Switch to rules tables in Validate

docs/examples/errors.csv

@@ -1,15 +1,15 @@
-table,cell,rule ID,message
-immune_exposures.csv,D8,immune_exposures!D3,"Cell is empty but rule: ""is-required true"" does not allow this."
-immune_exposures.csv,F9,immune_exposures!F3,"Cell is empty but rule: ""is-required true"" does not allow this."
-immune_exposures.csv,B10,immune_exposures!B3,"Validation failed for rule: ""Dengue virus equivalent-to (NCBITaxon:11060)""."
-immune_exposures.csv,C10,immune_exposures!C3,"Validation failed for rule: ""NCBITaxon:11060 equivalent-to 'Dengue virus'""."
-immune_exposures.csv,D11,immune_exposures!D3,"Validation failed for rule: ""Dengue virus 2 subclass-of disease""."
-immune_exposures.csv,D11,immune_exposures!D3,"Validation failed for rule: ""Dengue virus 2 subclass-of 'has material basis in' some 'Dengue virus'""."
-immune_exposures.csv,B12,immune_exposures!B3,"Validation failed for rule: ""blood or 'Hepacivirus C' equivalent-to (UBERON:0000178)""."
-immune_exposures.csv,C12,immune_exposures!C3,"Validation failed for rule: ""UBERON:0000178 equivalent-to (blood or 'Hepacivirus C')""."
-immune_exposures.csv,F12,immune_exposures!F3,"Cell is non-empty (""Chronic"") but rule: ""is-excluded true"" does not allow this."
-immune_exposures.csv,D13,immune_exposures!D3,"Validation failed for rule: ""wheat allergy equivalent-to (DOID:12206)""."
-immune_exposures.csv,D13,immune_exposures!D3,"Validation failed for rule: ""dengue hemorrhagic fever equivalent-to (DOID:3660)""."
-immune_exposures.csv,D13,immune_exposures!D3,"Validation failed for rule: ""wheat allergy subclass-of 'has material basis in' some 'Dengue virus'""."
-immune_exposures.csv,E13,immune_exposures!E3,"Validation failed for rule: ""DOID:3660 equivalent-to 'dengue hemorrhagic fever'""."
-immune_exposures.csv,E13,immune_exposures!E3,"Validation failed for rule: ""DOID:12206 equivalent-to 'wheat allergy'""."
+table,cell,rule,message
+immune_exposures,D7,is-required,"Cell is empty but rule: ""is-required true"" does not allow this."
+immune_exposures,F8,is-required,"Cell is empty but rule: ""is-required true"" does not allow this."
+immune_exposures,B9,equivalent-to,"Validation failed for rule: ""Dengue virus equivalent-to (NCBITaxon:11060)""."
+immune_exposures,C9,equivalent-to,"Validation failed for rule: ""NCBITaxon:11060 equivalent-to 'Dengue virus'""."
+immune_exposures,D10,subclass-of,"Validation failed for rule: ""Dengue virus 2 subclass-of disease""."
+immune_exposures,D10,subclass-of,"Validation failed for rule: ""Dengue virus 2 subclass-of 'has material basis in' some 'Dengue virus'""."
+immune_exposures,B11,equivalent-to,"Validation failed for rule: ""blood or 'Hepacivirus C' equivalent-to (UBERON:0000178)""."
+immune_exposures,C11,equivalent-to,"Validation failed for rule: ""UBERON:0000178 equivalent-to (blood or 'Hepacivirus C')""."
+immune_exposures,F11,is-excluded,"Cell is non-empty (""Chronic"") but rule: ""is-excluded true"" does not allow this."
+immune_exposures,D12,equivalent-to,"Validation failed for rule: ""wheat allergy equivalent-to (DOID:12206)""."
+immune_exposures,D12,equivalent-to,"Validation failed for rule: ""dengue hemorrhagic fever equivalent-to (DOID:3660)""."
+immune_exposures,D12,subclass-of,"Validation failed for rule: ""wheat allergy subclass-of 'has material basis in' some 'Dengue virus'""."
+immune_exposures,E12,equivalent-to,"Validation failed for rule: ""DOID:3660 equivalent-to 'dengue hemorrhagic fever'""."
+immune_exposures,E12,equivalent-to,"Validation failed for rule: ""DOID:12206 equivalent-to 'wheat allergy'""."

docs/examples/immune_exposures.csv

@@ -1,5 +1,4 @@
 exposure process reported,exposure material reported,exposure material id,disease reported,disease ontology id,disease stage reported
-is-required; subclass-of 'exposure process';,subclass-of|equivalent-to 'material entity'; equivalent-to %3; is-required (when %1 subclass-of ('administering substance in vivo' or 'exposure to substance without evidence for disease' or 'occurrence of infectious disease' or 'occurrence of allergic disease')); is-excluded (when %1 equivalent-to 'occurrence of disease'); is-excluded (when %1 subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer' or 'no exposure' or unknown)),equivalent-to %2,subclass-of disease; subclass-of 'has material basis in' some %2 (when %1 not-subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer')); equivalent-to %5; is-required (when %1 subclass-of 'occurrence of disease'); is-excluded (when %1 equivalent-to 'administering substance in vivo'); is-excluded (when %1 subclass-of (vaccination or 'transplant or transfusion' or 'exposure to substance without evidence for disease' or 'no exposure' or unknown)),equivalent-to %4,subclass-of 'disease stage'; is-required (when %1 subclass-of 'occurrence of disease'); is-excluded (when %1 not-subclass-of 'occurrence of disease')
 unknown,,,,,
 administering substance in vivo,Hepacivirus C,NCBITaxon:11103,,,
 exposure to substance without evidence for disease,Dengue virus,NCBITaxon:12637,,,

docs/examples/immune_exposures.html

@@ -15,16 +15,6 @@
 	<th>disease ontology id</th>
 	<th>disease stage reported</th>
 </tr>
-</thead>
-<thead class="bg-secondary text-white">
-<tr>
-	<th>is-required; subclass-of 'exposure process';</th>
-	<th>subclass-of|equivalent-to 'material entity'; equivalent-to %3; is-required (when %1 subclass-of ('administering substance in vivo' or 'exposure to substance without evidence for disease' or 'occurrence of infectious disease' or 'occurrence of allergic disease')); is-excluded (when %1 equivalent-to 'occurrence of disease'); is-excluded (when %1 subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer' or 'no exposure' or unknown))</th>
-	<th>equivalent-to %2</th>
-	<th>subclass-of disease; subclass-of 'has material basis in' some %2 (when %1 not-subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer')); equivalent-to %5; is-required (when %1 subclass-of 'occurrence of disease'); is-excluded (when %1 equivalent-to 'administering substance in vivo'); is-excluded (when %1 subclass-of (vaccination or 'transplant or transfusion' or 'exposure to substance without evidence for disease' or 'no exposure' or unknown))</th>
-	<th>equivalent-to %4</th>
-	<th>subclass-of 'disease stage'; is-required (when %1 subclass-of 'occurrence of disease'); is-excluded (when %1 not-subclass-of 'occurrence of disease')</th>
-</tr>
 </thead>
 	<tr>
 		<td><a href="ONTIE:0003310">unknown</a></td>

docs/examples/immune_exposures.txt

@@ -1,14 +1,14 @@
-At immune_exposures.csv row 8, column 4: Cell is empty but rule: "is-required true" does not allow this.
-At immune_exposures.csv row 9, column 6: Cell is empty but rule: "is-required true" does not allow this.
-At immune_exposures.csv row 10, column 2: Validation failed for rule: "Dengue virus equivalent-to (NCBITaxon:11060)".
-At immune_exposures.csv row 10, column 3: Validation failed for rule: "NCBITaxon:11060 equivalent-to 'Dengue virus'".
-At immune_exposures.csv row 11, column 4: Validation failed for rule: "Dengue virus 2 subclass-of disease".
-At immune_exposures.csv row 11, column 4: Validation failed for rule: "Dengue virus 2 subclass-of 'has material basis in' some 'Dengue virus'".
-At immune_exposures.csv row 12, column 2: Validation failed for rule: "blood or 'Hepacivirus C' equivalent-to (UBERON:0000178)".
-At immune_exposures.csv row 12, column 3: Validation failed for rule: "UBERON:0000178 equivalent-to (blood or 'Hepacivirus C')".
-At immune_exposures.csv row 12, column 6: Cell is non-empty ("Chronic") but rule: "is-excluded true" does not allow this.
-At immune_exposures.csv row 13, column 4: Validation failed for rule: "wheat allergy equivalent-to (DOID:12206)".
-At immune_exposures.csv row 13, column 4: Validation failed for rule: "dengue hemorrhagic fever equivalent-to (DOID:3660)".
-At immune_exposures.csv row 13, column 4: Validation failed for rule: "wheat allergy subclass-of 'has material basis in' some 'Dengue virus'".
-At immune_exposures.csv row 13, column 5: Validation failed for rule: "DOID:3660 equivalent-to 'dengue hemorrhagic fever'".
-At immune_exposures.csv row 13, column 5: Validation failed for rule: "DOID:12206 equivalent-to 'wheat allergy'".
+At immune_exposures.csv row 7, column 4: Cell is empty but rule: "is-required true" does not allow this.
+At immune_exposures.csv row 8, column 6: Cell is empty but rule: "is-required true" does not allow this.
+At immune_exposures.csv row 9, column 2: Validation failed for rule: "Dengue virus equivalent-to (NCBITaxon:11060)".
+At immune_exposures.csv row 9, column 3: Validation failed for rule: "NCBITaxon:11060 equivalent-to 'Dengue virus'".
+At immune_exposures.csv row 10, column 4: Validation failed for rule: "Dengue virus 2 subclass-of disease".
+At immune_exposures.csv row 10, column 4: Validation failed for rule: "Dengue virus 2 subclass-of 'has material basis in' some 'Dengue virus'".
+At immune_exposures.csv row 11, column 2: Validation failed for rule: "blood or 'Hepacivirus C' equivalent-to (UBERON:0000178)".
+At immune_exposures.csv row 11, column 3: Validation failed for rule: "UBERON:0000178 equivalent-to (blood or 'Hepacivirus C')".
+At immune_exposures.csv row 11, column 6: Cell is non-empty ("Chronic") but rule: "is-excluded true" does not allow this.
+At immune_exposures.csv row 12, column 4: Validation failed for rule: "wheat allergy equivalent-to (DOID:12206)".
+At immune_exposures.csv row 12, column 4: Validation failed for rule: "dengue hemorrhagic fever equivalent-to (DOID:3660)".
+At immune_exposures.csv row 12, column 4: Validation failed for rule: "wheat allergy subclass-of 'has material basis in' some 'Dengue virus'".
+At immune_exposures.csv row 12, column 5: Validation failed for rule: "DOID:3660 equivalent-to 'dengue hemorrhagic fever'".
+At immune_exposures.csv row 12, column 5: Validation failed for rule: "DOID:12206 equivalent-to 'wheat allergy'".

docs/examples/immune_exposures_2.csv

@@ -1,5 +1,4 @@
 exposure process reported,exposure material reported,exposure material id,disease reported,disease ontology id,disease stage reported
-is-required; subclass-of 'exposure process';,subclass-of|equivalent-to 'material entity'; equivalent-to %3; is-required (when %1 subclass-of ('administering substance in vivo' or 'exposure to substance without evidence for disease' or 'occurrence of infectious disease' or 'occurrence of allergic disease')); is-excluded (when %1 equivalent-to 'occurrence of disease'); is-excluded (when %1 subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer' or 'no exposure' or unknown)),equivalent-to %2,subclass-of disease; subclass-of 'has material basis in' some %2 (when %1 not-subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer')); equivalent-to %5; is-required (when %1 subclass-of 'occurrence of disease'); is-excluded (when %1 equivalent-to 'administering substance in vivo'); is-excluded (when %1 subclass-of (vaccination or 'transplant or transfusion' or 'exposure to substance without evidence for disease' or 'no exposure' or unknown)),equivalent-to %4,subclass-of 'disease stage'; is-required (when %1 subclass-of 'occurrence of disease'); is-excluded (when %1 not-subclass-of 'occurrence of disease')
 vaccination,Varicella-zoster virus vaccine,VO:0000669,,,
 infectious challenge,Hepacivirus C,NCBITaxon:11103,,,
 transplant or transfusion,blood,UBERON:0000178,,,

docs/examples/immune_exposures_2.html

@@ -15,16 +15,6 @@
 	<th>disease ontology id</th>
 	<th>disease stage reported</th>
 </tr>
-</thead>
-<thead class="bg-secondary text-white">
-<tr>
-	<th>is-required; subclass-of 'exposure process';</th>
-	<th>subclass-of|equivalent-to 'material entity'; equivalent-to %3; is-required (when %1 subclass-of ('administering substance in vivo' or 'exposure to substance without evidence for disease' or 'occurrence of infectious disease' or 'occurrence of allergic disease')); is-excluded (when %1 equivalent-to 'occurrence of disease'); is-excluded (when %1 subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer' or 'no exposure' or unknown))</th>
-	<th>equivalent-to %2</th>
-	<th>subclass-of disease; subclass-of 'has material basis in' some %2 (when %1 not-subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer')); equivalent-to %5; is-required (when %1 subclass-of 'occurrence of disease'); is-excluded (when %1 equivalent-to 'administering substance in vivo'); is-excluded (when %1 subclass-of (vaccination or 'transplant or transfusion' or 'exposure to substance without evidence for disease' or 'no exposure' or unknown))</th>
-	<th>equivalent-to %4</th>
-	<th>subclass-of 'disease stage'; is-required (when %1 subclass-of 'occurrence of disease'); is-excluded (when %1 not-subclass-of 'occurrence of disease')</th>
-</tr>
 </thead>
 	<tr>
 		<td><a href="ONTIE:0003304">vaccination</a></td>

docs/examples/immune_exposures_rules.csv

@@ -0,0 +1,13 @@
+table,column,validation
+immune_exposures,exposure process reported,is-required; subclass-of 'exposure process';
+immune_exposures,exposure material reported,subclass-of|equivalent-to 'material entity'; equivalent-to {exposure material id}; is-required (when {exposure process reported} subclass-of ('administering substance in vivo' or 'exposure to substance without evidence for disease' or 'occurrence of infectious disease' or 'occurrence of allergic disease')); is-excluded (when {exposure process reported} equivalent-to 'occurrence of disease'); is-excluded (when {exposure process reported} subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer' or 'no exposure' or unknown))
+immune_exposures,exposure material id,equivalent-to {exposure material reported}
+immune_exposures,disease reported,subclass-of disease; subclass-of 'has material basis in' some {exposure material reported} (when {exposure process reported} not-subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer')); equivalent-to {disease ontology id}; is-required (when {exposure process reported} subclass-of 'occurrence of disease'); is-excluded (when {exposure process reported} equivalent-to 'administering substance in vivo'); is-excluded (when {exposure process reported} subclass-of (vaccination or 'transplant or transfusion' or 'exposure to substance without evidence for disease' or 'no exposure' or unknown))
+immune_exposures,disease ontology id,equivalent-to {disease reported}
+immune_exposures,disease stage reported,subclass-of 'disease stage'; is-required (when {exposure process reported} subclass-of 'occurrence of disease'); is-excluded (when {exposure process reported} not-subclass-of 'occurrence of disease')
+immune_exposures_2,exposure process reported,is-required; subclass-of 'exposure process';
+immune_exposures_2,exposure material reported,subclass-of|equivalent-to 'material entity'; equivalent-to {exposure material id}; is-required (when {exposure process reported} subclass-of ('administering substance in vivo' or 'exposure to substance without evidence for disease' or 'occurrence of infectious disease' or 'occurrence of allergic disease')); is-excluded (when {exposure process reported} equivalent-to 'occurrence of disease'); is-excluded (when {exposure process reported} subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer' or 'no exposure' or unknown))
+immune_exposures_2,exposure material id,equivalent-to {exposure material reported}
+immune_exposures_2,disease reported,subclass-of disease; subclass-of 'has material basis in' some {exposure material reported} (when {exposure process reported} not-subclass-of ('occurrence of autoimmune disease' or 'occurrence of cancer')); equivalent-to {disease ontology id}; is-required (when {exposure process reported} subclass-of 'occurrence of disease'); is-excluded (when {exposure process reported} equivalent-to 'administering substance in vivo'); is-excluded (when {exposure process reported} subclass-of (vaccination or 'transplant or transfusion' or 'exposure to substance without evidence for disease' or 'no exposure' or unknown))
+immune_exposures_2,disease ontology id,equivalent-to {disease reported}
+immune_exposures_2,disease stage reported,subclass-of 'disease stage'; is-required (when {exposure process reported} subclass-of 'occurrence of disease'); is-excluded (when {exposure process reported} not-subclass-of 'occurrence of disease')