fixup correct diagnostic diagnosis

README.org

@@ -5,8 +5,8 @@ Git ommix creates patient-level repositories to store sample references, version
 Large files are only retrieved on demand thanks to *git annex*, decorrelating navigating the history from actually downloading all of it.
 
 Git ommix also stores a representation of the provenance of each of those entities using the PROV ontology.
-Git ommix allows querying the repository structure, implementing multiple useful operations. These operations can apply to the whole patient's history or be constrained to one or multiple specific objects (sample/data/result/diagnostic)
-- list the objects contributing to the target (the data contributing to a result or to a diagnostic, samples contributing to diagnostics)
+Git ommix allows querying the repository structure, implementing multiple useful operations. These operations can apply to the whole patient's history or be constrained to one or multiple specific objects (sample/data/result/diagnosis)
+- list the objects contributing to the target (the data contributing to a result or to a diagnosis, samples contributing to diagnosiss)
 - get the most recent version of the target
 - get the PROV-O prevenance of the target, as turtle triplets or as a visual graph
 - display a timeline of diagnoses
@@ -80,7 +80,7 @@ New result files can be a *revision of* previous /<result>/ in the same /<sample
 
 *** Diagnosis
 
-git ommix add diagnostic -p|--patient <patient> --use <result|diagnostic> [--revision_of <diagnostic>] [--invalidate <diagnostic>]
+git ommix add diagnosis -p|--patient <patient> --use <result|diagnosis> [--revision_of <diagnosis>] [--invalidate <diagnosis>]
 
 Diagonses live outside of samples and can be used to tie multiple results from diffferent samples into a clinically coherent history
 A diagnosis *derives from* (use) a <result> or a previous <diagnosis>
@@ -96,11 +96,11 @@ git ommix list patient
 
 List all the patients known in the local store
 
-*** Sample/Data/Result/Diagnostic
+*** Sample/Data/Result/Diagnosis
 
-git ommix list sample|data|result|diagnostic -p|--patient <patient> [ref]
+git ommix list sample|data|result|diagnosis -p|--patient <patient> [ref]
 
-List all the sample|data|result|diagnostic objects in <patient>
+List all the sample|data|result|diagnosis objects in <patient>
 [ref] limits the list to the history of [ref]
 [ref] can be expressed as a commit hash or an object name (type:id or id)
 Multiple [ref] can be provided

gitommix-completions

@@ -21,7 +21,7 @@ function _completions
         local VERB="${words[1]}"
         case $VERB in
             list) OPTIONS="all " ;&
-            add) OPTIONS+="patient sample data result diagnostic" ;;
+            add) OPTIONS+="patient sample data result diagnosis" ;;
             get) OPTIONS="prov graph timeline last sparql log file object" ;;
         esac
     elif [[ "$cword" -gt 2 ]];then
@@ -35,7 +35,7 @@ function _completions
         case $VERB in
             add)
                 case $OBJECT in
-                    diagnostic|result) OPTIONS+="--use " ;&
+                    diagnosis|result) OPTIONS+="--use " ;&
                     data) OPTIONS+="--revision_of --invalidate " ;&
                     sample) OPTIONS+="--patient " ;&
                     patient) OPTIONS+="--id --method --provider --date --message ";;
@@ -68,9 +68,9 @@ function _completions
             -s|--sample) OPTIONS="$(git ommix list sample --patient $PATIENT)" ;;
             --use) if [[ "$OBJECT" == "result" ]];then
                        OPTIONS="$(git ommix list data --patient $PATIENT)"
-                   elif [[ "$OBJECT" == "diagnostic" ]];then
+                   elif [[ "$OBJECT" == "diagnosis" ]];then
                        OPTIONS="$(git ommix list result --patient $PATIENT)
-$(git ommix list diagnostic --patient $PATIENT)"
+$(git ommix list diagnosis --patient $PATIENT)"
                    fi ;;
             --invalidate|--revision_of) OPTIONS="$(git ommix list $OBJECT --patient $PATIENT)" ;;
         esac

tests/HPV.test

@@ -23,11 +23,11 @@ git-ommix add patient --id $PATIENT
 git-ommix add sample --id Anal_biopsy
 git-ommix add data -s Anal_biopsy --id Anal_pathology data_anal_path
 git-ommix add result -s Anal_biopsy --use Anal_pathology --method pathology --provider "Badoual <cecile.badoual@aphp.fr>" --id Anal_pathology result_anal_path
-git-ommix add diagnostic --use Anal_pathology --id Anal_carcinoma_T2
+git-ommix add diagnosis --use Anal_pathology --id Anal_carcinoma_T2
 
 git-ommix add data -s Anal_biopsy --id Anal_NGS data_anal_NGS
 git-ommix add result -s Anal_biopsy --use Anal_NGS --method HPV_capture --provider "Veyer <david.veyer@aphp.fr>" --id Anal_NGS result_anal_ngs
-git-ommix add diagnostic --use Anal_NGS --id Anal_carcinoma_T2_HPV --revision_of Anal_carcinoma_T2
+git-ommix add diagnosis --use Anal_NGS --id Anal_carcinoma_T2_HPV --revision_of Anal_carcinoma_T2
 
 git-ommix add sample --id blood1
 git-ommix add data -s blood1 --id blood1 data_blood1
@@ -44,10 +44,10 @@ git-ommix add result -s blood3 --use blood3 --method HPV_capture --provider "Vey
 git-ommix add sample --id Bone_biopsy
 git-ommix add data -s Bone_biopsy --id Bone_pathology data_bone_path
 git-ommix add result -s Bone_biopsy --use Bone_pathology --method pathology --provider "Badoual <cecile.badoual@aphp.fr>" --id Bone_pathology result_bone_path
-git-ommix add diagnostic --use Bone_pathology --id Bone_carcinoma_T1
+git-ommix add diagnosis --use Bone_pathology --id Bone_carcinoma_T1
 
 git-ommix add data -s Bone_biopsy --id Bone_NGS data_bone_NGS
 git-ommix add result -s Bone_biopsy --use Bone_NGS --method HPV_capture --provider "Veyer <david.veyer@aphp.fr>" --id Bone_NGS result_bone_ngs
-git-ommix add diagnostic --use Bone_NGS --use Bone_carcinoma_T1 --revision_of Bone_carcinoma_T1 --revision_of Anal_carcinoma_T2_HPV --invalidate Bone_carcinoma_T1 --id Anal_metastasis_T2M1_HPV 
+git-ommix add diagnosis --use Bone_NGS --use Bone_carcinoma_T1 --revision_of Bone_carcinoma_T1 --revision_of Anal_carcinoma_T2_HPV --invalidate Bone_carcinoma_T1 --id Anal_metastasis_T2M1_HPV 
 
-git-ommix add diagnostic --revision_of Anal_metastasis_T2M1_HPV --use blood1 --use blood2 --use blood3 --id HPV_HGAIN_T2N1M1
+git-ommix add diagnosis --revision_of Anal_metastasis_T2M1_HPV --use blood1 --use blood2 --use blood3 --id HPV_HGAIN_T2N1M1

tests/complex.test

@@ -24,25 +24,25 @@ rm ~/GitOmmix/$PATIENT -rf
 ../../git-ommix add sample --id b1
 ../../git-ommix add data -s b1 --id b1 data_b1
 ../../git-ommix add result -s b1 --use b1 --id b1 result_b1
-../../git-ommix add diagnostic --use b1 --id GastricT2
+../../git-ommix add diagnosis --use b1 --id GastricT2
 
 ../../git-ommix add sample --id b2
 ../../git-ommix add data -s b2 --id b2 data_b2
 ../../git-ommix add result -s b2 --use b2 --id b2 result_b2
-../../git-ommix add diagnostic --use b2 --id LungT1
+../../git-ommix add diagnosis --use b2 --id LungT1
 
 ../../git-ommix add sample --id b3
 ../../git-ommix add data -s b3 --id b3 data_b3
 ../../git-ommix add result -s b3 --use b3 --id b3 result_b3
-../../git-ommix add diagnostic --use b3 --id BoneT1
+../../git-ommix add diagnosis --use b3 --id BoneT1
 
 ../../git-ommix add sample --id blood
 ../../git-ommix add data -s blood --id blood data_blood
 ../../git-ommix add result -s blood --use blood --id blood --method ddPCR result_blood
-../../git-ommix add diagnostic --revision_of LungT1 --use blood --id LungT1N1
-../../git-ommix add diagnostic --revision_of GastricT2 --use blood --id GastricT2N1
+../../git-ommix add diagnosis --revision_of LungT1 --use blood --id LungT1N1
+../../git-ommix add diagnosis --revision_of GastricT2 --use blood --id GastricT2N1
 
 echo "Markers compatible with malignant gastric cells circulating DNA" > result_b3
 ../../git-ommix add result -s b3 --use b3 --id b3_ctDNA result_b3
 
-../../git-ommix add diagnostic --revision_of GastricT2N1 --use b3_ctDNA --use BoneT1 --invalidate BoneT1 --id GastricT2N1M1
+../../git-ommix add diagnosis --revision_of GastricT2N1 --use b3_ctDNA --use BoneT1 --invalidate BoneT1 --id GastricT2N1M1

tests/simple.test

@@ -34,5 +34,5 @@ echo "A2" > result_a
 ../../git-ommix add data -s s_a --revision_of d_a --id d_a2 data_a
 ../../git-ommix add result -s s_a --revision_of r_a --invalidate r_a --use d_a2 --id r_a2 result_a
 
-../../git-ommix add diagnostic --use r_a2 --use r_b --id diag1
-../../git-ommix add diagnostic --revision_of diag1 --use r_c --id diag1b
+../../git-ommix add diagnosis --use r_a2 --use r_b --id diag1
+../../git-ommix add diagnosis --revision_of diag1 --use r_c --id diag1b

tests/simple_complete.test

@@ -24,5 +24,5 @@ echo "A2" > result
 ../../git-ommix add data -s sample --revision_of data --id data2 data
 ../../git-ommix add result -s sample --revision_of result --invalidate result --use data2 --id result2 result
 
-../../git-ommix add diagnostic --use result --id diag
-../../git-ommix add diagnostic --revision_of diag --use result2 --id diag2 --provider "MD <md@hospital>" --method "Clinical_acumen"
+../../git-ommix add diagnosis --use result --id diag
+../../git-ommix add diagnosis --revision_of diag --use result2 --id diag2 --provider "MD <md@hospital>" --method "Clinical_acumen"

tests/simple_large.test

@@ -36,5 +36,5 @@ echo "A2" > result_a
 ../../git-ommix add data -s s_a --revision_of d_a --id d_a2 data_a
 ../../git-ommix add result -s s_a --revision_of r_a --invalidate r_a --use d_a2 --id r_a2 result_a
 
-../../git-ommix add diagnostic --use r_a2 --use r_b --id diag1
-../../git-ommix add diagnostic --revision_of diag1 --use r_c --id diag1b
+../../git-ommix add diagnosis --use r_a2 --use r_b --id diag1
+../../git-ommix add diagnosis --revision_of diag1 --use r_c --id diag1b