Merge pull request #90 from thehyve/test-data-update

ewelinagr · web-flow · commit ae2ad1695752 · 2019-11-07T16:47:10.000+01:00
Update test data after csr model update
diff --git a/requirements/requirements.txt b/requirements/requirements.txt
@@ -1,4 +1,4 @@
-csr2transmart==0.0.26
+csr2transmart==0.0.27
 docutils==0.14
 lockfile==0.12.2
 luigi==2.8.0
diff --git a/test_data/E2E_TEST_DATA/config/ontology_config.json b/test_data/E2E_TEST_DATA/config/ontology_config.json
@@ -39,19 +39,7 @@
               "concept_code": "Individual.ic_withdrawn_date"
             },
             {
-              "name": "04. Informed consent material",
-              "concept_code": "Individual.ic_material"
-            },
-            {
-              "name": "05. Informed consent data",
-              "concept_code": "Individual.ic_data"
-            },
-            {
-              "name": "06. Informed consent linking external database",
-              "concept_code": "Individual.ic_linking_ext"
-            },
-            {
-              "name": "07. Report hereditary susceptibility",
+              "name": "04. Report hereditary susceptibility",
               "concept_code": "Individual.report_her_susc"
             }
           ]
@@ -83,7 +71,7 @@
         },
         {
           "name": "05. Center of treatment",
-          "concept_code": "Diagnosis.center_treatment"
+          "concept_code": "Diagnosis.diagnosis_center"
         }
       ]
     },
diff --git a/test_data/E2E_TEST_DATA/config/sources_config.json b/test_data/E2E_TEST_DATA/config/sources_config.json
@@ -74,33 +74,6 @@
             }
           ]
         },
-        {
-          "name": "ic_material",
-          "sources": [
-            {
-              "file": "individual.tsv",
-              "column": "ic_material"
-            }
-          ]
-        },
-        {
-          "name": "ic_data",
-          "sources": [
-            {
-              "file": "individual.tsv",
-              "column": "ic_data"
-            }
-          ]
-        },
-        {
-          "name": "ic_linking_ext",
-          "sources": [
-            {
-              "file": "individual.tsv",
-              "column": "ic_linking_ext"
-            }
-          ]
-        },
         {
           "name": "report_her_susc",
           "sources": [
@@ -180,7 +153,7 @@
           ]
         },
         {
-          "name": "center_treatment",
+          "name": "diagnosis_center",
           "sources": [
             {
               "file": "diagnosis.tsv"
diff --git a/test_data/E2E_TEST_DATA/dropzone/diagnosis.tsv b/test_data/E2E_TEST_DATA/dropzone/diagnosis.tsv
@@ -1,4 +1,4 @@
-diagnosis_id	individual_id	topography	treatment_protocol	tumor_type	tumor_stage	diagnosis_date	center_treatment
+diagnosis_id	individual_id	topography	treatment_protocol	tumor_type	tumor_stage	diagnosis_date	diagnosis_center
 D1	PMCBS000BCA	liver	chemo	neuroblastoma	IV	2016-05-01	Center 1
 D2	PMCBM000BAB	kidney	surgery	nephroblastoma	III	2016-07-02	Center 2
 D3	PMCBM000BAB	bone marrow	Protocol 1	hepatoblastoma	IV	2016-11-03	Center 3
diff --git a/test_data/E2E_TEST_DATA/dropzone/individual.tsv b/test_data/E2E_TEST_DATA/dropzone/individual.tsv
@@ -1,3 +1,3 @@
-individual_id	taxonomy	birth_date	gender	death_date	ic_type	ic_given_date	ic_withdrawn_date	ic_material	ic_data	ic_linking_ext	report_her_susc	report_inc_findings
-PMCBS000BCA	Human	1993-02-01	f		yes	2017-03-01		yes	yes	NA	yes	yes
-PMCBM000BAB	Human	1994-04-03	m		yes	2017-05-11	2017-10-14	yes	NA	not applicable	yes	yes
+individual_id	taxonomy	birth_date	gender	death_date	ic_type	ic_given_date	ic_withdrawn_date	report_her_susc	report_inc_findings
+PMCBS000BCA	Human	1993-02-01	f		yes	2017-03-01		yes	yes
+PMCBM000BAB	Human	1994-04-03	m		yes	2017-05-11	2017-10-14	yes	yes
diff --git a/test_data/test_logic/config/ontology_config.json b/test_data/test_logic/config/ontology_config.json
@@ -39,19 +39,7 @@
               "concept_code": "Individual.ic_withdrawn_date"
             },
             {
-              "name": "04. Informed consent material",
-              "concept_code": "Individual.ic_material"
-            },
-            {
-              "name": "05. Informed consent data",
-              "concept_code": "Individual.ic_data"
-            },
-            {
-              "name": "06. Informed consent linking external database",
-              "concept_code": "Individual.ic_linking_ext"
-            },
-            {
-              "name": "07. Report hereditary susceptibility",
+              "name": "04. Report hereditary susceptibility",
               "concept_code": "Individual.report_her_susc"
             }
           ]
@@ -83,7 +71,7 @@
         },
         {
           "name": "05. Center of treatment",
-          "concept_code": "Diagnosis.center_treatment"
+          "concept_code": "Diagnosis.diagnosis_center"
         }
       ]
     },
diff --git a/test_data/test_logic/config/sources_config.json b/test_data/test_logic/config/sources_config.json
@@ -108,33 +108,6 @@
               "date_format": "%d/%m/%Y"
             }
           ]
-        },
-        {
-          "name": "ic_material",
-          "sources": [
-            {
-              "file": "studies/PMCST000AAA_individual.txt",
-              "column": "IFCMAT"
-            }
-          ]
-        },
-        {
-          "name": "ic_data",
-          "sources": [
-            {
-              "file": "studies/PMCST000AAA_individual.txt",
-              "column": "IFCGIV"
-            }
-          ]
-        },
-        {
-          "name": "ic_linking_ext",
-          "sources": [
-            {
-              "file": "studies/PMCST000AAA_individual.txt",
-              "column": "IFCCOM"
-            }
-          ]
         }
       ]
     },
@@ -196,7 +169,7 @@
           ]
         },
         {
-          "name": "center_treatment",
+          "name": "diagnosis_center",
           "sources": [
             {
               "file": "studies/PMCST000AAA_diagnosis.txt",

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-csr2transmart==0.0.26`
	`1`	`+csr2transmart==0.0.27`
`2`	`2`	`docutils==0.14`
`3`	`3`	`lockfile==0.12.2`
`4`	`4`	`luigi==2.8.0`
Original file line number	Diff line number	Diff line change
`@@ -39,19 +39,7 @@`
`39`	`39`	`"concept_code": "Individual.ic_withdrawn_date"`
`40`	`40`	`},`
`41`	`41`	`{`
`42`		`- "name": "04. Informed consent material",`
`43`		`- "concept_code": "Individual.ic_material"`
`44`		`- },`
`45`		`- {`
`46`		`- "name": "05. Informed consent data",`
`47`		`- "concept_code": "Individual.ic_data"`
`48`		`- },`
`49`		`- {`
`50`		`- "name": "06. Informed consent linking external database",`
`51`		`- "concept_code": "Individual.ic_linking_ext"`
`52`		`- },`
`53`		`- {`
`54`		`- "name": "07. Report hereditary susceptibility",`
	`42`	`+ "name": "04. Report hereditary susceptibility",`
`55`	`43`	`"concept_code": "Individual.report_her_susc"`
`56`	`44`	`}`
`57`	`45`	`]`
`@@ -83,7 +71,7 @@`
`83`	`71`	`},`
`84`	`72`	`{`
`85`	`73`	`"name": "05. Center of treatment",`
`86`		`- "concept_code": "Diagnosis.center_treatment"`
	`74`	`+ "concept_code": "Diagnosis.diagnosis_center"`
`87`	`75`	`}`
`88`	`76`	`]`
`89`	`77`	`},`