From 43de2baf021eaea66d793b637cc318c0e44150df Mon Sep 17 00:00:00 2001 From: mereolog Date: Fri, 8 Sep 2023 16:16:30 +0200 Subject: [PATCH 01/21] uc1_cq2 for GSRS Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 6 +++++ .../uc1_cq2_amlodipine_expected_results.json | 22 +++++++++++++++++++ 2 files changed, 28 insertions(+) create mode 100644 etc/unit_tests/cq_expected_results/GSRS/uc1_cq2_amlodipine_expected_results.json diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index 58675d38..fb24852b 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -3,3 +3,9 @@ uc1_cq1_tests: parameters: uc1_cq1_parameter_1: "" expected_output: "cq_expected_results/GSRS/uc1_cq1_expected_results.json" + + uc1_cq2_tests_amlodipine: + sparql_template: "cq_templates/uc1_cq2.sparql" + parameters: + uc1_cq2_parameter_1: "" + expected_output: "cq_expected_results/IDMP/uc1_cq2_amlodipine_expected_results.json" diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq2_amlodipine_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq2_amlodipine_expected_results.json new file mode 100644 index 00000000..39322586 --- /dev/null +++ b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq2_amlodipine_expected_results.json @@ -0,0 +1,22 @@ +{ + "results": { + "bindings": [ + { + "ActiveMoiety": { + "type": "uri", + "value": "https://gsrs.ncats.nih.gov/api/v1/substances/1J444QC288" + }, + "ActiveMoietyName": { + "type": "literal", + "value": "AMLODIPINE" + } + } + ] + }, + "head": { + "vars": [ + "ActiveMoiety", + "ActiveMoietyName" + ] + } +} \ No newline at end of file From 3e962ed8f48bbfeb2ef1f6d0a3e5dae9100cd1df Mon Sep 17 00:00:00 2001 From: mereolog Date: Fri, 8 Sep 2023 16:25:26 +0200 Subject: [PATCH 02/21] fix to previous commit Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index fb24852b..f17e4015 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -4,7 +4,7 @@ uc1_cq1_tests: uc1_cq1_parameter_1: "" expected_output: "cq_expected_results/GSRS/uc1_cq1_expected_results.json" - uc1_cq2_tests_amlodipine: +uc1_cq2_tests: sparql_template: "cq_templates/uc1_cq2.sparql" parameters: uc1_cq2_parameter_1: "" From dc2a540cd6a66cbf4cae68bfd5d7f3efc08a2cdf Mon Sep 17 00:00:00 2001 From: mereolog Date: Fri, 8 Sep 2023 16:34:36 +0200 Subject: [PATCH 03/21] update of GSRS version in unit tests Signed-off-by: mereolog --- .github/workflows/unit_tests_run.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/unit_tests_run.yml b/.github/workflows/unit_tests_run.yml index 31146e30..930dd5ea 100644 --- a/.github/workflows/unit_tests_run.yml +++ b/.github/workflows/unit_tests_run.yml @@ -48,8 +48,7 @@ jobs: path: AboutIDMPDev-ReferenceIndividuals.ttl GSRS: runs-on: ubuntu-latest - env: - GSRS_VERSION: ${{ inputs.gsrs_version || '2022-12-15' }} + GSRS_VERSION: ${{ inputs.gsrs_version || '2023-07-08' }} steps: - uses: actions/checkout@v3 - name: Set up Java 11 From b49c6caceb480142ae86d4f8c1c69a37e3d7dbb3 Mon Sep 17 00:00:00 2001 From: mereolog Date: Fri, 8 Sep 2023 16:35:56 +0200 Subject: [PATCH 04/21] update of GSRS version in unit tests Signed-off-by: mereolog --- .github/workflows/unit_tests_run.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/unit_tests_run.yml b/.github/workflows/unit_tests_run.yml index 930dd5ea..cf18ad57 100644 --- a/.github/workflows/unit_tests_run.yml +++ b/.github/workflows/unit_tests_run.yml @@ -48,6 +48,7 @@ jobs: path: AboutIDMPDev-ReferenceIndividuals.ttl GSRS: runs-on: ubuntu-latest + env: GSRS_VERSION: ${{ inputs.gsrs_version || '2023-07-08' }} steps: - uses: actions/checkout@v3 From 1c15ed51047ce2c53b201622801dfb2194911955 Mon Sep 17 00:00:00 2001 From: mereolog Date: Fri, 8 Sep 2023 16:38:10 +0200 Subject: [PATCH 05/21] update of GSRS version in unit tests Signed-off-by: mereolog --- .github/workflows/unit_tests_run.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/unit_tests_run.yml b/.github/workflows/unit_tests_run.yml index cf18ad57..fafeb2b2 100644 --- a/.github/workflows/unit_tests_run.yml +++ b/.github/workflows/unit_tests_run.yml @@ -49,7 +49,7 @@ jobs: GSRS: runs-on: ubuntu-latest env: - GSRS_VERSION: ${{ inputs.gsrs_version || '2023-07-08' }} + GSRS_VERSION: ${{ inputs.gsrs_version || '2022-12-22' }} steps: - uses: actions/checkout@v3 - name: Set up Java 11 From c05746c5f5849e45457ace503416551d2ea36187 Mon Sep 17 00:00:00 2001 From: mereolog Date: Fri, 8 Sep 2023 16:40:06 +0200 Subject: [PATCH 06/21] Revert "fix to previous commit" This reverts commit 3e962ed8f48bbfeb2ef1f6d0a3e5dae9100cd1df. --- etc/unit_tests/configs/gsrs_tests_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index f17e4015..fb24852b 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -4,7 +4,7 @@ uc1_cq1_tests: uc1_cq1_parameter_1: "" expected_output: "cq_expected_results/GSRS/uc1_cq1_expected_results.json" -uc1_cq2_tests: + uc1_cq2_tests_amlodipine: sparql_template: "cq_templates/uc1_cq2.sparql" parameters: uc1_cq2_parameter_1: "" From 30a99528413f01cd3bed951b191881051b4ce3da Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 09:25:02 +0200 Subject: [PATCH 07/21] revert to last version of GSRS Signed-off-by: mereolog --- .github/workflows/unit_tests_run.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/unit_tests_run.yml b/.github/workflows/unit_tests_run.yml index fafeb2b2..31146e30 100644 --- a/.github/workflows/unit_tests_run.yml +++ b/.github/workflows/unit_tests_run.yml @@ -49,7 +49,7 @@ jobs: GSRS: runs-on: ubuntu-latest env: - GSRS_VERSION: ${{ inputs.gsrs_version || '2022-12-22' }} + GSRS_VERSION: ${{ inputs.gsrs_version || '2022-12-15' }} steps: - uses: actions/checkout@v3 - name: Set up Java 11 From bcdd854734e7d451c6be28680ab20d7470b895e0 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 09:50:03 +0200 Subject: [PATCH 08/21] revert to last version of GSRS Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index fb24852b..df395bdf 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -4,7 +4,7 @@ uc1_cq1_tests: uc1_cq1_parameter_1: "" expected_output: "cq_expected_results/GSRS/uc1_cq1_expected_results.json" - uc1_cq2_tests_amlodipine: +uc1_cq2_tests_amlodipine: sparql_template: "cq_templates/uc1_cq2.sparql" parameters: uc1_cq2_parameter_1: "" From 71c94609f9baf6c66732c8225b10b769821a0ebc Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 11:31:12 +0200 Subject: [PATCH 09/21] fix to gsrs unit tests config Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index df395bdf..ffddd16e 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -8,4 +8,4 @@ uc1_cq2_tests_amlodipine: sparql_template: "cq_templates/uc1_cq2.sparql" parameters: uc1_cq2_parameter_1: "" - expected_output: "cq_expected_results/IDMP/uc1_cq2_amlodipine_expected_results.json" + expected_output: "cq_expected_results/GSRS/uc1_cq2_amlodipine_expected_results.json" From d8d03054ec9aa341401836330dc6aa06f3fc3efb Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 11:50:54 +0200 Subject: [PATCH 10/21] uc1_cq4 for GSRS unit test added Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 9 ++++++++- ...ults.json => uc1_cq2_expected_results.json} | 0 .../GSRS/uc1_cq4_expected_results.json | 18 ++++++++++++++++++ 3 files changed, 26 insertions(+), 1 deletion(-) rename etc/unit_tests/cq_expected_results/GSRS/{uc1_cq2_amlodipine_expected_results.json => uc1_cq2_expected_results.json} (100%) create mode 100644 etc/unit_tests/cq_expected_results/GSRS/uc1_cq4_expected_results.json diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index ffddd16e..7a8d6083 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -8,4 +8,11 @@ uc1_cq2_tests_amlodipine: sparql_template: "cq_templates/uc1_cq2.sparql" parameters: uc1_cq2_parameter_1: "" - expected_output: "cq_expected_results/GSRS/uc1_cq2_amlodipine_expected_results.json" + expected_output: "cq_expected_results/GSRS/uc1_cq2_expected_results.json" + +uc1_cq2_tests_amlodipine: + sparql_template: "cq_templates/uc1_cq4.sparql" + parameters: + uc1_cq2_parameter_1: "" + uc1_cq2_parameter_2: "<" + expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json" diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq2_amlodipine_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq2_expected_results.json similarity index 100% rename from etc/unit_tests/cq_expected_results/GSRS/uc1_cq2_amlodipine_expected_results.json rename to etc/unit_tests/cq_expected_results/GSRS/uc1_cq2_expected_results.json diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq4_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq4_expected_results.json new file mode 100644 index 00000000..32d30a26 --- /dev/null +++ b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq4_expected_results.json @@ -0,0 +1,18 @@ +{ "head": { + "vars": [ "Code" , "CodeName" , "CodeText" ] + } , + "results": { + "bindings": [ + { + "Code": { "type": "uri" , "value": "https://data.pistoiaalliance.org/id/FDA_UNII/1J444QC288" } , + "CodeName": { "type": "literal" , "value": "" } , + "CodeText": { "type": "literal" , "value": "1J444QC288" } + }, + { + "Code": { "type": "uri" , "value": "https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/UNII-1J444QC288" } , + "CodeName": { "type": "literal" , "value": "1J444QC288" } , + "CodeText": { "type": "literal" , "value": "1J444QC288" } + } + ] + } +} From cf0915ba2348cfc426151cf548aa703e207158b3 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 11:57:46 +0200 Subject: [PATCH 11/21] uc1_cq4 for GSRS unit test added Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index 7a8d6083..4dbf789d 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -14,5 +14,5 @@ uc1_cq2_tests_amlodipine: sparql_template: "cq_templates/uc1_cq4.sparql" parameters: uc1_cq2_parameter_1: "" - uc1_cq2_parameter_2: "<" + uc1_cq2_parameter_2: "" expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json" From 0579e5f4705e716ce94e1da3c85254bc254febe0 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 12:05:20 +0200 Subject: [PATCH 12/21] uc1_cq4 for GSRS unit test added Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index 4dbf789d..8cafac38 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -4,15 +4,15 @@ uc1_cq1_tests: uc1_cq1_parameter_1: "" expected_output: "cq_expected_results/GSRS/uc1_cq1_expected_results.json" -uc1_cq2_tests_amlodipine: +uc1_cq2_tests: sparql_template: "cq_templates/uc1_cq2.sparql" parameters: uc1_cq2_parameter_1: "" expected_output: "cq_expected_results/GSRS/uc1_cq2_expected_results.json" -uc1_cq2_tests_amlodipine: +uc1_cq2_tests: sparql_template: "cq_templates/uc1_cq4.sparql" parameters: - uc1_cq2_parameter_1: "" - uc1_cq2_parameter_2: "" + uc1_cq4_parameter_1: "" + uc1_cq4_parameter_2: "" expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json" From 1b35aaebc5fdd8b81794e9b1ffdb8bd26ddf3b85 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 12:31:05 +0200 Subject: [PATCH 13/21] uc1_cq4 for GSRS unit test added Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 2 +- .../cq_expected_results/GSRS/uc1_cq4_expected_results.json | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index 8cafac38..436ba37d 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -10,7 +10,7 @@ uc1_cq2_tests: uc1_cq2_parameter_1: "" expected_output: "cq_expected_results/GSRS/uc1_cq2_expected_results.json" -uc1_cq2_tests: +uc1_cq4_tests: sparql_template: "cq_templates/uc1_cq4.sparql" parameters: uc1_cq4_parameter_1: "" diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq4_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq4_expected_results.json index 32d30a26..dba2c62f 100644 --- a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq4_expected_results.json +++ b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq4_expected_results.json @@ -4,13 +4,12 @@ "results": { "bindings": [ { - "Code": { "type": "uri" , "value": "https://data.pistoiaalliance.org/id/FDA_UNII/1J444QC288" } , - "CodeName": { "type": "literal" , "value": "" } , + "Code": { "type": "uri" , "value": "https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/UNII-1J444QC288" } , + "CodeName": { "type": "literal" , "value": "1J444QC288" } , "CodeText": { "type": "literal" , "value": "1J444QC288" } }, { - "Code": { "type": "uri" , "value": "https://spec.pistoiaalliance.org/idmp/ontology/EXT/Examples/AmlodipineExample/UNII-1J444QC288" } , - "CodeName": { "type": "literal" , "value": "1J444QC288" } , + "Code": { "type": "uri" , "value": "https://data.pistoiaalliance.org/id/FDA_UNII/1J444QC288" } , "CodeText": { "type": "literal" , "value": "1J444QC288" } } ] From fe81ade9e93d90d02d735cb4f904cdd1e73cbaf8 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 12:55:48 +0200 Subject: [PATCH 14/21] uc1_cq9 for GSRS unit test added Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 6 ++++++ .../GSRS/uc1_cq9_expected_results.json | 19 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index 436ba37d..c8e22208 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -16,3 +16,9 @@ uc1_cq4_tests: uc1_cq4_parameter_1: "" uc1_cq4_parameter_2: "" expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json" + +uc1_cq9_tests_amlodipine: + sparql_template: "cq_templates/uc1_cq9.sparql" + parameters: + uc1_cq9_parameter_1: "" + expected_output: "cq_expected_results/GSRS/uc1_cq9_expected_results.json" diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json new file mode 100644 index 00000000..a5b3e149 --- /dev/null +++ b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json @@ -0,0 +1,19 @@ +{ + "results": { + "bindings": [ + { + "Structure": { + "type": "uri", + "value": "https://data.pistoiaalliance.org/idmp/gsrs/molfile/02b5d803-9961-49cb-ae4c-db5cbc1d8a58" + } + } + ] + }, + "head": { + "vars": [ + "Structure", + "StructureName", + "StructureText" + ] + } +} \ No newline at end of file From db4710c9a0754681723b318476eae18ce1f2cc79 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 14:00:54 +0200 Subject: [PATCH 15/21] uc1_cq9 for GSRS unit test added Signed-off-by: mereolog --- .../GSRS/uc1_cq9_expected_results.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json index a5b3e149..4d5c44ea 100644 --- a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json +++ b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json @@ -1,4 +1,11 @@ { + "head": { + "vars": [ + "Structure", + "StructureName", + "StructureText" + ] + }, "results": { "bindings": [ { @@ -8,12 +15,5 @@ } } ] - }, - "head": { - "vars": [ - "Structure", - "StructureName", - "StructureText" - ] } } \ No newline at end of file From a8345ce3807b6d156d8bd0f685ca6f1db2679db1 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 14:12:05 +0200 Subject: [PATCH 16/21] uc1_cq9 for GSRS unit test added Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 2 +- .../GSRS/uc1_cq9_expected_results.json | 28 +++++++++---------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index c8e22208..e55956ac 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -17,7 +17,7 @@ uc1_cq4_tests: uc1_cq4_parameter_2: "" expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json" -uc1_cq9_tests_amlodipine: +uc1_cq9_tests: sparql_template: "cq_templates/uc1_cq9.sparql" parameters: uc1_cq9_parameter_1: "" diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json index 4d5c44ea..abb3fbe3 100644 --- a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json +++ b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json @@ -1,19 +1,19 @@ { "head": { - "vars": [ - "Structure", - "StructureName", - "StructureText" - ] + "vars": [ + "Structure", + "StructureName", + "StructureText" + ] }, "results": { - "bindings": [ - { - "Structure": { - "type": "uri", - "value": "https://data.pistoiaalliance.org/idmp/gsrs/molfile/02b5d803-9961-49cb-ae4c-db5cbc1d8a58" - } - } - ] + "bindings": [ + { + "Structure": { + "type": "uri", + "value": "https://data.pistoiaalliance.org/idmp/gsrs/molfile/02b5d803-9961-49cb-ae4c-db5cbc1d8a58" + } + } + ] } -} \ No newline at end of file + } \ No newline at end of file From b13e73df45ad67ec408c7ab1b88d15b043e633f6 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 14:37:24 +0200 Subject: [PATCH 17/21] temp report for unittest runner Signed-off-by: mereolog --- etc/unit_tests/UnitTestRunner.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/etc/unit_tests/UnitTestRunner.java b/etc/unit_tests/UnitTestRunner.java index a49cd9ab..68571743 100644 --- a/etc/unit_tests/UnitTestRunner.java +++ b/etc/unit_tests/UnitTestRunner.java @@ -152,7 +152,8 @@ private static boolean isResultExpected(String actual, String expected) { JsonNode expectedJson = objectMapper.readTree(expected); JsonNode diff = JsonDiff.asJson(actualJson, expectedJson); - + System.out.println(actualJson); + System.out.println(expectedJson); if (diff.size() > 0) { System.out.println("Differences found:"); System.out.println(diff); From a45784f5d1e0c45e31bf25a7d329700a32637613 Mon Sep 17 00:00:00 2001 From: mereolog Date: Mon, 11 Sep 2023 14:51:37 +0200 Subject: [PATCH 18/21] rollback of previous commit Signed-off-by: mereolog --- etc/unit_tests/UnitTestRunner.java | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/etc/unit_tests/UnitTestRunner.java b/etc/unit_tests/UnitTestRunner.java index 68571743..38cb67e5 100644 --- a/etc/unit_tests/UnitTestRunner.java +++ b/etc/unit_tests/UnitTestRunner.java @@ -152,8 +152,7 @@ private static boolean isResultExpected(String actual, String expected) { JsonNode expectedJson = objectMapper.readTree(expected); JsonNode diff = JsonDiff.asJson(actualJson, expectedJson); - System.out.println(actualJson); - System.out.println(expectedJson); + if (diff.size() > 0) { System.out.println("Differences found:"); System.out.println(diff); From e2c6e14bafc5a773513684126d316d4cbdb8947a Mon Sep 17 00:00:00 2001 From: mereolog Date: Thu, 14 Sep 2023 12:10:35 +0200 Subject: [PATCH 19/21] fix to uc1_cq9 expected results for GSRS Signed-off-by: mereolog --- .../cq_expected_results/GSRS/uc1_cq9_expected_results.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json index abb3fbe3..7e6501f9 100644 --- a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json +++ b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json @@ -11,7 +11,7 @@ { "Structure": { "type": "uri", - "value": "https://data.pistoiaalliance.org/idmp/gsrs/molfile/02b5d803-9961-49cb-ae4c-db5cbc1d8a58" + "value": "https://data.pistoiaalliance.org/idmp/gsrs/molfile/50875c99-6080-4eb7-867c-4c077d62da8c" } } ] From ef16a60e1dbca00b1debfc2aee6a110019900381 Mon Sep 17 00:00:00 2001 From: mereolog Date: Thu, 14 Sep 2023 12:32:13 +0200 Subject: [PATCH 20/21] more detail unit failure reporting added Signed-off-by: mereolog --- etc/unit_tests/UnitTestRunner.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/etc/unit_tests/UnitTestRunner.java b/etc/unit_tests/UnitTestRunner.java index 38cb67e5..4aa3d753 100644 --- a/etc/unit_tests/UnitTestRunner.java +++ b/etc/unit_tests/UnitTestRunner.java @@ -156,6 +156,10 @@ private static boolean isResultExpected(String actual, String expected) { if (diff.size() > 0) { System.out.println("Differences found:"); System.out.println(diff); + System.out.println("Actual results:"); + System.out.println(actualJson); + System.out.println("Expected results:"); + System.out.println(expectedJson); return false; } } catch (IOException e) { From f59010ca0ebb37343d8b21fd0661a2f151d69254 Mon Sep 17 00:00:00 2001 From: mereolog Date: Thu, 14 Sep 2023 13:28:17 +0200 Subject: [PATCH 21/21] uc1_cq9 removed from GSRS tests Signed-off-by: mereolog --- etc/unit_tests/configs/gsrs_tests_config.yaml | 8 +------- .../GSRS/uc1_cq9_expected_results.json | 19 ------------------- 2 files changed, 1 insertion(+), 26 deletions(-) delete mode 100644 etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json diff --git a/etc/unit_tests/configs/gsrs_tests_config.yaml b/etc/unit_tests/configs/gsrs_tests_config.yaml index e55956ac..753004e1 100644 --- a/etc/unit_tests/configs/gsrs_tests_config.yaml +++ b/etc/unit_tests/configs/gsrs_tests_config.yaml @@ -15,10 +15,4 @@ uc1_cq4_tests: parameters: uc1_cq4_parameter_1: "" uc1_cq4_parameter_2: "" - expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json" - -uc1_cq9_tests: - sparql_template: "cq_templates/uc1_cq9.sparql" - parameters: - uc1_cq9_parameter_1: "" - expected_output: "cq_expected_results/GSRS/uc1_cq9_expected_results.json" + expected_output: "cq_expected_results/GSRS/uc1_cq4_expected_results.json" \ No newline at end of file diff --git a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json b/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json deleted file mode 100644 index 7e6501f9..00000000 --- a/etc/unit_tests/cq_expected_results/GSRS/uc1_cq9_expected_results.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "head": { - "vars": [ - "Structure", - "StructureName", - "StructureText" - ] - }, - "results": { - "bindings": [ - { - "Structure": { - "type": "uri", - "value": "https://data.pistoiaalliance.org/idmp/gsrs/molfile/50875c99-6080-4eb7-867c-4c077d62da8c" - } - } - ] - } - } \ No newline at end of file