diff --git a/CHANGELOG.md b/CHANGELOG.md
index c333e4d54..ab060cf7a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fix how Template adds entities to the QuotedEntityChecker [#1104]
- [`merge`] and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies [#1171]
- Handle IRIs that are not entities in export [#1168]
+- Fix integration tests [#1181]
## [1.9.5] - 2023-09-20
@@ -382,6 +383,7 @@ First official release of ROBOT!
[`template`]: http://robot.obolibrary.org/template
[`validate`]: http://robot.obolibrary.org/validate
+[#1181]: https://github.com/ontodev/robot/pull/1181
[#1171]: https://github.com/ontodev/robot/pull/1171
[#1168]: https://github.com/ontodev/robot/pull/1168
[#1160]: https://github.com/ontodev/robot/pull/1160
diff --git a/docs/examples/dropped_axiom.owl b/docs/examples/dropped_axiom.owl
deleted file mode 100644
index 7675e191d..000000000
--- a/docs/examples/dropped_axiom.owl
+++ /dev/null
@@ -1,52 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- part of
-
-
-
-
-
-
-
diff --git a/docs/examples/unmerged.owl b/docs/examples/unmerged.owl
index 95191dfad..5535a4796 100644
--- a/docs/examples/unmerged.owl
+++ b/docs/examples/unmerged.owl
@@ -1,14 +1,14 @@
+ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
@@ -70,6 +70,12 @@
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_definition
+
+
+
+ An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
+
+
@@ -85,6 +91,12 @@
This annotation property may be replaced with an annotation property from an external ontology such as IAO
homology_notes
+
+
+
+ Notes on the homology status of this class.
+
+
@@ -113,6 +125,12 @@
taxon_notes
taxon_notes
+
+
+
+ Notes on the how instances of this class vary across species.
+
+
@@ -128,6 +146,12 @@
function_notes
function_notes
+
+
+
+ Notes on the evolved function of instances of this class.
+
+
@@ -143,6 +167,30 @@
external_ontology_notes
external_ontology_notes
+
+
+
+ Notes on how similar or equivalent classes are represented in other ontologies.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -188,6 +236,12 @@
+
+
+
+
+
+
@@ -206,12 +260,24 @@
+
+
+
+
+
+
+
+
+
+
+
+
@@ -307,6 +373,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
anatomical structure
+
+
+
+ Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
+ CARO:0000003
+
@@ -345,6 +417,30 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
organ
+
+
+
+ UMLS:C0178784
+ ncithesaurus:Organ
+
+
+
+
+ element
+ UBERON:cjm
+
+
+
+
+ Anatomical structure that performs a specific function or group of functions [WP].
+
+
+
+
+
+ Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
+ GO:0048513
+
@@ -374,6 +470,18 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
organ part
+
+
+
+ Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA].
+ FMA:82472
+
+
+
+
+ regional part of organ
+ NIF_GrossAnatomy:birnlex_16
+
@@ -398,6 +506,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
material anatomical entity
+
+
+
+ Anatomical entity that has mass.
+ CARO:MAH
+
@@ -451,6 +565,32 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
anatomical system
+
+
+
+ Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia].
+
+ CARO:0000011
+ CARO:MAH
+
+
+
+
+ system
+ GO:0048731
+
+
+
+
+ UMLS:C0460002
+ ncithesaurus:Organ_System
+
+
+
+
+ body system
+ NIF_GrossAnatomy:birnlex_14
+
@@ -503,6 +643,38 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
multicellular organism
+
+
+
+ Anatomical structure that is an individual member of a species and consists of more than one cell.
+
+ CARO:0000012
+ CARO:MAH
+
+
+
+
+ multi-cellular organism
+ CARO:0000012
+
+
+
+
+ animal
+ BTO:0000042
+
+
+
+
+ Koerper
+ BTO:0001489
+
+
+
+
+ whole body
+ BTO:0001489
+
@@ -549,6 +721,38 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
organism subdivision
+
+
+
+ Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
+ CARO:0000032
+ CARO:DOS
+ CARO:MAH
+
+
+
+
+ UMLS:C0229962
+ ncithesaurus:Body_Part
+
+
+
+
+ anatomic region
+ MA:0002433
+
+
+
+
+ body region
+ FMA:7153
+
+
+
+
+ cardinal body part
+ FMA:7153
+
@@ -573,6 +777,13 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
anatomical group
+
+
+
+ Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.
+ CARO:0000054
+ CARO:MAH
+
@@ -615,6 +826,24 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
abdomen
+
+
+
+ The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
+ UBERON:cjm
+
+
+
+
+ abdominopelvic region
+ FMA:9577
+
+
+
+
+ abdominopelvis
+ FMA:9577
+
@@ -656,6 +885,44 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
endocrine system
+
+
+
+ Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
+
+ NLM:endocrine+system
+
+
+
+
+ Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
+ 2012-06-20
+ AAO:0010279
+ AAO
+ AAO:BJB
+
+
+
+
+ Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
+ 2012-09-17
+ VHOG:0000098
+ VHOG
+
+ DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)
+
+
+
+
+ UMLS:C0014136
+ ncithesaurus:Endocrine_System
+
+
+
+
+ endocrine glandular system
+ EHDAA2:0002224
+
@@ -686,6 +953,19 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
anatomical entity
+
+
+
+ Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
+ CARO:MAH
+ FMA:62955
+
+
+
+
+ UMLS:C1515976
+ ncithesaurus:Anatomic_Structure_System_or_Substance
+
@@ -740,6 +1020,41 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
+
+
+
+ Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted].
+
+
+
+
+
+ All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
+ 2012-09-17
+ VHOG:0001481
+ VHOG
+
+ ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9
+
+
+
+
+ UMLS:C0001613
+ ncithesaurus:Adrenal_Cortex
+
+
+
+
+ cortex glandulae suprarenalis
+
+
+
+
+
+
+ cortex glandulae suprarenalis
+ BTO:0000045
+
@@ -769,6 +1084,24 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
cortex
+
+
+
+ Outermost layer of an organ[WP].
+
+
+
+
+
+ this class is used more generically than in FMA, and includes e.g. cortex of hair
+ FMA
+
+
+
+
+ cortex
+ FMA:61109
+
@@ -817,6 +1150,50 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
trunk
+
+
+
+ Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
+
+ TAO:0001115
+ UBERONREF:0000006
+
+
+
+
+ Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
+ 2012-06-20
+ AAO:0010339
+ AAO
+ AAO:BJB
+
+
+
+
+ Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
+ 2012-08-14
+ TAO:0001115
+ TAO
+ ZFIN:curator
+
+
+
+
+ UMLS:C0460005
+ ncithesaurus:Trunk
+
+
+
+
+ trunk region
+ XAO:0000054
+
+
+
+
+ Rumpf
+ BTO:0001493
+
@@ -868,6 +1245,37 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
endocrine gland
+
+
+
+ Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
+
+
+
+
+
+ UMLS:C0014133
+ ncithesaurus:Endocrine_Gland
+
+
+
+
+ ductless gland
+ AEO:0000098
+
+
+
+
+ ductless gland
+
+
+
+
+
+ glandulae endocrinae
+
+
+
@@ -933,6 +1341,107 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
+
+
+
+ Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
+
+ BTO:0000047
+
+
+
+
+ Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]
+ 2012-06-20
+ AAO:0010551
+ AAO
+ AAO:BJB
+
+
+
+
+ All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
+ 2012-09-17
+ VHOG:0001141
+ VHOG
+
+ ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9
+
+
+
+
+ UMLS:C0001625
+ ncithesaurus:Adrenal_Gland
+
+
+
+
+ glandula adrenalis
+
+
+
+
+
+
+ glandula suprarenalis
+
+
+
+
+
+
+ adrenal
+ BTO:0000047
+
+
+
+
+ adrenal capsule
+ BTO:0000047
+
+
+
+
+ atrabiliary capsule
+ BTO:0000047
+
+
+
+
+ epinephric gland
+
+
+
+
+
+ epinephros
+ BTO:0000047
+
+
+
+
+ glandula suprarenalis
+ BTO:0000047
+
+
+
+
+ interrenal gland
+ GO:0030325
+
+
+
+
+
+ suprarenal capsule
+ BTO:0000047
+
+
+
+
+ suprarenal gland
+
+
@@ -954,6 +1463,30 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
UBERON:0002417
abdominal segment of trunk
+
+
+
+ The abdominal segment of the torso.
+
+
+
+
+
+ abdomen/pelvis/perineum
+ MA:0000021
+
+
+
+
+ lower body
+ MA:0000021
+
+
+
+
+ lumbar region
+
+
@@ -996,6 +1529,37 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
gland
+
+
+
+ A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO].
+
+
+
+
+
+ UMLS:C1285092
+ ncithesaurus:Gland
+
+
+
+
+ Druese
+ BTO:0000522
+
+
+
+
+ glandula
+
+
+
+
+
+
+ glandula
+ BTO:0000522
+
@@ -1023,6 +1587,40 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
adrenal/interrenal gland
+
+
+
+ This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]
+ GO:0030325
+
+
+
+
+ All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
+ 2012-09-17
+ VHOG:0001141
+ VHOG
+
+ ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9
+
+
+
+
+ adrenal gland - interrenal gland
+ VHOG:0001141
+
+
+
+
+ adrenal - interrenal gland
+ VHOG:0001141
+
+
+
+
+ suprarenal gland - interrenal gland
+ VHOG:0001141
+
@@ -1045,6 +1643,18 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
subdivision of trunk
+
+
+
+ region of trunk
+ FMA:25054
+
+
+
+
+ trunk subdivision
+ FMA:25054
+
@@ -1061,6 +1671,18 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
multicellular anatomical structure
+
+
+
+ An anatomical structure that has more than one cell as a part.
+ CARO:0010000
+
+
+
+
+ multicellular structure
+ FBbt:00100313
+
@@ -1084,6 +1706,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
subdivision of organism along main body axis
+
+
+
+ A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
+
+
@@ -1096,6 +1724,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
UBERON:0013701
main body axis
+
+
+
+ A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
+
+
@@ -1121,9 +1755,33 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000
body proper
+
+
+
+ The region of the organism associated with the visceral organs.
+ AEO:0000103
+
+
+
+
+ Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
+ FMA:231424
+
+
+
+
+ body
+ AEO:0000103
+
+
+
+
+ whole body
+ BTO:0001489
+
-
+
diff --git a/docs/examples/xref-repaired.obo b/docs/examples/xref-repaired.obo
index 96f4e3f82..0c77bf6ab 100644
--- a/docs/examples/xref-repaired.obo
+++ b/docs/examples/xref-repaired.obo
@@ -1,9 +1,10 @@
+format-version: 1.2
ontology: xref-need-of-repair
[Term]
id: GO:1
name: leaf node
-is_a: GO:3
+is_a: GO:3 ! replacement parent
[Term]
id: GO:2
@@ -22,3 +23,4 @@ id: GO:4
name: other term
is_obsolete: true
replaced_by: GO:3
+
diff --git a/robot-command/src/test/java/org/obolibrary/robot/CommandLineIT.java b/robot-command/src/test/java/org/obolibrary/robot/CommandLineIT.java
index e5ce8e031..238f5dbec 100644
--- a/robot-command/src/test/java/org/obolibrary/robot/CommandLineIT.java
+++ b/robot-command/src/test/java/org/obolibrary/robot/CommandLineIT.java
@@ -76,6 +76,10 @@ private List extractCommands(File docFile) throws IOException {
}
}
}
+ // Catch test blocks at the end of the file.
+ if (collecting && collected != null) {
+ commands.add(collected);
+ }
return commands;
}
@@ -232,18 +236,6 @@ public void testExecute() throws Exception {
runCommand(command);
}
- // Regression test for dropped axiom should fail:
- // https://github.com/ontodev/robot/issues/98
- boolean passed = true;
- try {
- runCommand("robot convert -i dropped_axiom.owl -o " + "results/dropped_axiom.owl");
- } catch (Exception e) {
- passed = false;
- }
- if (passed) {
- throw new Exception("dropped_axiom.owl test should fail but it passed");
- }
-
compareResults();
}
}