Grm 55/literature vil

builds.json

@@ -1,6 +1,68 @@
 {
   "builds" :
   [
+    {
+      "version": "7.9",
+      "packages": [
+        {
+          "package": "org.ga4gh.models",
+          "python_package": "ga4gh",
+          "version": "3.1.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.gel.models.metrics.avro",
+          "python_package": "metrics",
+          "version": "1.2.2",
+          "dependencies": [
+            "org.gel.models.participant.avro"
+          ]
+        },
+        {
+          "package": "org.gel.models.participant.avro",
+          "python_package": "participant",
+          "version": "1.3.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.gel.models.report.avro",
+          "python_package": "reports",
+          "version": "6.2.1",
+          "dependencies": [
+            "org.gel.models.participant.avro"
+          ]
+        },
+        {
+          "package": "org.gel.models.system.avro",
+          "python_package": "system",
+          "version": "0.1.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.opencb.biodata.models.variant.avro",
+          "python_package": "opencb",
+          "version": "1.3.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.gel.models.coverage.avro",
+          "python_package": "coverage",
+          "version": "0.1.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.gel.models.cva.avro",
+          "python_package": "cva",
+          "version": "1.5.3",
+          "dependencies": [
+            "org.gel.models.report.avro",
+            "org.gel.models.participant.avro",
+            "org.gel.models.system.avro",
+            "org.opencb.biodata.models.variant.avro"
+          ]
+        }
+      ]
+    },
     {
       "version": "7.8",
       "packages": [

pom.xml

@@ -7,11 +7,11 @@
 
     <groupId>org.gel.models</groupId>
     <artifactId>gel-models</artifactId>
-    <version>7.8.0</version>
+    <version>7.9.0</version>
     <packaging>${p.type}</packaging>
 
     <properties>
-        <models.version>7.8</models.version>
+        <models.version>7.9</models.version>
         <opencb.models.version>1.3.0</opencb.models.version>
         <opencb.models.package>org.opencb.biodata.models.variant.avro</opencb.models.package>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

protocols/resources/builds.json

@@ -1,6 +1,68 @@
 {
   "builds" :
   [
+    {
+      "version": "7.9",
+      "packages": [
+        {
+          "package": "org.ga4gh.models",
+          "python_package": "ga4gh",
+          "version": "3.1.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.gel.models.metrics.avro",
+          "python_package": "metrics",
+          "version": "1.2.2",
+          "dependencies": [
+            "org.gel.models.participant.avro"
+          ]
+        },
+        {
+          "package": "org.gel.models.participant.avro",
+          "python_package": "participant",
+          "version": "1.3.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.gel.models.report.avro",
+          "python_package": "reports",
+          "version": "6.2.1",
+          "dependencies": [
+            "org.gel.models.participant.avro"
+          ]
+        },
+        {
+          "package": "org.gel.models.system.avro",
+          "python_package": "system",
+          "version": "0.1.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.opencb.biodata.models.variant.avro",
+          "python_package": "opencb",
+          "version": "1.3.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.gel.models.coverage.avro",
+          "python_package": "coverage",
+          "version": "0.1.0",
+          "dependencies": []
+        },
+        {
+          "package": "org.gel.models.cva.avro",
+          "python_package": "cva",
+          "version": "1.5.3",
+          "dependencies": [
+            "org.gel.models.report.avro",
+            "org.gel.models.participant.avro",
+            "org.gel.models.system.avro",
+            "org.opencb.biodata.models.variant.avro"
+          ]
+        }
+      ]
+    },
     {
       "version": "7.8",
       "packages": [

protocols/tests/test_util/test_dependency_manager.py

@@ -5,7 +5,7 @@
 import protocols.reports_5_0_0
 import protocols.reports_4_2_0
 import protocols.reports_4_0_0
-import protocols.reports_6_2_0
+import protocols.reports_6_2_1
 
 
 class TestDependencyManager(TestCase):
@@ -15,7 +15,7 @@ def test_dependency_manager(self):
         assert dependency_manager is not None
         latest_dependencies = dependency_manager.get_latest_version_dependencies()
         assert isinstance(latest_dependencies, dict)
-        assert latest_dependencies["org.gel.models.report.avro"] == protocols.reports_6_2_0
+        assert latest_dependencies["org.gel.models.report.avro"] == protocols.reports_6_2_1
         dependencies_400 = dependency_manager.get_version_dependencies("4.0.0")
         assert isinstance(dependencies_400, dict)
         assert dependencies_400["org.gel.models.report.avro"] == protocols.reports_4_0_0

protocols/util/dependency_manager.py

@@ -4,7 +4,7 @@
 import inspect
 from protocols.util.singleton import Singleton
 
-VERSION_78 = "7.8"
+VERSION_79 = "7.9"
 VERSION_77 = "7.7"
 VERSION_76 = "7.6"
 VERSION_74 = "7.4"

schemas/IDLs/org.gel.models.cva.avro/1.5.3/Comment.avdl

@@ -0,0 +1,22 @@
+@namespace("org.gel.models.cva.avro")
+
+protocol CommentProtocol {
+
+    /**
+    A generic comment.
+    */
+    record Comment {
+        /**
+        The text of the comment
+        */
+        string text;
+        /**
+        Date in format yyyyMMddhhmm
+        */
+        string `date`;
+        /**
+        The author of the curation event
+        */
+        string userid;
+    }
+}

schemas/IDLs/org.gel.models.cva.avro/1.5.3/CvaEvidence.avdl

@@ -0,0 +1,159 @@
+@namespace("org.gel.models.cva.avro")
+
+protocol EvidencesProtocol {
+
+    // CVA references
+    import idl "Comment.avdl";
+    import idl "ReportEvent.avdl";
+    import idl "CvaVariant.avdl";
+    // Report models references
+    import idl "CommonInterpreted.avdl";
+    // OpenCB references
+    import idl "variant.avdl";
+    import idl "evidence.avdl";
+
+
+    /**
+    The curation record contains all information that might be stored from a curation event.
+    */
+    record Curation {
+        /**
+        The heritable phenotype to which the curation refers.
+        */
+        org.opencb.biodata.models.variant.avro.HeritableTrait heritableTrait;
+        /**
+        The transcript to which the curation refers
+        */
+        union {null, org.opencb.biodata.models.variant.avro.GenomicFeature} genomicFeature;
+        /**
+        The assembly to which the curation refers
+        */
+        union {null, org.gel.models.report.avro.Assembly} assembly;
+        /**
+        The variant's classification.
+        */
+        union{null, org.opencb.biodata.models.variant.avro.VariantClassification} variantClassification;
+        /**
+        The curation confidence.
+        */
+        union {null, org.opencb.biodata.models.variant.avro.Confidence} confidence;
+        /**
+        The automatic consistency status. The value is automatically inferred from evidences.
+        */
+        org.opencb.biodata.models.variant.avro.ConsistencyStatus automaticConsistencyStatus;
+        /**
+        The manual consistency status. The value is optionally provided by a curator.
+        */
+        union {null, org.opencb.biodata.models.variant.avro.ConsistencyStatus} manualConsistencyStatus;
+        /**
+        The penetrance of the phenotype for this genotype. Value in the range [0, 1]
+        */
+        union {null, org.opencb.biodata.models.variant.avro.Penetrance} penetrance;
+        /**
+        Variable expressivity of a given phenotype for the same genotype
+        */
+        union {null, boolean} variableExpressivity;
+        /**
+        Can this variant be reported as a secondary finding?
+        */
+        union {null, boolean} reportableAsSecondaryFinding;
+        /**
+        Is this variant actionable?
+        */
+        union {null, boolean} actionable;
+        /**
+        Confirmation flag to support two-step curation
+        */
+        union {null, boolean} confirmed;
+        /**
+        A list of additional properties in the form name-value.
+        */
+        array<org.opencb.biodata.models.variant.avro.Property> additionalProperties = [];
+        /**
+        Bibliography
+        */
+        array<string> bibliography = [];
+    }
+
+    /**
+    A curation history entry, stores previous and new curation state, the date of the change and the author.
+    */
+    record CurationHistoryEntry {
+        /**
+        Date in format yyyyMMddhhmm
+        */
+        string `date`;
+        /**
+        The current curation at date
+        */
+        Curation curation;
+        /**
+        The author of the curation event
+        */
+        string userId;
+    }
+
+    /**
+    A curation for a known variant contains the current curation state and the curation history.
+    Must be unique by `curation.phenotype` and `curation.inheritanceMode`.
+    */
+    record CurationEntry {
+        /**
+        Date in format yyyyMMddhhmm
+        */
+        string `date`;
+        /**
+        The current curation state
+        */
+        Curation curation;
+        /**
+        The curation history
+        */
+        array<CurationHistoryEntry> history = [];
+        /**
+        Comments on the curation event
+        */
+        array<Comment> comments = [];
+    }
+
+    /*
+    An enum of property names.
+    */
+    /*
+    enum PropertyName {
+        OBI_0001617,                            // pubmed id, http://purl.obolibrary.org/obo/OBI_0001617
+        SIO_001066,                             // study, http://semanticscience.org/resource/SIO_001066
+        SIO_001315,                             // author list, http://semanticscience.org/resource/SIO_001315
+        SIO_000160,                             // journal, http://semanticscience.org/resource/SIO_000160
+        STATO_0000088,                          // study group population size, http://purl.obolibrary.org/obo/STATO_0000088
+        OBI_0000175,                            // pvalue,http://purl.obolibrary.org/obo/OBI_0000175
+        OBI_0001265,                            // FWER_adjusted_pvalue, http://purl.obolibrary.org/obo/OBI_0001265
+        OBI_0001442,                            // qvalue, http://purl.obolibrary.org/obo/OBI_0001442
+        STATO_0000200,                          // study_power, http://purl.obolibrary.org/obo/STATO_0000200
+        STATO_0000053,                          //false_positive_report_probability, http://purl.obolibrary.org/obo/STATO_0000053
+        STATO_0000182,                          //odds_ratio, http://purl.obolibrary.org/obo/STATO_0000182
+        STATO_0000245,                          //relative_risk, http://purl.obolibrary.org/obo/STATO_0000245
+        STATO_0000196,                          //confidence_interval, http://purl.obolibrary.org/obo/STATO_0000196
+        OBI_0000789,                           //OBI_0000789, http://purl.obolibrary.org/obo/OBI_0000789
+        STATO_0000254                           //population_allele_frequency, http://purl.obolibrary.org/obo/STATO_0000254
+    }
+    */
+
+    /**
+    A curation and the variants coordinates to which it corresponds
+    */
+    record CurationAndVariants {
+        VariantsCoordinates variantsCoordinates;
+        Curation curation;
+    }
+
+    /**
+    An evidence entry and the variants coordinates to which it corresponds
+    */
+    record EvidenceEntryAndVariants {
+        VariantsCoordinates variantsCoordinates;
+        union {null, VariantsCoordinates} markersCoordinates;
+        org.opencb.biodata.models.variant.avro.EvidenceEntry evidenceEntry;
+        union {null, org.gel.models.report.avro.Actions} actions;
+    }
+}