update to ECDC uploader

.classpath

@@ -6,5 +6,52 @@
 	<classpathentry kind="lib" path="C:/lib/ftp4j-1.7.2/ftp4j-1.7.2.jar"/>
 	<classpathentry kind="lib" path="C:/lib/commons-io-2.6/commons-io-2.6.jar"/>
 	<classpathentry kind="lib" path="C:/lib/commons-cli-1.4/commons-cli-1.4.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jcifs-1.3.19.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/commons-codec-1.10.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/commons-logging-1.2.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/fluent-hc-4.5.5.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/httpclient-4.5.5.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/httpclient-cache-4.5.5.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/httpclient-win-4.5.5.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/httpcore-4.4.9.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/httpmime-4.5.5.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/jna-4.4.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/httpcomponents-client-4.5.5/lib/jna-platform-4.4.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/apache commons vfs/commons-vfs2-2.2.jar"/>
+	<classpathentry kind="lib" path="C:/lib/apache commons vfs/commons-vfs2-2.2-javadoc.jar"/>
+	<classpathentry kind="lib" path="C:/lib/apache commons vfs/jsch-0.1.54.jar"/>
+	<classpathentry kind="lib" path="C:/lib/sqlite-jdbc-3.21.0.jar"/>
+	<classpathentry kind="lib" path="C:/sql/sqljdbc_6.0/enu/jre8/sqljdbc42.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/jdom-2.0.6.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/jdom-2.0.6-contrib.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/jdom-2.0.6-javadoc.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/jdom-2.0.6-junit.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/jdom-2.0.6-sources.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/lib/jaxen-1.1.6.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/lib/xercesImpl.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/lib/xml-apis.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/lib/xalan/serializer-2.7.2.jar"/>
+	<classpathentry kind="lib" path="C:/lib/jdom/lib/xalan/xalan-2.7.2.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/poi-4.0.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/poi-ooxml-4.0.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/poi-examples-4.0.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/poi-excelant-4.0.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/poi-ooxml-schemas-4.0.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/poi-scratchpad-4.0.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/ooxml-lib/xmlbeans-3.0.1.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/commons-collections4-4.2.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/ooxml-lib/curvesapi-1.05.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/activation-1.1.1.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/commons-codec-1.11.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/commons-logging-1.2.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/commons-math3-3.6.1.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/jaxb-api-2.3.0.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/jaxb-core-2.3.0.1.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/jaxb-impl-2.3.0.1.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/junit-4.12.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/log4j-1.2.17.jar"/>
+	<classpathentry kind="lib" path="C:/lib/poi-4.0.0/lib/commons-compress-1.18.jar"/>
+	<classpathentry kind="lib" path="C:/lib/mysql-connector-java-5.1.47/mysql-connector-java-5.1.47.jar"/>
+	<classpathentry kind="lib" path="C:/lib/postgresql-42.2.5.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

ECOLIISO.meta

@@ -0,0 +1,16 @@
+RecordId
+SampleId
+DateOfSampling
+DateOfReceiptSourceLab
+DateOfReceiptReferenceLab
+Gender=M,F,UNK
+Age
+AgeMonth
+SampleOrigin
+Specimen
+PlaceOfResidence
+Imported=Y,N,UNK
+ProbableCountryOfInfection
+Serotype
+WgsProtocol=MISEQ_2X300,MISEQ_2x250,MISEQ_2X150,NEXTSEQ_2X150,HISEQ_2X100,MINISEQ_2X150,IONTORRENT
+WgsAssembler=SPADES,VELVET,MAP_TO_LOCI1

ERC000028.txt

@@ -0,0 +1,7 @@
+serovar
+collected_by
+collection_date
+country
+host_associated
+specific_host
+host_disease_status

ERC000028b.txt

@@ -0,0 +1,8 @@
+serovar
+collected_by
+collection_date
+country
+host_associated
+specific_host
+host_disease_status
+test

ERC000044.txt

@@ -0,0 +1,4 @@
+collection_date
+collected_by
+geographic location (country and/or sea)
+host scientific name

ERC000045.txt

@@ -0,0 +1,2 @@
+collection_date
+isolation_source

LISTISO.meta

@@ -0,0 +1,15 @@
+RecordId
+SampleId
+DateOfSampling
+DateOfReceiptSourceLab
+DateOfReceiptReferenceLab
+Gender=M,F,UNK
+Age
+AgeMonth
+SampleOrigin
+Specimen
+PlaceOfResidence
+Imported=Y,N,UNK
+ProbableCountryOfInfection
+WgsProtocol=MISEQ_2X300,MISEQ_2x250,MISEQ_2X150,NEXTSEQ_2X150,HISEQ_2X100,MINISEQ_2X150,IONTORRENT
+WgsAssembler=SPADES,VELVET,MAP_TO_LOCI1

SALMISO.meta

@@ -0,0 +1,16 @@
+RecordId
+SampleId
+DateOfSampling
+DateOfReceiptSourceLab
+DateOfReceiptReferenceLab
+Gender=M,F,UNK
+Age
+AgeMonth
+SampleOrigin
+Specimen
+PlaceOfResidence
+Imported
+ProbableCountryOfInfection
+Serotype
+WgsProtocol=MISEQ_2X300,MISEQ_2x250,MISEQ_2X150,NEXTSEQ_2X150,HISEQ_2X100,MINISEQ_2X150,IONTORRENT
+WgsAssembler=SPADES,VELVET,MAP_TO_LOCI1

TESSy

@@ -0,0 +1,8 @@
+DateUsedForStatistics
+ReportingCountry
+Gender
+Age
+Imported
+DateOfSampling
+DateOfReceiptReferenceLab
+ProbableCountryOfInfection

checklist.txt

@@ -0,0 +1 @@
+ERC000028