diff --git a/MIPMap Report.docx b/MIPMap Report.docx new file mode 100644 index 0000000..9496d2b Binary files /dev/null and b/MIPMap Report.docx differ diff --git a/MIPMap Report.pdf b/MIPMap Report.pdf deleted file mode 100644 index e651d99..0000000 Binary files a/MIPMap Report.pdf and /dev/null differ diff --git a/MIPMap Tutorial.pdf b/MIPMap Tutorial.docx similarity index 90% rename from MIPMap Tutorial.pdf rename to MIPMap Tutorial.docx index 9a7dd82..6aa0789 100644 Binary files a/MIPMap Tutorial.pdf and b/MIPMap Tutorial.docx differ diff --git a/MIPMap tests.zip b/MIPMap tests.zip deleted file mode 100755 index 29304d3..0000000 Binary files a/MIPMap tests.zip and /dev/null differ diff --git a/MIPMap tests/Datasets/DS1/hospitalExam.csv b/MIPMap tests/Datasets/DS1/hospitalExam.csv new file mode 100755 index 0000000..5e93e9b --- /dev/null +++ b/MIPMap tests/Datasets/DS1/hospitalExam.csv @@ -0,0 +1,27 @@ +patient_ipp,measurement_id,measurement_value,date +2561591,APOE4,0,19/6/2006 +763227,CDRSB,"9,7",29/11/2006 +1040371,MMSE,"24,8",21/6/2007 +286768,CDRSB,"0,2",10/12/2007 +1033854,APOE4,1,17/6/2008 +593656,MMSE,28,1/12/2008 +2619235,APOE4,1,18/1/2010 +166595,MOCA,24,10/1/2011 +629792,MMSE,26,17/1/2006 +163081,CDRSB,0,11/7/2006 +559677,APOE4,1,11/1/2007 +2742705,CDRSB,3,19/7/2007 +2877889,MOCA,26,8/1/2008 +678884,MOCA,28,7/7/2008 +2326096,APOE4,1,14/1/2009 +481145,MOCA,24,18/1/2011 +2684672,MMSE,28,21/7/2011 +448702,MOCA,24,9/1/2012 +2746803,APOE4,2,27/6/2012 +960386,MOCA,28,2/2/2006 +260428,APOE4,0,1/9/2006 +861093,MOCA,25,19/3/2007 +604704,MMSE,24,16/8/2007 +919019,CDRSB,3,4/1/2006 +910023,APOE4,1,7/7/2006 +2567891,MMSE,22,12/1/2007 \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS1/hospitalPatient.csv b/MIPMap tests/Datasets/DS1/hospitalPatient.csv new file mode 100755 index 0000000..90114aa --- /dev/null +++ b/MIPMap tests/Datasets/DS1/hospitalPatient.csv @@ -0,0 +1,25 @@ +patient_ipp,first_name,last_name,gender,date_of_birth +2561591,Peter,Quill,Male,25/3/1927 +2684672,Vincent,Nichols,Male,24/9/1982 +260428,Derrick,Matthews,Male,26/1/1977 +861093,Matilda,Webster,Female,30/6/1942 +604704,Effie,Evans,Female,14/9/1963 +163081,Charlotte,Bailey,Female,2/4/1957 +559677,George,Harrington,Male,26/6/1943 +2742705,Esther,Silva,Female,20/11/1967 +629792,Rebecca,Barrett,Female,28/3/1965 +418877,Roger,Bryan,Male,21/8/1928 +2326096,Mary,Nunez,Female,27/6/1929 +481145,Susan,Wagner,Female,16/5/1924 +2877889,John,Mann,Male,19/9/1973 +763227,Rosetta,Schultz,Female,26/8/1992 +1040371,Edward,Webster,Male,16/3/1939 +286768,Leon,Newman,Male,31/3/1962 +1033854,Bertha,Yates,Female,18/3/1963 +448702,Trevor,Sandoval,Male,9/12/1946 +2746803,Isabelle,Pierce,Female,3/7/1953 +960386,Matthew,Delgado,Male,15/11/1921 +593656,Emily,Logan,Female,24/4/1938 +2619235,Amy,Morgan,Female,8/12/1976 +166595,Florence,Cook,Female,16/2/1943 +919019,Gordon,Leonard,Male,13/10/1982 \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS1/hospitalToPatient.xml b/MIPMap tests/Datasets/DS1/hospitalToPatient.xml new file mode 100755 index 0000000..40db552 --- /dev/null +++ b/MIPMap tests/Datasets/DS1/hospitalToPatient.xml @@ -0,0 +1,64 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + hospitalSchema + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + CSV + + patientSchema + + + patient_exams.csv + + + + + + + + + + + + + + diff --git a/MIPMap tests/Datasets/DS1/patient_exams.csv b/MIPMap tests/Datasets/DS1/patient_exams.csv new file mode 100755 index 0000000..5e429e1 --- /dev/null +++ b/MIPMap tests/Datasets/DS1/patient_exams.csv @@ -0,0 +1,88 @@ +id,pid,viscode,examdate,Measurement,Value +"10","3","bl","12/9/2005","APOE4","1" +"10","3","bl","12/9/2005","CDRSB","4,5" +"10","3","bl","12/9/2005","MMSE","20" +"11","3","m06","13/3/2006","APOE4","1" +"11","3","m06","13/3/2006","CDRSB","6" +"11","3","m06","13/3/2006","MMSE","24" +"12","3","m12","12/9/2006","APOE4","1" +"12","3","m12","12/9/2006","CDRSB","3,5" +"12","3","m12","12/9/2006","MMSE","17" +"13","3","m18","12/3/2007","APOE4","1" +"13","3","m18","12/3/2007","CDRSB","NA" +"13","3","m18","12/3/2007","MMSE","NA" +"14","3","m24","12/9/2007","APOE4","1" +"14","3","m24","12/9/2007","CDRSB","8" +"14","3","m24","12/9/2007","MMSE","19" +"21","5","bl","7/9/2005","APOE4","0" +"21","5","bl","7/9/2005","CDRSB","0" +"21","5","bl","7/9/2005","MMSE","29" +"22","5","m06","9/3/2006","APOE4","0" +"22","5","m06","9/3/2006","CDRSB","0" +"22","5","m06","9/3/2006","MMSE","29" +"23","5","m12","5/9/2006","APOE4","0" +"23","5","m12","5/9/2006","CDRSB","1,5" +"23","5","m12","5/9/2006","MMSE","30" +"24","5","m18","9/3/2007","APOE4","0" +"24","5","m18","9/3/2007","CDRSB","NA" +"24","5","m18","9/3/2007","MMSE","NA" +"25","5","m24","7/9/2007","APOE4","0" +"25","5","m24","7/9/2007","CDRSB","0" +"25","5","m24","7/9/2007","MMSE","29" +"26","5","m30","2/5/2008","APOE4","0" +"26","5","m30","2/5/2008","CDRSB","NA" +"26","5","m30","2/5/2008","MMSE","NA" +"27","5","m36","10/9/2008","APOE4","0" +"27","5","m36","10/9/2008","CDRSB","1" +"27","5","m36","10/9/2008","MMSE","30" +"51","10","bl","10/11/2005","APOE4","1" +"51","10","bl","10/11/2005","CDRSB","5" +"51","10","bl","10/11/2005","MMSE","24" +"52","10","m06","9/5/2006","APOE4","1" +"52","10","m06","9/5/2006","CDRSB","2,5" +"52","10","m06","9/5/2006","MMSE","26" +"53","10","m12","9/11/2006","APOE4","1" +"53","10","m12","9/11/2006","CDRSB","4" +"53","10","m12","9/11/2006","MMSE","25" +"54","10","m18","10/5/2007","APOE4","1" +"54","10","m18","10/5/2007","CDRSB","NA" +"54","10","m18","10/5/2007","MMSE","NA" +"55","10","m24","7/11/2007","APOE4","1" +"55","10","m24","7/11/2007","CDRSB","5" +"55","10","m24","7/11/2007","MMSE","28" +"62","15","bl","18/10/2005","APOE4","1" +"62","15","bl","18/10/2005","CDRSB","0" +"62","15","bl","18/10/2005","MMSE","29" +"63","15","m06","18/4/2006","APOE4","1" +"63","15","m06","18/4/2006","CDRSB","0" +"63","15","m06","18/4/2006","MMSE","30" +"64","15","m12","13/10/2006","APOE4","1" +"64","15","m12","13/10/2006","CDRSB","0" +"64","15","m12","13/10/2006","MMSE","27" +"65","15","m18","10/4/2007","APOE4","1" +"65","15","m18","10/4/2007","CDRSB","NA" +"65","15","m18","10/4/2007","MMSE","NA" +"66","15","m24","11/10/2007","APOE4","1" +"66","15","m24","11/10/2007","CDRSB","0" +"66","15","m24","11/10/2007","MMSE","29" +"67","15","m30","7/4/2008","APOE4","1" +"67","15","m30","7/4/2008","CDRSB","NA" +"67","15","m30","7/4/2008","MMSE","NA" +"68","15","m36","28/10/2008","APOE4","1" +"68","15","m36","28/10/2008","CDRSB","0" +"68","15","m36","28/10/2008","MMSE","30" +"69","15","m72","3/11/2011","APOE4","1" +"69","15","m72","3/11/2011","CDRSB","1" +"69","15","m72","3/11/2011","MMSE","29" +"70","15","m78","10/4/2012","APOE4","1" +"70","15","m78","10/4/2012","CDRSB","NA" +"70","15","m78","10/4/2012","MMSE","NA" +"71","16","bl","13/10/2005","APOE4","1" +"71","16","bl","13/10/2005","CDRSB","0" +"71","16","bl","13/10/2005","MMSE","28" +"72","16","m06","12/4/2006","APOE4","1" +"72","16","m06","12/4/2006","CDRSB","0" +"72","16","m06","12/4/2006","MMSE","29" +"73","16","m12","11/10/2006","APOE4","1" +"73","16","m12","11/10/2006","CDRSB","0" +"73","16","m12","11/10/2006","MMSE","30" diff --git a/MIPMap tests/Datasets/DS2/hospitalExam.csv b/MIPMap tests/Datasets/DS2/hospitalExam.csv new file mode 100755 index 0000000..5e93e9b --- /dev/null +++ b/MIPMap tests/Datasets/DS2/hospitalExam.csv @@ -0,0 +1,27 @@ +patient_ipp,measurement_id,measurement_value,date +2561591,APOE4,0,19/6/2006 +763227,CDRSB,"9,7",29/11/2006 +1040371,MMSE,"24,8",21/6/2007 +286768,CDRSB,"0,2",10/12/2007 +1033854,APOE4,1,17/6/2008 +593656,MMSE,28,1/12/2008 +2619235,APOE4,1,18/1/2010 +166595,MOCA,24,10/1/2011 +629792,MMSE,26,17/1/2006 +163081,CDRSB,0,11/7/2006 +559677,APOE4,1,11/1/2007 +2742705,CDRSB,3,19/7/2007 +2877889,MOCA,26,8/1/2008 +678884,MOCA,28,7/7/2008 +2326096,APOE4,1,14/1/2009 +481145,MOCA,24,18/1/2011 +2684672,MMSE,28,21/7/2011 +448702,MOCA,24,9/1/2012 +2746803,APOE4,2,27/6/2012 +960386,MOCA,28,2/2/2006 +260428,APOE4,0,1/9/2006 +861093,MOCA,25,19/3/2007 +604704,MMSE,24,16/8/2007 +919019,CDRSB,3,4/1/2006 +910023,APOE4,1,7/7/2006 +2567891,MMSE,22,12/1/2007 \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS2/hospitalPatient.csv b/MIPMap tests/Datasets/DS2/hospitalPatient.csv new file mode 100755 index 0000000..3602ff5 --- /dev/null +++ b/MIPMap tests/Datasets/DS2/hospitalPatient.csv @@ -0,0 +1,25 @@ +patient_ipp;first_name;last_name;gender;date_of_birth +2561591;Peter;Quill;Male;25/3/1927 +2684672;Vincent;Nichols;Male;24/9/1982 +260428;Derrick;Matthews;Male;26/1/1977 +861093;Matilda;Webster;Female;30/6/1942 +604704;Effie;Evans;Female;14/9/1963 +163081;Charlotte;Bailey;Female;2/4/1957 +559677;George;Harrington;Male;26/6/1943 +2742705;Esther;Silva;Female;20/11/1967 +629792;Rebecca;Barrett;Female;28/3/1965 +418877;Roger;Bryan;Male;21/8/1928 +2326096;Mary;Nunez;Female;27/6/1929 +481145;Susan;Wagner;Female;16/5/1924 +2877889;John;Mann;Male;19/9/1973 +763227;Rosetta;Schultz;Female;26/8/1992 +1040371;Edward;Webster;Male;16/3/1939 +286768;Leon;Newman;Male;31/3/1962 +1033854;Bertha;Yates;Female;18/3/1963 +448702;Trevor;Sandoval;Male;9/12/1946 +2746803;Isabelle;Pierce;Female;3/7/1953 +960386;Matthew;Delgado;Male;15/11/1921 +593656;Emily;Logan;Female;24/4/1938 +2619235;Amy;Morgan;Female;8/12/1976 +166595;Florence;Cook;Female;16/2/1943 +919019;Gordon;Leonard;Male;13/10/1982 \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS2/hospitalToPatient.xml b/MIPMap tests/Datasets/DS2/hospitalToPatient.xml new file mode 100755 index 0000000..40db552 --- /dev/null +++ b/MIPMap tests/Datasets/DS2/hospitalToPatient.xml @@ -0,0 +1,64 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + hospitalSchema + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + CSV + + patientSchema + + + patient_exams.csv + + + + + + + + + + + + + + diff --git a/MIPMap tests/Datasets/DS2/patient_exams.csv b/MIPMap tests/Datasets/DS2/patient_exams.csv new file mode 100755 index 0000000..5e429e1 --- /dev/null +++ b/MIPMap tests/Datasets/DS2/patient_exams.csv @@ -0,0 +1,88 @@ +id,pid,viscode,examdate,Measurement,Value +"10","3","bl","12/9/2005","APOE4","1" +"10","3","bl","12/9/2005","CDRSB","4,5" +"10","3","bl","12/9/2005","MMSE","20" +"11","3","m06","13/3/2006","APOE4","1" +"11","3","m06","13/3/2006","CDRSB","6" +"11","3","m06","13/3/2006","MMSE","24" +"12","3","m12","12/9/2006","APOE4","1" +"12","3","m12","12/9/2006","CDRSB","3,5" +"12","3","m12","12/9/2006","MMSE","17" +"13","3","m18","12/3/2007","APOE4","1" +"13","3","m18","12/3/2007","CDRSB","NA" +"13","3","m18","12/3/2007","MMSE","NA" +"14","3","m24","12/9/2007","APOE4","1" +"14","3","m24","12/9/2007","CDRSB","8" +"14","3","m24","12/9/2007","MMSE","19" +"21","5","bl","7/9/2005","APOE4","0" +"21","5","bl","7/9/2005","CDRSB","0" +"21","5","bl","7/9/2005","MMSE","29" +"22","5","m06","9/3/2006","APOE4","0" +"22","5","m06","9/3/2006","CDRSB","0" +"22","5","m06","9/3/2006","MMSE","29" +"23","5","m12","5/9/2006","APOE4","0" +"23","5","m12","5/9/2006","CDRSB","1,5" +"23","5","m12","5/9/2006","MMSE","30" +"24","5","m18","9/3/2007","APOE4","0" +"24","5","m18","9/3/2007","CDRSB","NA" +"24","5","m18","9/3/2007","MMSE","NA" +"25","5","m24","7/9/2007","APOE4","0" +"25","5","m24","7/9/2007","CDRSB","0" +"25","5","m24","7/9/2007","MMSE","29" +"26","5","m30","2/5/2008","APOE4","0" +"26","5","m30","2/5/2008","CDRSB","NA" +"26","5","m30","2/5/2008","MMSE","NA" +"27","5","m36","10/9/2008","APOE4","0" +"27","5","m36","10/9/2008","CDRSB","1" +"27","5","m36","10/9/2008","MMSE","30" +"51","10","bl","10/11/2005","APOE4","1" +"51","10","bl","10/11/2005","CDRSB","5" +"51","10","bl","10/11/2005","MMSE","24" +"52","10","m06","9/5/2006","APOE4","1" +"52","10","m06","9/5/2006","CDRSB","2,5" +"52","10","m06","9/5/2006","MMSE","26" +"53","10","m12","9/11/2006","APOE4","1" +"53","10","m12","9/11/2006","CDRSB","4" +"53","10","m12","9/11/2006","MMSE","25" +"54","10","m18","10/5/2007","APOE4","1" +"54","10","m18","10/5/2007","CDRSB","NA" +"54","10","m18","10/5/2007","MMSE","NA" +"55","10","m24","7/11/2007","APOE4","1" +"55","10","m24","7/11/2007","CDRSB","5" +"55","10","m24","7/11/2007","MMSE","28" +"62","15","bl","18/10/2005","APOE4","1" +"62","15","bl","18/10/2005","CDRSB","0" +"62","15","bl","18/10/2005","MMSE","29" +"63","15","m06","18/4/2006","APOE4","1" +"63","15","m06","18/4/2006","CDRSB","0" +"63","15","m06","18/4/2006","MMSE","30" +"64","15","m12","13/10/2006","APOE4","1" +"64","15","m12","13/10/2006","CDRSB","0" +"64","15","m12","13/10/2006","MMSE","27" +"65","15","m18","10/4/2007","APOE4","1" +"65","15","m18","10/4/2007","CDRSB","NA" +"65","15","m18","10/4/2007","MMSE","NA" +"66","15","m24","11/10/2007","APOE4","1" +"66","15","m24","11/10/2007","CDRSB","0" +"66","15","m24","11/10/2007","MMSE","29" +"67","15","m30","7/4/2008","APOE4","1" +"67","15","m30","7/4/2008","CDRSB","NA" +"67","15","m30","7/4/2008","MMSE","NA" +"68","15","m36","28/10/2008","APOE4","1" +"68","15","m36","28/10/2008","CDRSB","0" +"68","15","m36","28/10/2008","MMSE","30" +"69","15","m72","3/11/2011","APOE4","1" +"69","15","m72","3/11/2011","CDRSB","1" +"69","15","m72","3/11/2011","MMSE","29" +"70","15","m78","10/4/2012","APOE4","1" +"70","15","m78","10/4/2012","CDRSB","NA" +"70","15","m78","10/4/2012","MMSE","NA" +"71","16","bl","13/10/2005","APOE4","1" +"71","16","bl","13/10/2005","CDRSB","0" +"71","16","bl","13/10/2005","MMSE","28" +"72","16","m06","12/4/2006","APOE4","1" +"72","16","m06","12/4/2006","CDRSB","0" +"72","16","m06","12/4/2006","MMSE","29" +"73","16","m12","11/10/2006","APOE4","1" +"73","16","m12","11/10/2006","CDRSB","0" +"73","16","m12","11/10/2006","MMSE","30" diff --git a/MIPMap tests/Datasets/DS3/MIPMap_demo.sql b/MIPMap tests/Datasets/DS3/MIPMap_demo.sql new file mode 100755 index 0000000..51210ea --- /dev/null +++ b/MIPMap tests/Datasets/DS3/MIPMap_demo.sql @@ -0,0 +1,78 @@ +CREATE DATABASE "MIPMap_demo" + WITH OWNER = postgres + ENCODING = 'UTF8' + TABLESPACE = pg_default + LC_COLLATE = 'Greek_Greece.1253' + LC_CTYPE = 'Greek_Greece.1253' + CONNECTION LIMIT = -1; + + -- Table: exam_measurement + +-- DROP TABLE exam_measurement; + +CREATE TABLE exam_measurement +( + id character varying(16) NOT NULL, + lab_id character varying(16), + variable_name character varying(32), + loinc_num character varying(10), + description character varying(512), + record_creation timestamp without time zone DEFAULT now(), + CONSTRAINT exam_measurement_pkey PRIMARY KEY (id) +) +WITH ( + OIDS=FALSE +); +ALTER TABLE exam_measurement + OWNER TO postgres; + + -- Table: patient + +-- DROP TABLE patient; + +CREATE TABLE patient +( + id character varying(32) NOT NULL, + year_of_birth integer, + gender character varying(16), + city character varying(32), + extracted_from character varying(32), + extraction_method character varying(32), + description character varying(512), + record_creation timestamp without time zone DEFAULT now(), + CONSTRAINT patient_pkey PRIMARY KEY (id) +) +WITH ( + OIDS=FALSE +); +ALTER TABLE patient + OWNER TO postgres; + + -- Table: exam_value + +-- DROP TABLE exam_value; + +CREATE TABLE exam_value +( + patient_id character varying(32), + exam_measurement_id character varying(16), + value character varying(32), + variable_name character varying(32), + status character varying(32), + exam_date date, + extracted_from character varying(32), + extraction_method character varying(32), + description character varying(512), + record_creation timestamp without time zone DEFAULT now(), + CONSTRAINT exam_value_exam_measurement_id_fkey FOREIGN KEY (exam_measurement_id) + REFERENCES exam_measurement (id) MATCH SIMPLE + ON UPDATE NO ACTION ON DELETE NO ACTION, + CONSTRAINT exam_value_patient_id_fkey FOREIGN KEY (patient_id) + REFERENCES patient (id) MATCH SIMPLE + ON UPDATE NO ACTION ON DELETE NO ACTION +) +WITH ( + OIDS=FALSE +); +ALTER TABLE exam_value + OWNER TO postgres; diff --git a/MIPMap tests/Datasets/DS3/mipmap_test.sql b/MIPMap tests/Datasets/DS3/mipmap_test.sql new file mode 100755 index 0000000..93fcb3f --- /dev/null +++ b/MIPMap tests/Datasets/DS3/mipmap_test.sql @@ -0,0 +1,52 @@ +create database mipmap_test; + +use mipmap_test; + +CREATE TABLE `patients` ( + `idpatients` int(11) NOT NULL, + `name` varchar(45) DEFAULT NULL, + `gender` varchar(45) DEFAULT NULL, + PRIMARY KEY (`idpatients`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8; + +CREATE TABLE `exams` ( + `idexams` int(11) NOT NULL, + `patient` int(11) DEFAULT NULL, + `exam_measurement` varchar(45) DEFAULT NULL, + `exam_value` varchar(45) DEFAULT NULL, + `exam_date` date DEFAULT NULL, + PRIMARY KEY (`idexams`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8 + +insert into patients values (2561591,"Peter Quill", "Male"), +(2684672,"Vincent Nichols","Male"), +(260428,"Derrick Matthews","Male"), +(861093,"Matilda Webster","Female"), +(604704,"Effie Evans","Female"), +(163081,"Charlotte Bailey","Female"), +(559677,"George Harrington","Male"), +(2742705,"Esther Silva","Female"), +(629792,"Rebecca Barrett","Female"), +(418877,"Roger Bryan","Male"), +(2326096,"Mary Nunez","Female"), +(481145,"Susan Wagner","Female"), +(2877889,"John Mann","Male"), +(763227,"Rosetta Schultz","Female"), +(1040371,"Edward Webster","Male"), +(286768,"Leon Newman","Male"), +(1033854,"Bertha Yates","Female"), +(448702,"Trevor Sandoval","Male"), +(2746803,"Isabelle Pierce","Female"), +(960386,"Matthew Delgado","Male"), +(593656,"Emily Logan","Female"), +(2619235,"Amy Morgan","Female"), +(166595,"Florence Cook","Female"), +(919019,"Gordon Leonard","Male"); + +insert into exams values (2,629792,"CDRSB",3,"2010-03-25"), +(3,2746803,"MOCA",28,"2010-03-25"), +(4,559677,"CDRSB",3,"2010-03-26"), +(5,2561591,"APOE4",1,"2010-03-26"), +(6,1033854,"MOCA",28,"2010-03-28"), +(7,593656,"APOE4",0,"2010-03-29"), +(8,2561591,"CDRSB",3,"2010-04-02"); diff --git a/MIPMap tests/Datasets/DS4/MIP_Database.sql b/MIPMap tests/Datasets/DS4/MIP_Database.sql new file mode 100755 index 0000000..7140d46 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/MIP_Database.sql @@ -0,0 +1,39 @@ +-- Table: patient +-- DROP TABLE patient; + +CREATE TABLE patient +( + id text NOT NULL, + name text, + year_of_birth integer, + gender text, + extraction_method text, + record_creation timestamp without time zone, + CONSTRAINT patient_pkey PRIMARY KEY (id) +) +WITH ( + OIDS=FALSE +); +ALTER TABLE patient + OWNER TO postgres; + +-- Table: exam_value +-- DROP TABLE exam_value; + +CREATE TABLE exam_value +( + patient_id text, + measurement_id text, + value text, + exam_date date, + extraction_method text, + extracted_from text, + CONSTRAINT exam_value_patient_id_fkey FOREIGN KEY (patient_id) + REFERENCES patient (id) MATCH SIMPLE + ON UPDATE NO ACTION ON DELETE NO ACTION +) +WITH ( + OIDS=FALSE +); +ALTER TABLE exam_value + OWNER TO postgres; \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS4/hospitalExam.csv b/MIPMap tests/Datasets/DS4/hospitalExam.csv new file mode 100755 index 0000000..03d10c8 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/hospitalExam.csv @@ -0,0 +1,27 @@ +patient_ipp,measurement_id,measurement_value,date +2561591,APOE4,0,19/6/2006 +763227,CDRSB,9,29/11/2006 +1040371,MMSE,24,21/6/2007 +286768,CDRSB,0,10/12/2007 +1033854,APOE4,1,17/6/2008 +593656,MMSE,28,1/12/2008 +2619235,APOE4,1,18/1/2010 +166595,MOCA,24,10/1/2011 +629792,MMSE,26,17/1/2006 +163081,CDRSB,0,11/7/2006 +559677,APOE4,1,11/1/2007 +2742705,CDRSB,3,19/7/2007 +2877889,MOCA,26,8/1/2008 +678884,MOCA,28,7/7/2008 +2326096,APOE4,1,14/1/2009 +481145,MOCA,24,18/1/2011 +2684672,MMSE,28,21/7/2011 +448702,MOCA,24,9/1/2012 +2746803,APOE4,2,27/6/2012 +960386,MOCA,28,2/2/2006 +260428,APOE4,0,1/9/2006 +861093,MOCA,25,19/3/2007 +604704,MMSE,24,16/8/2007 +919019,CDRSB,3,4/1/2006 +910023,APOE4,1,7/7/2006 +2567891,MMSE,22,12/1/2007 \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS4/hospitalPatient.csv b/MIPMap tests/Datasets/DS4/hospitalPatient.csv new file mode 100755 index 0000000..90114aa --- /dev/null +++ b/MIPMap tests/Datasets/DS4/hospitalPatient.csv @@ -0,0 +1,25 @@ +patient_ipp,first_name,last_name,gender,date_of_birth +2561591,Peter,Quill,Male,25/3/1927 +2684672,Vincent,Nichols,Male,24/9/1982 +260428,Derrick,Matthews,Male,26/1/1977 +861093,Matilda,Webster,Female,30/6/1942 +604704,Effie,Evans,Female,14/9/1963 +163081,Charlotte,Bailey,Female,2/4/1957 +559677,George,Harrington,Male,26/6/1943 +2742705,Esther,Silva,Female,20/11/1967 +629792,Rebecca,Barrett,Female,28/3/1965 +418877,Roger,Bryan,Male,21/8/1928 +2326096,Mary,Nunez,Female,27/6/1929 +481145,Susan,Wagner,Female,16/5/1924 +2877889,John,Mann,Male,19/9/1973 +763227,Rosetta,Schultz,Female,26/8/1992 +1040371,Edward,Webster,Male,16/3/1939 +286768,Leon,Newman,Male,31/3/1962 +1033854,Bertha,Yates,Female,18/3/1963 +448702,Trevor,Sandoval,Male,9/12/1946 +2746803,Isabelle,Pierce,Female,3/7/1953 +960386,Matthew,Delgado,Male,15/11/1921 +593656,Emily,Logan,Female,24/4/1938 +2619235,Amy,Morgan,Female,8/12/1976 +166595,Florence,Cook,Female,16/2/1943 +919019,Gordon,Leonard,Male,13/10/1982 \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS4/mapping_task_1.xml b/MIPMap tests/Datasets/DS4/mapping_task_1.xml new file mode 100755 index 0000000..90114ed --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_1.xml @@ -0,0 +1,90 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_10.xml b/MIPMap tests/Datasets/DS4/mapping_task_10.xml new file mode 100755 index 0000000..05cdbd5 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_10.xml @@ -0,0 +1,107 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_11.xml b/MIPMap tests/Datasets/DS4/mapping_task_11.xml new file mode 100755 index 0000000..5b9a65f --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_11.xml @@ -0,0 +1,97 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_12.xml b/MIPMap tests/Datasets/DS4/mapping_task_12.xml new file mode 100755 index 0000000..522695d --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_12.xml @@ -0,0 +1,115 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + + MIP_Database.exam_value.exam_valueTuple.measurement_id + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + + MIP_Database.exam_value.exam_valueTuple.value + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_13.xml b/MIPMap tests/Datasets/DS4/mapping_task_13.xml new file mode 100755 index 0000000..9f72cbc --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_13.xml @@ -0,0 +1,115 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + true + true + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + + MIP_Database.exam_value.exam_valueTuple.measurement_id + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + + MIP_Database.exam_value.exam_valueTuple.value + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_14.xml b/MIPMap tests/Datasets/DS4/mapping_task_14.xml new file mode 100755 index 0000000..ab5e6ce --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_14.xml @@ -0,0 +1,115 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + true + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + + MIP_Database.exam_value.exam_valueTuple.measurement_id + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + + MIP_Database.exam_value.exam_valueTuple.value + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_15.xml b/MIPMap tests/Datasets/DS4/mapping_task_15.xml new file mode 100755 index 0000000..1bcb488 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_15.xml @@ -0,0 +1,245 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + Hospitals_Data.patient_exams + (Hospitals_Data.patient_exams.patient_examsTuple.viscode == "bl") + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + true + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + MIP_Database.exam_value + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + + MIP_Database.exam_value_1_.exam_valueTuple.measurement_id + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + + MIP_Database.exam_value_1_.exam_valueTuple.value + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.date + + MIP_Database.exam_value_1_.exam_valueTuple.exam_date + Hospitals_Data.hospitalExam.hospitalExamTuple.date + 1.0 + + + + "Hospital A" + MIP_Database.exam_value.exam_valueTuple.extracted_from + "Hospital A" + 1.0 + + + + "Hospital B" + MIP_Database.exam_value_1_.exam_valueTuple.extracted_from + "Hospital B" + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + + MIP_Database.exam_value_1_.exam_valueTuple.patient_id + append("hospitalB_", Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp) + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.pid + + MIP_Database.exam_value.exam_valueTuple.patient_id + append("hospitalA_", Hospitals_Data.patient_exams.patient_examsTuple.pid) + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.examdate + + MIP_Database.exam_value.exam_valueTuple.exam_date + Hospitals_Data.patient_exams.patient_examsTuple.examdate + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.Measurement + + MIP_Database.exam_value.exam_valueTuple.measurement_id + Hospitals_Data.patient_exams.patient_examsTuple.Measurement + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.Value + + MIP_Database.exam_value.exam_valueTuple.value + Hospitals_Data.patient_exams.patient_examsTuple.Value + 1.0 + + + + "MIPMap" + MIP_Database.exam_value.exam_valueTuple.extraction_method + "MIPMap" + 1.0 + + + + "MIPMap" + MIP_Database.patient.patientTuple.extraction_method + "MIPMap" + 1.0 + + + + "MIPMap" + MIP_Database.exam_value_1_.exam_valueTuple.extraction_method + "MIPMap" + 1.0 + + + + datetime() + MIP_Database.patient.patientTuple.record_creation + datetime() + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.pid + + MIP_Database.patient.patientTuple.id + append("hospitalA_", Hospitals_Data.patient_exams.patient_examsTuple.pid) + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.gender + + MIP_Database.patient.patientTuple.gender + Hospitals_Data.hospitalPatient.hospitalPatientTuple.gender + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + MIP_Database.patient.patientTuple.id + append("hospitalB_", Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp) + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.first_name + Hospitals_Data.hospitalPatient.hospitalPatientTuple.last_name + + MIP_Database.patient.patientTuple.name + append(Hospitals_Data.hospitalPatient.hospitalPatientTuple.first_name, append(" ", Hospitals_Data.hospitalPatient.hospitalPatientTuple.last_name)) + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.date_of_birth + + MIP_Database.patient.patientTuple.year_of_birth + substring(Hospitals_Data.hospitalPatient.hospitalPatientTuple.date_of_birth, (len(Hospitals_Data.hospitalPatient.hospitalPatientTuple.date_of_birth) - 4)) + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_16.xml b/MIPMap tests/Datasets/DS4/mapping_task_16.xml new file mode 100755 index 0000000..857bd6a --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_16.xml @@ -0,0 +1,151 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + MIP_Database.exam_value + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + + MIP_Database.exam_value_1_.exam_valueTuple.measurement_id + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + + MIP_Database.exam_value_1_.exam_valueTuple.value + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.date + + MIP_Database.exam_value_1_.exam_valueTuple.exam_date + Hospitals_Data.hospitalExam.hospitalExamTuple.date + 1.0 + + + + "Hospital A" + MIP_Database.exam_value.exam_valueTuple.extracted_from + "Hospital A" + 1.0 + + + + "Hospital B" + MIP_Database.exam_value_1_.exam_valueTuple.extracted_from + "Hospital B" + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + + MIP_Database.exam_value_1_.exam_valueTuple.patient_id + append("hospitalB_", Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp) + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.pid + + MIP_Database.exam_value.exam_valueTuple.patient_id + append("hospitalA_", Hospitals_Data.patient_exams.patient_examsTuple.pid) + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.examdate + + MIP_Database.exam_value.exam_valueTuple.exam_date + Hospitals_Data.patient_exams.patient_examsTuple.examdate + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.Measurement + + MIP_Database.exam_value.exam_valueTuple.measurement_id + Hospitals_Data.patient_exams.patient_examsTuple.Measurement + 1.0 + + + + Hospitals_Data.patient_exams.patient_examsTuple.Value + + MIP_Database.exam_value.exam_valueTuple.value + Hospitals_Data.patient_exams.patient_examsTuple.Value + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_17.xml b/MIPMap tests/Datasets/DS4/mapping_task_17.xml new file mode 100755 index 0000000..9e9c287 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_17.xml @@ -0,0 +1,105 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + false + true + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + + MIP_Database.exam_value.exam_valueTuple.measurement_id + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + + MIP_Database.exam_value.exam_valueTuple.value + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.gender + + MIP_Database.patient.patientTuple.gender + Hospitals_Data.hospitalPatient.hospitalPatientTuple.gender + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_18.xml b/MIPMap tests/Datasets/DS4/mapping_task_18.xml new file mode 100755 index 0000000..33d1aff --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_18.xml @@ -0,0 +1,107 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.date_of_birth + + MIP_Database.patient.patientTuple.year_of_birth + Hospitals_Data.hospitalPatient.hospitalPatientTuple.date_of_birth + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + MIP_Database.patient.patientTuple.id + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_19.xml b/MIPMap tests/Datasets/DS4/mapping_task_19.xml new file mode 100755 index 0000000..279f4b6 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_19.xml @@ -0,0 +1,108 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.gender + + MIP_Database.patient.patientTuple.gender + Hospitals_Data.hospitalPatient.hospitalPatientTuple.gender + 1.0 + + + + Hospitals_Data.hospitalPatient.hospitalPatientTuple.first_name + Hospitals_Data.hospitalPatient.hospitalPatientTuple.last_name + + MIP_Database.patient.patientTuple.name + append(Hospitals_Data.hospitalPatient.hospitalPatientTuple.first_name, append(" ", Hospitals_Data.hospitalPatient.hospitalPatientTuple.last_name)) + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_2.xml b/MIPMap tests/Datasets/DS4/mapping_task_2.xml new file mode 100755 index 0000000..ed29856 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_2.xml @@ -0,0 +1,99 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_3.xml b/MIPMap tests/Datasets/DS4/mapping_task_3.xml new file mode 100755 index 0000000..c12af4d --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_3.xml @@ -0,0 +1,106 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + 1.0 + + + + "MIPMap" + MIP_Database.exam_value.exam_valueTuple.extraction_method + "MIPMap" + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_4.xml b/MIPMap tests/Datasets/DS4/mapping_task_4.xml new file mode 100755 index 0000000..1bd561e --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_4.xml @@ -0,0 +1,113 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + 1.0 + + + + "MIPMap" + MIP_Database.exam_value.exam_valueTuple.extraction_method + "MIPMap" + 1.0 + + + + date() + MIP_Database.exam_value.exam_valueTuple.exam_date + date() + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_5.xml b/MIPMap tests/Datasets/DS4/mapping_task_5.xml new file mode 100755 index 0000000..90181a0 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_5.xml @@ -0,0 +1,98 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + "MIPMap" + MIP_Database.exam_value.exam_valueTuple.extraction_method + "MIPMap" + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_6.xml b/MIPMap tests/Datasets/DS4/mapping_task_6.xml new file mode 100755 index 0000000..b8c7a3b --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_6.xml @@ -0,0 +1,99 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + + MIP_Database.exam_value.exam_valueTuple.patient_id + append("HospitalB_", Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp) + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_7.xml b/MIPMap tests/Datasets/DS4/mapping_task_7.xml new file mode 100755 index 0000000..5d4c93a --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_7.xml @@ -0,0 +1,100 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.first_name + + MIP_Database.exam_value.exam_valueTuple.patient_id + append(append("HospitalB_", Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp), Hospitals_Data.hospitalPatient.hospitalPatientTuple.first_name) + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_8.xml b/MIPMap tests/Datasets/DS4/mapping_task_8.xml new file mode 100755 index 0000000..66fd3c2 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_8.xml @@ -0,0 +1,90 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.first_name + + MIP_Database.exam_value.exam_valueTuple.patient_id + append(append("HospitalB_", Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp), Hospitals_Data.hospitalPatient.hospitalPatientTuple.first_name) + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/mapping_task_9.xml b/MIPMap tests/Datasets/DS4/mapping_task_9.xml new file mode 100755 index 0000000..296a0c1 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/mapping_task_9.xml @@ -0,0 +1,107 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospitals_Data + + + hospitalExam.csv + + + hospitalExam.csv + true + + + + + patient_exams.csv + + + patient_exams.csv + true + + + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + + + + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.patient_ipp + Hospitals_Data.hospitalPatient.hospitalPatientTuple.patient_ipp + + false + false + false + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + MIP_Database.exam_value.exam_valueTuple.patient_id + MIP_Database.patient.patientTuple.id + + true + false + false + + + + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + + MIP_Database.exam_value.exam_valueTuple.measurement_id + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_id + 1.0 + + + + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + + MIP_Database.exam_value.exam_valueTuple.measurement_id + Hospitals_Data.hospitalExam.hospitalExamTuple.measurement_value + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS4/patient_exams.csv b/MIPMap tests/Datasets/DS4/patient_exams.csv new file mode 100755 index 0000000..5e429e1 --- /dev/null +++ b/MIPMap tests/Datasets/DS4/patient_exams.csv @@ -0,0 +1,88 @@ +id,pid,viscode,examdate,Measurement,Value +"10","3","bl","12/9/2005","APOE4","1" +"10","3","bl","12/9/2005","CDRSB","4,5" +"10","3","bl","12/9/2005","MMSE","20" +"11","3","m06","13/3/2006","APOE4","1" +"11","3","m06","13/3/2006","CDRSB","6" +"11","3","m06","13/3/2006","MMSE","24" +"12","3","m12","12/9/2006","APOE4","1" +"12","3","m12","12/9/2006","CDRSB","3,5" +"12","3","m12","12/9/2006","MMSE","17" +"13","3","m18","12/3/2007","APOE4","1" +"13","3","m18","12/3/2007","CDRSB","NA" +"13","3","m18","12/3/2007","MMSE","NA" +"14","3","m24","12/9/2007","APOE4","1" +"14","3","m24","12/9/2007","CDRSB","8" +"14","3","m24","12/9/2007","MMSE","19" +"21","5","bl","7/9/2005","APOE4","0" +"21","5","bl","7/9/2005","CDRSB","0" +"21","5","bl","7/9/2005","MMSE","29" +"22","5","m06","9/3/2006","APOE4","0" +"22","5","m06","9/3/2006","CDRSB","0" +"22","5","m06","9/3/2006","MMSE","29" +"23","5","m12","5/9/2006","APOE4","0" +"23","5","m12","5/9/2006","CDRSB","1,5" +"23","5","m12","5/9/2006","MMSE","30" +"24","5","m18","9/3/2007","APOE4","0" +"24","5","m18","9/3/2007","CDRSB","NA" +"24","5","m18","9/3/2007","MMSE","NA" +"25","5","m24","7/9/2007","APOE4","0" +"25","5","m24","7/9/2007","CDRSB","0" +"25","5","m24","7/9/2007","MMSE","29" +"26","5","m30","2/5/2008","APOE4","0" +"26","5","m30","2/5/2008","CDRSB","NA" +"26","5","m30","2/5/2008","MMSE","NA" +"27","5","m36","10/9/2008","APOE4","0" +"27","5","m36","10/9/2008","CDRSB","1" +"27","5","m36","10/9/2008","MMSE","30" +"51","10","bl","10/11/2005","APOE4","1" +"51","10","bl","10/11/2005","CDRSB","5" +"51","10","bl","10/11/2005","MMSE","24" +"52","10","m06","9/5/2006","APOE4","1" +"52","10","m06","9/5/2006","CDRSB","2,5" +"52","10","m06","9/5/2006","MMSE","26" +"53","10","m12","9/11/2006","APOE4","1" +"53","10","m12","9/11/2006","CDRSB","4" +"53","10","m12","9/11/2006","MMSE","25" +"54","10","m18","10/5/2007","APOE4","1" +"54","10","m18","10/5/2007","CDRSB","NA" +"54","10","m18","10/5/2007","MMSE","NA" +"55","10","m24","7/11/2007","APOE4","1" +"55","10","m24","7/11/2007","CDRSB","5" +"55","10","m24","7/11/2007","MMSE","28" +"62","15","bl","18/10/2005","APOE4","1" +"62","15","bl","18/10/2005","CDRSB","0" +"62","15","bl","18/10/2005","MMSE","29" +"63","15","m06","18/4/2006","APOE4","1" +"63","15","m06","18/4/2006","CDRSB","0" +"63","15","m06","18/4/2006","MMSE","30" +"64","15","m12","13/10/2006","APOE4","1" +"64","15","m12","13/10/2006","CDRSB","0" +"64","15","m12","13/10/2006","MMSE","27" +"65","15","m18","10/4/2007","APOE4","1" +"65","15","m18","10/4/2007","CDRSB","NA" +"65","15","m18","10/4/2007","MMSE","NA" +"66","15","m24","11/10/2007","APOE4","1" +"66","15","m24","11/10/2007","CDRSB","0" +"66","15","m24","11/10/2007","MMSE","29" +"67","15","m30","7/4/2008","APOE4","1" +"67","15","m30","7/4/2008","CDRSB","NA" +"67","15","m30","7/4/2008","MMSE","NA" +"68","15","m36","28/10/2008","APOE4","1" +"68","15","m36","28/10/2008","CDRSB","0" +"68","15","m36","28/10/2008","MMSE","30" +"69","15","m72","3/11/2011","APOE4","1" +"69","15","m72","3/11/2011","CDRSB","1" +"69","15","m72","3/11/2011","MMSE","29" +"70","15","m78","10/4/2012","APOE4","1" +"70","15","m78","10/4/2012","CDRSB","NA" +"70","15","m78","10/4/2012","MMSE","NA" +"71","16","bl","13/10/2005","APOE4","1" +"71","16","bl","13/10/2005","CDRSB","0" +"71","16","bl","13/10/2005","MMSE","28" +"72","16","m06","12/4/2006","APOE4","1" +"72","16","m06","12/4/2006","CDRSB","0" +"72","16","m06","12/4/2006","MMSE","29" +"73","16","m12","11/10/2006","APOE4","1" +"73","16","m12","11/10/2006","CDRSB","0" +"73","16","m12","11/10/2006","MMSE","30" diff --git a/MIPMap tests/Datasets/DS5/EMBLGene.csv b/MIPMap tests/Datasets/DS5/EMBLGene.csv new file mode 100755 index 0000000..cd0b346 --- /dev/null +++ b/MIPMap tests/Datasets/DS5/EMBLGene.csv @@ -0,0 +1,3 @@ +gname,pname +"14-A","14-A-antigen" +"15-B","alpha-precursor" \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS5/GeneProtein.csv b/MIPMap tests/Datasets/DS5/GeneProtein.csv new file mode 100755 index 0000000..4cb1207 --- /dev/null +++ b/MIPMap tests/Datasets/DS5/GeneProtein.csv @@ -0,0 +1 @@ +gname,proteinId,pname \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS5/PDBGene.csv b/MIPMap tests/Datasets/DS5/PDBGene.csv new file mode 100755 index 0000000..97f72fa --- /dev/null +++ b/MIPMap tests/Datasets/DS5/PDBGene.csv @@ -0,0 +1,3 @@ +gname,protId +"14-A","p1" +"16-ACC","p2" \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS5/PDBProtein.csv b/MIPMap tests/Datasets/DS5/PDBProtein.csv new file mode 100755 index 0000000..a3e9da4 --- /dev/null +++ b/MIPMap tests/Datasets/DS5/PDBProtein.csv @@ -0,0 +1,3 @@ +id,pname +"p1","14-A-antigen" +"p2","ACC synthase" \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS5/mapping_task.xml b/MIPMap tests/Datasets/DS5/mapping_task.xml new file mode 100755 index 0000000..01a3abb --- /dev/null +++ b/MIPMap tests/Datasets/DS5/mapping_task.xml @@ -0,0 +1,108 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + source + + + PDBProtein.csv + + + PDBProtein.csv + true + + + + + PDBGene.csv + + + PDBGene.csv + true + + + + + EMBLGene.csv + + + EMBLGene.csv + true + + + + + + + + + + + + + + source.PDBGene.PDBGeneTuple.protId + source.PDBProtein.PDBProteinTuple.id + + true + false + false + + + + + CSV + + target + + + GeneProtein.csv + + + + + + + + + + + + + + + source.PDBGene.PDBGeneTuple.protId + + target.GeneProtein.GeneProteinTuple.proteinId + source.PDBGene.PDBGeneTuple.protId + 1.0 + + + + source.PDBProtein.PDBProteinTuple.pname + + target.GeneProtein.GeneProteinTuple.pname + source.PDBProtein.PDBProteinTuple.pname + 1.0 + + + + source.PDBGene.PDBGeneTuple.gname + + target.GeneProtein.GeneProteinTuple.gname + source.PDBGene.PDBGeneTuple.gname + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS6/EMBLGene.csv b/MIPMap tests/Datasets/DS6/EMBLGene.csv new file mode 100755 index 0000000..cd0b346 --- /dev/null +++ b/MIPMap tests/Datasets/DS6/EMBLGene.csv @@ -0,0 +1,3 @@ +gname,pname +"14-A","14-A-antigen" +"15-B","alpha-precursor" \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS6/GeneOriginal.csv b/MIPMap tests/Datasets/DS6/GeneOriginal.csv new file mode 100755 index 0000000..f1819be --- /dev/null +++ b/MIPMap tests/Datasets/DS6/GeneOriginal.csv @@ -0,0 +1 @@ +gname,proteinId \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS6/PDBGene.csv b/MIPMap tests/Datasets/DS6/PDBGene.csv new file mode 100755 index 0000000..97f72fa --- /dev/null +++ b/MIPMap tests/Datasets/DS6/PDBGene.csv @@ -0,0 +1,3 @@ +gname,protId +"14-A","p1" +"16-ACC","p2" \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS6/PDBProtein.csv b/MIPMap tests/Datasets/DS6/PDBProtein.csv new file mode 100755 index 0000000..a3e9da4 --- /dev/null +++ b/MIPMap tests/Datasets/DS6/PDBProtein.csv @@ -0,0 +1,3 @@ +id,pname +"p1","14-A-antigen" +"p2","ACC synthase" \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS6/ProteinOriginal.csv b/MIPMap tests/Datasets/DS6/ProteinOriginal.csv new file mode 100755 index 0000000..c54f602 --- /dev/null +++ b/MIPMap tests/Datasets/DS6/ProteinOriginal.csv @@ -0,0 +1 @@ +id,pname \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS6/mapping_task.xml b/MIPMap tests/Datasets/DS6/mapping_task.xml new file mode 100755 index 0000000..3c87bec --- /dev/null +++ b/MIPMap tests/Datasets/DS6/mapping_task.xml @@ -0,0 +1,136 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + source + + + PDBProtein.csv + + + PDBProtein.csv + true + + + + + PDBGene.csv + + + PDBGene.csv + true + + + + + EMBLGene.csv + + + EMBLGene.csv + true + + + + + + + + + + + + + + CSV + + target + + + GeneOriginal.csv + + + + ProteinOriginal.csv + + + + + + + + + + + + + target.GeneOriginal.GeneOriginalTuple.proteinId + target.ProteinOriginal.ProteinOriginalTuple.id + + true + false + false + + + + + + + source.PDBProtein.PDBProteinTuple.id + + target.ProteinOriginal.ProteinOriginalTuple.id + source.PDBProtein.PDBProteinTuple.id + 1.0 + + + + source.PDBProtein.PDBProteinTuple.pname + + target.ProteinOriginal.ProteinOriginalTuple.pname + source.PDBProtein.PDBProteinTuple.pname + 1.0 + + + + source.PDBGene.PDBGeneTuple.gname + + target.GeneOriginal.GeneOriginalTuple.gname + source.PDBGene.PDBGeneTuple.gname + 1.0 + + + + source.PDBGene.PDBGeneTuple.protId + + target.GeneOriginal.GeneOriginalTuple.proteinId + source.PDBGene.PDBGeneTuple.protId + 1.0 + + + + source.EMBLGene.EMBLGeneTuple.gname + + target.GeneOriginal.GeneOriginalTuple.gname + source.EMBLGene.EMBLGeneTuple.gname + 1.0 + + + + source.EMBLGene.EMBLGeneTuple.pname + + target.ProteinOriginal.ProteinOriginalTuple.pname + source.EMBLGene.EMBLGeneTuple.pname + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS7/MIP_Database.sql b/MIPMap tests/Datasets/DS7/MIP_Database.sql new file mode 100755 index 0000000..7140d46 --- /dev/null +++ b/MIPMap tests/Datasets/DS7/MIP_Database.sql @@ -0,0 +1,39 @@ +-- Table: patient +-- DROP TABLE patient; + +CREATE TABLE patient +( + id text NOT NULL, + name text, + year_of_birth integer, + gender text, + extraction_method text, + record_creation timestamp without time zone, + CONSTRAINT patient_pkey PRIMARY KEY (id) +) +WITH ( + OIDS=FALSE +); +ALTER TABLE patient + OWNER TO postgres; + +-- Table: exam_value +-- DROP TABLE exam_value; + +CREATE TABLE exam_value +( + patient_id text, + measurement_id text, + value text, + exam_date date, + extraction_method text, + extracted_from text, + CONSTRAINT exam_value_patient_id_fkey FOREIGN KEY (patient_id) + REFERENCES patient (id) MATCH SIMPLE + ON UPDATE NO ACTION ON DELETE NO ACTION +) +WITH ( + OIDS=FALSE +); +ALTER TABLE exam_value + OWNER TO postgres; \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS7/mapping_task_1.xml b/MIPMap tests/Datasets/DS7/mapping_task_1.xml new file mode 100755 index 0000000..4fe5546 --- /dev/null +++ b/MIPMap tests/Datasets/DS7/mapping_task_1.xml @@ -0,0 +1,85 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospital_data + + + patient_exams.csv + + + patient_exams.csv + true + + + + + + + + + + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIPMap_demo + postgres + 0000 + + + + + + + + + + + + Hospital_data.patient_exams.patient_examsTuple.pid + + MIPMap_demo.exam_value.exam_valueTuple.patient_id + Hospital_data.patient_exams.patient_examsTuple.pid + 1.0 + + + + Hospital_data.patient_exams.patient_examsTuple.Measurement + + MIPMap_demo.exam_value.exam_valueTuple.exam_measurement_id + Hospital_data.patient_exams.patient_examsTuple.Measurement + 1.0 + + + + Hospital_data.patient_exams.patient_examsTuple.Value + + MIPMap_demo.exam_value.exam_valueTuple.value + Hospital_data.patient_exams.patient_examsTuple.Value + 1.0 + + + + Hospital_data.patient_exams.patient_examsTuple.examdate + + MIPMap_demo.exam_value.exam_valueTuple.exam_date + Hospital_data.patient_exams.patient_examsTuple.examdate + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS7/mapping_task_2.xml b/MIPMap tests/Datasets/DS7/mapping_task_2.xml new file mode 100755 index 0000000..f93db5b --- /dev/null +++ b/MIPMap tests/Datasets/DS7/mapping_task_2.xml @@ -0,0 +1,89 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Hospital_data + + + patient_exams.csv + + + patient_exams.csv + true + + + patient_exams_2.csv + true + + + + + + + + + + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIPMap_demo + postgres + 0000 + + + + + + + + + + + + Hospital_data.patient_exams.patient_examsTuple.pid + + MIPMap_demo.exam_value.exam_valueTuple.patient_id + Hospital_data.patient_exams.patient_examsTuple.pid + 1.0 + + + + Hospital_data.patient_exams.patient_examsTuple.Measurement + + MIPMap_demo.exam_value.exam_valueTuple.exam_measurement_id + Hospital_data.patient_exams.patient_examsTuple.Measurement + 1.0 + + + + Hospital_data.patient_exams.patient_examsTuple.Value + + MIPMap_demo.exam_value.exam_valueTuple.value + Hospital_data.patient_exams.patient_examsTuple.Value + 1.0 + + + + Hospital_data.patient_exams.patient_examsTuple.examdate + + MIPMap_demo.exam_value.exam_valueTuple.exam_date + Hospital_data.patient_exams.patient_examsTuple.examdate + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS7/patient_exams.csv b/MIPMap tests/Datasets/DS7/patient_exams.csv new file mode 100755 index 0000000..f889054 --- /dev/null +++ b/MIPMap tests/Datasets/DS7/patient_exams.csv @@ -0,0 +1,52 @@ +id,pid,viscode,examdate,Measurement,Value +"51","10","bl","10/11/2005","APOE4","1" +"51","10","bl","10/11/2005","CDRSB","5" +"51","10","bl","10/11/2005","MMSE","24" +"52","10","m06","9/5/2006","APOE4","1" +"52","10","m06","9/5/2006","CDRSB","2,5" +"52","10","m06","9/5/2006","MMSE","26" +"53","10","m12","9/11/2006","APOE4","1" +"53","10","m12","9/11/2006","CDRSB","4" +"53","10","m12","9/11/2006","MMSE","25" +"54","10","m18","10/5/2007","APOE4","1" +"54","10","m18","10/5/2007","CDRSB","NA" +"54","10","m18","10/5/2007","MMSE","NA" +"55","10","m24","7/11/2007","APOE4","1" +"55","10","m24","7/11/2007","CDRSB","5" +"55","10","m24","7/11/2007","MMSE","28" +"62","15","bl","18/10/2005","APOE4","1" +"62","15","bl","18/10/2005","CDRSB","0" +"62","15","bl","18/10/2005","MMSE","29" +"63","15","m06","18/4/2006","APOE4","1" +"63","15","m06","18/4/2006","CDRSB","0" +"63","15","m06","18/4/2006","MMSE","30" +"64","15","m12","13/10/2006","APOE4","1" +"64","15","m12","13/10/2006","CDRSB","0" +"64","15","m12","13/10/2006","MMSE","27" +"65","15","m18","10/4/2007","APOE4","1" +"65","15","m18","10/4/2007","CDRSB","NA" +"65","15","m18","10/4/2007","MMSE","NA" +"66","15","m24","11/10/2007","APOE4","1" +"66","15","m24","11/10/2007","CDRSB","0" +"66","15","m24","11/10/2007","MMSE","29" +"67","15","m30","7/4/2008","APOE4","1" +"67","15","m30","7/4/2008","CDRSB","NA" +"67","15","m30","7/4/2008","MMSE","NA" +"68","15","m36","28/10/2008","APOE4","1" +"68","15","m36","28/10/2008","CDRSB","0" +"68","15","m36","28/10/2008","MMSE","30" +"69","15","m72","3/11/2011","APOE4","1" +"69","15","m72","3/11/2011","CDRSB","1" +"69","15","m72","3/11/2011","MMSE","29" +"70","15","m78","10/4/2012","APOE4","1" +"70","15","m78","10/4/2012","CDRSB","NA" +"70","15","m78","10/4/2012","MMSE","NA" +"71","16","bl","13/10/2005","APOE4","1" +"71","16","bl","13/10/2005","CDRSB","0" +"71","16","bl","13/10/2005","MMSE","28" +"72","16","m06","12/4/2006","APOE4","1" +"72","16","m06","12/4/2006","CDRSB","0" +"72","16","m06","12/4/2006","MMSE","29" +"73","16","m12","11/10/2006","APOE4","1" +"73","16","m12","11/10/2006","CDRSB","0" +"73","16","m12","11/10/2006","MMSE","30" \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS7/patient_exams_2.csv b/MIPMap tests/Datasets/DS7/patient_exams_2.csv new file mode 100755 index 0000000..d2d7423 --- /dev/null +++ b/MIPMap tests/Datasets/DS7/patient_exams_2.csv @@ -0,0 +1,37 @@ +id,pid,viscode,examdate,Measurement,Value +"10","3","bl","12/9/2005","APOE4","1" +"10","3","bl","12/9/2005","CDRSB","4,5" +"10","3","bl","12/9/2005","MMSE","20" +"11","3","m06","13/3/2006","APOE4","1" +"11","3","m06","13/3/2006","CDRSB","6" +"11","3","m06","13/3/2006","MMSE","24" +"12","3","m12","12/9/2006","APOE4","1" +"12","3","m12","12/9/2006","CDRSB","3,5" +"12","3","m12","12/9/2006","MMSE","17" +"13","3","m18","12/3/2007","APOE4","1" +"13","3","m18","12/3/2007","CDRSB","NA" +"13","3","m18","12/3/2007","MMSE","NA" +"14","3","m24","12/9/2007","APOE4","1" +"14","3","m24","12/9/2007","CDRSB","8" +"14","3","m24","12/9/2007","MMSE","19" +"21","5","bl","7/9/2005","APOE4","0" +"21","5","bl","7/9/2005","CDRSB","0" +"21","5","bl","7/9/2005","MMSE","29" +"22","5","m06","9/3/2006","APOE4","0" +"22","5","m06","9/3/2006","CDRSB","0" +"22","5","m06","9/3/2006","MMSE","29" +"23","5","m12","5/9/2006","APOE4","0" +"23","5","m12","5/9/2006","CDRSB","1,5" +"23","5","m12","5/9/2006","MMSE","30" +"24","5","m18","9/3/2007","APOE4","0" +"24","5","m18","9/3/2007","CDRSB","NA" +"24","5","m18","9/3/2007","MMSE","NA" +"25","5","m24","7/9/2007","APOE4","0" +"25","5","m24","7/9/2007","CDRSB","0" +"25","5","m24","7/9/2007","MMSE","29" +"26","5","m30","2/5/2008","APOE4","0" +"26","5","m30","2/5/2008","CDRSB","NA" +"26","5","m30","2/5/2008","MMSE","NA" +"27","5","m36","10/9/2008","APOE4","0" +"27","5","m36","10/9/2008","CDRSB","1" +"27","5","m36","10/9/2008","MMSE","30" \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS8/MIP_Database.sql b/MIPMap tests/Datasets/DS8/MIP_Database.sql new file mode 100755 index 0000000..7140d46 --- /dev/null +++ b/MIPMap tests/Datasets/DS8/MIP_Database.sql @@ -0,0 +1,39 @@ +-- Table: patient +-- DROP TABLE patient; + +CREATE TABLE patient +( + id text NOT NULL, + name text, + year_of_birth integer, + gender text, + extraction_method text, + record_creation timestamp without time zone, + CONSTRAINT patient_pkey PRIMARY KEY (id) +) +WITH ( + OIDS=FALSE +); +ALTER TABLE patient + OWNER TO postgres; + +-- Table: exam_value +-- DROP TABLE exam_value; + +CREATE TABLE exam_value +( + patient_id text, + measurement_id text, + value text, + exam_date date, + extraction_method text, + extracted_from text, + CONSTRAINT exam_value_patient_id_fkey FOREIGN KEY (patient_id) + REFERENCES patient (id) MATCH SIMPLE + ON UPDATE NO ACTION ON DELETE NO ACTION +) +WITH ( + OIDS=FALSE +); +ALTER TABLE exam_value + OWNER TO postgres; \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS8/hospitalPatient.csv b/MIPMap tests/Datasets/DS8/hospitalPatient.csv new file mode 100755 index 0000000..761729f --- /dev/null +++ b/MIPMap tests/Datasets/DS8/hospitalPatient.csv @@ -0,0 +1,10 @@ +patient_ipp,first_name,last_name,gender,date_of_birth +2561591,Peter,Quill,Male,25/3/1927 +2684672,Vincent,Nichols,Male,24/9/1982 +260428,Derrick,Matthews,Male,26/1/1977 +861093,Matilda,Webster,Female,30/6/1942 +604704,Effie,Evans,Female,14/9/1963 +163081,Charlotte,Bailey,Female,2/4/1957 +559677,George,Harrington,Male,26/6/1943 +2742705,Esther,Silva,Female,20/11/1967 +629792,Rebecca,Barrett,Female,28/3/1965 \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS8/mapping_task.xml b/MIPMap tests/Datasets/DS8/mapping_task.xml new file mode 100755 index 0000000..add713f --- /dev/null +++ b/MIPMap tests/Datasets/DS8/mapping_task.xml @@ -0,0 +1,112 @@ + + + + true + true + true + false + -1 + -1 + false + + + CSV + + Patients + + + hospitalPatient.csv + + + hospitalPatient.csv + true + + + + + patients.csv + + + patients.csv + true + + + + + + + + + + + + + + Relational + + org.postgresql.Driver + jdbc:postgresql://localhost/MIP_Database + postgres + 0000 + + + + + + + + + + + + Patients.hospitalPatient.hospitalPatientTuple.patient_ipp + + MIP_Database.patient.patientTuple.id + Patients.hospitalPatient.hospitalPatientTuple.patient_ipp + 1.0 + + + + Patients.patients.patientsTuple.patient_id + + MIP_Database.patient.patientTuple.id + Patients.patients.patientsTuple.patient_id + 1.0 + + + + Patients.hospitalPatient.hospitalPatientTuple.gender + + MIP_Database.patient.patientTuple.gender + Patients.hospitalPatient.hospitalPatientTuple.gender + 1.0 + + + + Patients.patients.patientsTuple.gender + + MIP_Database.patient.patientTuple.gender + Patients.patients.patientsTuple.gender + 1.0 + + + + Patients.hospitalPatient.hospitalPatientTuple.first_name + Patients.hospitalPatient.hospitalPatientTuple.last_name + + MIP_Database.patient.patientTuple.name + append(Patients.hospitalPatient.hospitalPatientTuple.first_name, append(" ", Patients.hospitalPatient.hospitalPatientTuple.last_name)) + 1.0 + + + + Patients.patients.patientsTuple.fname + Patients.patients.patientsTuple.lname + + MIP_Database.patient.patientTuple.name + append(Patients.patients.patientsTuple.fname, append(" ", Patients.patients.patientsTuple.lname)) + 1.0 + + + + diff --git a/MIPMap tests/Datasets/DS8/patients.csv b/MIPMap tests/Datasets/DS8/patients.csv new file mode 100755 index 0000000..f349743 --- /dev/null +++ b/MIPMap tests/Datasets/DS8/patients.csv @@ -0,0 +1,11 @@ +patient_id,fname,lname,gender,year_of_birth +418877,Roger,Bryan,Male,1928 +2326096,Mary,Nunez,Female,1929 +481145,Susan,Wagner,Female,1924 +2877889,John,Mann,Male,1973 +763227,Rosetta,Schultz,Female,1992 +1040371,Edward,Webster,Male,1939 +286768,Leon,Newman,Male,1962 +861093,Matilda,Webster,Female,1942 +1033854,Bertha,Yates,Female,1963 +2561591,Peter,Quil,Male,1927 \ No newline at end of file diff --git a/MIPMap tests/Datasets/DS9/patient_exams_original.csv b/MIPMap tests/Datasets/DS9/patient_exams_original.csv new file mode 100755 index 0000000..8f45491 --- /dev/null +++ b/MIPMap tests/Datasets/DS9/patient_exams_original.csv @@ -0,0 +1 @@ +id,pid,viscode,examdate,APOE4,CDRSB,MMSE,MOCA "10","3","bl","12/9/2005","1","4,5","20","NA" "11","3","m06","13/3/2006","1","6","24","NA" "12","3","m12","12/9/2006","1","3,5","17","NA" "13","3","m18","12/3/2007","1","NA","NA","NA" "14","3","m24","12/9/2007","1","8","19","NA" "21","5","bl","7/9/2005","0","0","29","NA" "22","5","m06","9/3/2006","0","0","29","NA" "23","5","m12","5/9/2006","0","1,5","30","NA" "24","5","m18","9/3/2007","0","NA","NA","NA" "25","5","m24","7/9/2007","0","0","29","NA" "26","5","m30","2/5/2008","0","NA","NA","NA" "27","5","m36","10/9/2008","0","1","30","NA" "51","10","bl","10/11/2005","1","5","24","NA" "52","10","m06","9/5/2006","1","2,5","26","NA" "53","10","m12","9/11/2006","1","4","25","NA" "54","10","m18","10/5/2007","1","NA","NA","NA" "55","10","m24","7/11/2007","1","5","28","NA" "62","15","bl","18/10/2005","1","0","29","NA" "63","15","m06","18/4/2006","1","0","30","NA" "64","15","m12","13/10/2006","1","0","27","NA" "65","15","m18","10/4/2007","1","NA","NA","NA" "66","15","m24","11/10/2007","1","0","29","NA" "67","15","m30","7/4/2008","1","NA","NA","NA" "68","15","m36","28/10/2008","1","0","30","NA" "69","15","m72","3/11/2011","1","1","29","26" "70","15","m78","10/4/2012","1","NA","NA","NA" "71","16","bl","13/10/2005","1","0","28","NA" "72","16","m06","12/4/2006","1","0","29","NA" "73","16","m12","11/10/2006","1","0","30","NA" \ No newline at end of file diff --git a/MIPMap tests/MIPMap - Test Cases.xlsx b/MIPMap tests/MIPMap - Test Cases.xlsx new file mode 100755 index 0000000..75b99cf Binary files /dev/null and b/MIPMap tests/MIPMap - Test Cases.xlsx differ diff --git a/MIPMap tests/MIPMap - Testing Scenarios.docx b/MIPMap tests/MIPMap - Testing Scenarios.docx new file mode 100755 index 0000000..e4fef07 Binary files /dev/null and b/MIPMap tests/MIPMap - Testing Scenarios.docx differ