
<Waypoints>
143-
<Point elementId="c6acb" arrowHead="Undirected" x="501.73758652856577" y="406.2077846481381" elementRef="bc11b" relX="0.0" relY="1.0" />
144-
<Point elementId="f36e7" arrowHead="Directed" x="501.3687932642829" y="670.9924047776798" elementRef="ddf5c" relX="0.0" relY="-1.0" />
142+
<Point elementId="c10c1" arrowHead="Undirected" x="501.73758652856577" y="406.2077846481381" elementRef="bc11b" relX="0.0" relY="1.0" />
143+
<Point elementId="f0fb8" arrowHead="Directed" x="501.3687932642829" y="670.9924047776798" elementRef="ddf5c" relX="0.0" relY="-1.0" />
145144
<Anchor elementId="b91da" position="0.5" shapeType="None" />
146145
</Waypoints>
147146
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="12288" />
148147
</Interaction>
149148
<Interaction elementId="id206ac4ab">
150149
<Waypoints>
151-
<Point elementId="a666f" arrowHead="Undirected" x="543.5501653803749" y="538.0842992270277" elementRef="e8e55" relX="-1.0" relY="0.0" />
152-
<Point elementId="a28df" arrowHead="Catalysis" x="501.5531898964243" y="538.6000947129089" elementRef="b91da" relX="0.0" relY="0.0" />
150+
<Point elementId="a3253" arrowHead="Undirected" x="543.5501653803749" y="538.0842992270277" elementRef="e8e55" relX="-1.0" relY="0.0" />
151+
<Point elementId="a68c4" arrowHead="Catalysis" x="501.5531898964243" y="538.6000947129089" elementRef="b91da" relX="0.0" relY="0.0" />
153152
</Waypoints>
154153
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="12288" />
155154
</Interaction>
156155
<Interaction elementId="ida3507e27">
157156
<Waypoints>
158-
<Point elementId="b2cb4" arrowHead="Undirected" x="501.3687932642829" y="690.9924047776798" elementRef="ddf5c" relX="0.0" relY="1.0" />
159-
<Point elementId="cc140" arrowHead="Directed" x="501.73758652856577" y="915.4425607010502" elementRef="b9fc8" relX="0.0" relY="-1.0" />
157+
<Point elementId="c0b08" arrowHead="Undirected" x="501.3687932642829" y="690.9924047776798" elementRef="ddf5c" relX="0.0" relY="1.0" />
158+
<Point elementId="c1254" arrowHead="Directed" x="501.73758652856577" y="915.4425607010502" elementRef="b9fc8" relX="0.0" relY="-1.0" />
160159
<Anchor elementId="ce68b" position="0.5672174806337065" shapeType="None" />
161160
</Waypoints>
162161
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="12288" />
163162
</Interaction>
164163
<Interaction elementId="id471f45d8">
165164
<Waypoints>
166-
<Point elementId="f7359" arrowHead="Undirected" x="533.6273428886439" y="819.1639580023904" elementRef="ac174" relX="-1.0" relY="0.0" />
167-
<Point elementId="c8466" arrowHead="Catalysis" x="501.5779792505241" y="818.3044567483765" elementRef="ce68b" relX="0.0" relY="0.0" />
165+
<Point elementId="b8a2b" arrowHead="Undirected" x="533.6273428886439" y="819.1639580023904" elementRef="ac174" relX="-1.0" relY="0.0" />
166+
<Point elementId="ee007" arrowHead="Catalysis" x="501.5779792505241" y="818.3044567483765" elementRef="ce68b" relX="0.0" relY="0.0" />
168167
</Waypoints>
169168
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="12288" />
170169
</Interaction>
171170
<Interaction elementId="idb12262c">
172171
<Waypoints>
173-
<Point elementId="af15e" arrowHead="Undirected" x="447.87494490285985" y="456.5178500441604" elementRef="f7d12" relX="1.0" relY="0.0" />
174-
<Point elementId="d5431" arrowHead="Undirected" x="502.81690140845075" y="497.5589723785347" />
175-
<Point elementId="c2732" arrowHead="Directed" x="501.5531898964243" y="538.6000947129089" elementRef="b91da" relX="0.0" relY="0.0" />
172+
<Point elementId="a614d" arrowHead="Undirected" x="447.87494490285985" y="456.5178500441604" elementRef="f7d12" relX="1.0" relY="0.0" />
173+
<Point elementId="fa04d" arrowHead="Undirected" x="502.81690140845075" y="497.5589723785347" />
174+
<Point elementId="c3d47" arrowHead="Directed" x="501.5531898964243" y="538.6000947129089" elementRef="b91da" relX="0.0" relY="0.0" />
176175
</Waypoints>
177176
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Curved" zOrder="12288" />
178177
</Interaction>
179178
<Interaction elementId="id1e219796">
180179
<Waypoints>
181-
<Point elementId="bca1a" arrowHead="Undirected" x="501.5531898964243" y="538.6000947129089" elementRef="b91da" relX="0.0" relY="0.0" />
182-
<Point elementId="dc69d" arrowHead="Undirected" x="502.81690140845075" y="570.3563405290449" />
183-
<Point elementId="f21a7" arrowHead="Directed" x="437.0224445695248" y="602.1125863451811" elementRef="c0317" relX="1.0" relY="0.0" />
180+
<Point elementId="d8e53" arrowHead="Undirected" x="501.5531898964243" y="538.6000947129089" elementRef="b91da" relX="0.0" relY="0.0" />
181+
<Point elementId="add2b" arrowHead="Undirected" x="502.81690140845075" y="570.3563405290449" />
182+
<Point elementId="c98b5" arrowHead="Directed" x="437.0224445695248" y="602.1125863451811" elementRef="c0317" relX="1.0" relY="0.0" />
184183
</Waypoints>
185184
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Curved" zOrder="12288" />
186185
</Interaction>
187186
<Interaction elementId="id14ee7ceb">
188187
<Waypoints>
189-
<Point elementId="a303e" arrowHead="Undirected" x="445.07042253521126" y="181.33127845529467" elementRef="b77de" relX="1.0" relY="-0.5" />
190-
<Point elementId="df2ee" arrowHead="Undirected" x="498.59154929577466" y="207.74420685413935" />
191-
<Point elementId="fe4d2" arrowHead="Directed" x="501.6187932642829" y="234.15713525298403" elementRef="f34f8" relX="0.0" relY="0.0" />
188+
<Point elementId="b1158" arrowHead="Undirected" x="445.07042253521126" y="181.33127845529467" elementRef="b77de" relX="1.0" relY="-0.5" />
189+
<Point elementId="ee63d" arrowHead="Undirected" x="498.59154929577466" y="207.74420685413935" />
190+
<Point elementId="efe19" arrowHead="Directed" x="501.6187932642829" y="234.15713525298403" elementRef="f34f8" relX="0.0" relY="0.0" />
192191
</Waypoints>
193192
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Curved" zOrder="12288" />
194193
</Interaction>
195194
<Interaction elementId="id15a83c9f">
196195
<Waypoints>
197-
<Point elementId="e9db0" arrowHead="Undirected" x="427.0" y="72.10648585782997" elementRef="d120d" relX="-1.0" relY="0.0" />
198-
<Point elementId="ae8ef" arrowHead="Directed" x="161.2891099110305" y="241.53808599636506" elementRef="f0fdd" relX="0.0" relY="-1.0" />
196+
<Point elementId="d774a" arrowHead="Undirected" x="427.0" y="72.10648585782997" elementRef="d120d" relX="-1.0" relY="0.0" />
197+
<Point elementId="a5893" arrowHead="Directed" x="161.2891099110305" y="241.53808599636506" elementRef="f0fdd" relX="0.0" relY="-1.0" />
199198
</Waypoints>
200199
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Curved" zOrder="12288" />
201200
</Interaction>
202201
<Interaction elementId="idd5d26da">
203202
<Waypoints>
204-
<Point elementId="e8468" arrowHead="Undirected" x="834.5274289335271" y="232.23573727903857" elementRef="f76fa" relX="-1.0" relY="0.0" />
205-
<Point elementId="d6c27" arrowHead="Undirected" x="792.7643626033234" y="233.9420316163951" elementRef="a45cf" relX="1.0" relY="0.0" />
203+
<Point elementId="a28ec" arrowHead="Undirected" x="834.5274289335271" y="232.23573727903857" elementRef="f76fa" relX="-1.0" relY="0.0" />
204+
<Point elementId="b99d5" arrowHead="Undirected" x="792.7643626033234" y="233.9420316163951" elementRef="a45cf" relX="1.0" relY="0.0" />
206205
</Waypoints>
207206
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="12288" />
208207
</Interaction>
209208
<Interaction elementId="id1f159e35">
210209
<Waypoints>
211-
<Point elementId="ae5a5" arrowHead="Undirected" x="840.6600606238385" y="538.1726991016237" elementRef="d85f9" relX="-1.0" relY="0.0" />
212-
<Point elementId="a2cb9" arrowHead="Undirected" x="811.5735205056135" y="538.0842992270277" elementRef="e8e55" relX="1.0" relY="0.0" />
210+
<Point elementId="cf0e7" arrowHead="Undirected" x="840.6600606238385" y="538.1726991016237" elementRef="d85f9" relX="-1.0" relY="0.0" />
211+
<Point elementId="cae4e" arrowHead="Undirected" x="811.5735205056135" y="538.0842992270277" elementRef="e8e55" relX="1.0" relY="0.0" />
213212
</Waypoints>
214213
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="12288" />
215214
</Interaction>
216215
<Interaction elementId="idf1083275">
217216
<Waypoints>
218-
<Point elementId="c4f15" arrowHead="Undirected" x="848.667179042809" y="819.5290180584846" elementRef="fb9da" relX="-1.0" relY="0.0" />
219-
<Point elementId="f204e" arrowHead="Undirected" x="832.394366197183" y="819.1639580023904" elementRef="ac174" relX="1.0" relY="0.0" />
217+
<Point elementId="ae2e8" arrowHead="Undirected" x="848.667179042809" y="819.5290180584846" elementRef="fb9da" relX="-1.0" relY="0.0" />
218+
<Point elementId="f9bc0" arrowHead="Undirected" x="832.394366197183" y="819.1639580023904" elementRef="ac174" relX="1.0" relY="0.0" />
220219
</Waypoints>
221220
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="12288" />
222221
</Interaction>
223222
<Interaction elementId="d0763">
224223
<Waypoints>
225-
<Point elementId="e9cd0" arrowHead="Undirected" x="433.42721334053476" y="753.1492197710415" elementRef="eb4a5" relX="1.0" relY="0.0" />
226-
<Point elementId="e5bb6" arrowHead="Undirected" x="500.0" y="785.726838259709" />
227-
<Point elementId="b759c" arrowHead="Directed" x="501.5779792505241" y="818.3044567483765" elementRef="ce68b" relX="0.0" relY="0.0" />
224+
<Point elementId="b4cdb" arrowHead="Undirected" x="433.42721334053476" y="753.1492197710415" elementRef="eb4a5" relX="1.0" relY="0.0" />
225+
<Point elementId="e5354" arrowHead="Undirected" x="500.0" y="785.726838259709" />
226+
<Point elementId="a2458" arrowHead="Directed" x="501.5779792505241" y="818.3044567483765" elementRef="ce68b" relX="0.0" relY="0.0" />
228227
</Waypoints>
229228
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Curved" zOrder="32770" />
230229
</Interaction>
231230
<Interaction elementId="c8ee2">
232231
<Waypoints>
233-
<Point elementId="f06a5" arrowHead="Undirected" x="501.5779792505241" y="818.3044567483765" elementRef="ce68b" relX="0.0" relY="0.0" />
234-
<Point elementId="c6408" arrowHead="Undirected" x="501.4084507042254" y="851.7989399697261" />
235-
<Point elementId="e6d02" arrowHead="Directed" x="424.22345061821323" y="885.2934231910757" elementRef="b62ef" relX="1.0" relY="0.0" />
232+
<Point elementId="d3322" arrowHead="Undirected" x="501.5779792505241" y="818.3044567483765" elementRef="ce68b" relX="0.0" relY="0.0" />
233+
<Point elementId="cb29e" arrowHead="Undirected" x="501.4084507042254" y="851.7989399697261" />
234+
<Point elementId="a17fd" arrowHead="Directed" x="424.22345061821323" y="885.2934231910757" elementRef="b62ef" relX="1.0" relY="0.0" />
236235
</Waypoints>
237236
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Curved" zOrder="32771" />
238237
</Interaction>
239238
<Interaction elementId="c9038">
240239
<Waypoints>
241-
<Point elementId="f0cd5" arrowHead="Undirected" x="501.6187932642829" y="234.15713525298403" elementRef="f34f8" relX="0.0" relY="0.0" />
242-
<Point elementId="dbd2f" arrowHead="Undirected" x="502.81690140845075" y="271.8050571597256" />
243-
<Point elementId="adb3c" arrowHead="Directed" x="445.9206829524727" y="309.4529790664672" elementRef="aa664" relX="1.0" relY="0.0" />
240+
<Point elementId="f8246" arrowHead="Undirected" x="501.6187932642829" y="234.15713525298403" elementRef="f34f8" relX="0.0" relY="0.0" />
241+
<Point elementId="c45f2" arrowHead="Undirected" x="502.81690140845075" y="271.8050571597256" />
242+
<Point elementId="ff7d1" arrowHead="Directed" x="445.9206829524727" y="309.4529790664672" elementRef="aa664" relX="1.0" relY="0.0" />
244243
</Waypoints>
245244
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Curved" zOrder="32774" />
246245
</Interaction>
247246
<Interaction elementId="d039a">
248247
<Waypoints>
249-
<Point elementId="d6166" arrowHead="Undirected" x="501.5" y="82.10648585782997" elementRef="d120d" relX="0.0" relY="1.0" />
250-
<Point elementId="c49d1" arrowHead="Directed" x="501.73758652856577" y="386.2077846481381" elementRef="bc11b" relX="0.0" relY="-1.0" />
248+
<Point elementId="f3fde" arrowHead="Undirected" x="501.5" y="82.10648585782997" elementRef="d120d" relX="0.0" relY="1.0" />
249+
<Point elementId="f6552" arrowHead="Directed" x="501.73758652856577" y="386.2077846481381" elementRef="bc11b" relX="0.0" relY="-1.0" />
251250
<Anchor elementId="f34f8" position="0.5" shapeType="None" />
252251
</Waypoints>
253252
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="32787" />
254253
</Interaction>
255254
<Interaction elementId="de6d5">
256255
<Waypoints>
257-
<Point elementId="a0d5d" arrowHead="Undirected" x="541.4576247118068" y="233.9420316163951" elementRef="a45cf" relX="-1.0" relY="0.0" />
258-
<Point elementId="dc90e" arrowHead="Catalysis" x="501.6187932642829" y="234.15713525298403" elementRef="f34f8" relX="0.0" relY="0.0" />
256+
<Point elementId="cbcfa" arrowHead="Undirected" x="541.4576247118068" y="233.9420316163951" elementRef="a45cf" relX="-1.0" relY="0.0" />
257+
<Point elementId="fad25" arrowHead="Catalysis" x="501.6187932642829" y="234.15713525298403" elementRef="f34f8" relX="0.0" relY="0.0" />
259258
</Waypoints>
260259
<Graphics lineColor="000000" lineStyle="Solid" lineWidth="1.0" connectorType="Straight" zOrder="32788" />
261260
</Interaction>
@@ -272,10 +271,10 @@
272271
</Group>
273272
</Groups>
274273
<Annotations>
275-
<Annotation elementId="b2f1c" value="plant cell" type="Ontology">
274+
<Annotation elementId="ddc43" value="plant cell" type="Ontology">
276275
<Xref identifier="0000610" dataSource="CL" />
277276
</Annotation>
278-
<Annotation elementId="b1d73" value="diterpenoid biosynthetic pathway" type="Ontology">
277+
<Annotation elementId="fcfa8" value="diterpenoid biosynthetic pathway" type="Ontology">
279278
<Xref identifier="0000251" dataSource="PW" />
280279
</Annotation>
281280
</Annotations>

0 commit comments

Comments
 (0)