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UPDATE: Update how batches are inserted into db
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aueb-wim committed Dec 5, 2017
2 parents 569bf63 + 090a71e commit 615b4c7
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Showing 67 changed files with 3,634 additions and 4 deletions.
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27 changes: 27 additions & 0 deletions MIPMap tests/Datasets/DS1/hospitalExam.csv
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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
25 changes: 25 additions & 0 deletions MIPMap tests/Datasets/DS1/hospitalPatient.csv
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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
64 changes: 64 additions & 0 deletions MIPMap tests/Datasets/DS1/hospitalToPatient.xml
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<?xml version="1.0" encoding="UTF-8"?>
<mappingtask>
<config>
<rewriteSubsumptions>true</rewriteSubsumptions>
<rewriteCoverages>true</rewriteCoverages>
<rewriteSelfJoins>true</rewriteSelfJoins>
<rewriteEGDs>false</rewriteEGDs>
<sortStrategy>-1</sortStrategy>
<skolemTableStrategy>-1</skolemTableStrategy>
<useLocalSkolem>false</useLocalSkolem>
</config>
<source>
<type>CSV</type>
<csv>
<csv-db-name>hospitalSchema</csv-db-name>
<csv-tables>
<csv-table>
<schema>hospitalExam.csv</schema>
<instances>
<instance>
<path>hospitalExam.csv</path>
<column-names>true</column-names>
</instance>
</instances>
</csv-table>
<csv-table>
<schema>hospitalPatient.csv</schema>
<instances>
<instance>
<path>hospitalPatient.csv</path>
<column-names>true</column-names>
</instance>
</instances>
</csv-table>
</csv-tables>
</csv>
<inclusions />
<exclusions />
<duplications />
<functionalDependencies />
<selectionConditions />
<joinConditions />
</source>
<target>
<type>CSV</type>
<csv>
<csv-db-name>patientSchema</csv-db-name>
<csv-tables>
<csv-table>
<schema>patient_exams.csv</schema>
<instances />
</csv-table>
</csv-tables>
</csv>
<inclusions />
<exclusions />
<duplications />
<functionalDependencies />
<selectionConditions />
<joinConditions />
</target>
<correspondences />
</mappingtask>

88 changes: 88 additions & 0 deletions MIPMap tests/Datasets/DS1/patient_exams.csv
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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"
27 changes: 27 additions & 0 deletions MIPMap tests/Datasets/DS2/hospitalExam.csv
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Original file line number Diff line number Diff line change
@@ -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
25 changes: 25 additions & 0 deletions MIPMap tests/Datasets/DS2/hospitalPatient.csv
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Original file line number Diff line number Diff line change
@@ -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
64 changes: 64 additions & 0 deletions MIPMap tests/Datasets/DS2/hospitalToPatient.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,64 @@
<?xml version="1.0" encoding="UTF-8"?>
<mappingtask>
<config>
<rewriteSubsumptions>true</rewriteSubsumptions>
<rewriteCoverages>true</rewriteCoverages>
<rewriteSelfJoins>true</rewriteSelfJoins>
<rewriteEGDs>false</rewriteEGDs>
<sortStrategy>-1</sortStrategy>
<skolemTableStrategy>-1</skolemTableStrategy>
<useLocalSkolem>false</useLocalSkolem>
</config>
<source>
<type>CSV</type>
<csv>
<csv-db-name>hospitalSchema</csv-db-name>
<csv-tables>
<csv-table>
<schema>hospitalExam.csv</schema>
<instances>
<instance>
<path>hospitalExam.csv</path>
<column-names>true</column-names>
</instance>
</instances>
</csv-table>
<csv-table>
<schema>hospitalPatient.csv</schema>
<instances>
<instance>
<path>hospitalPatient.csv</path>
<column-names>true</column-names>
</instance>
</instances>
</csv-table>
</csv-tables>
</csv>
<inclusions />
<exclusions />
<duplications />
<functionalDependencies />
<selectionConditions />
<joinConditions />
</source>
<target>
<type>CSV</type>
<csv>
<csv-db-name>patientSchema</csv-db-name>
<csv-tables>
<csv-table>
<schema>patient_exams.csv</schema>
<instances />
</csv-table>
</csv-tables>
</csv>
<inclusions />
<exclusions />
<duplications />
<functionalDependencies />
<selectionConditions />
<joinConditions />
</target>
<correspondences />
</mappingtask>

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