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Hotfix sample #33

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merged 2 commits into from
Feb 27, 2023
Merged

Hotfix sample #33

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6fdf585
Merge pull request #30 from samply/release-1.2.3
PierreDelpy Feb 24, 2023
56a38bd
specify sample creation checks
Feb 27, 2023
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8 changes: 4 additions & 4 deletions src/main/resources/ADT2MDS_FHIR.xsl
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Original file line number Diff line number Diff line change
Expand Up @@ -131,12 +131,12 @@
</xsl:variable>
<xsl:value-of select="concat('bio', hash:hash($Patient_Id, '', string-join($attribute, '')))" />
</xsl:attribute>
<Entnahmedatum><xsl:value-of select="Entnahmedatum"/></Entnahmedatum>
<xsl:if test="Entnahmedatum"><Entnahmedatum><xsl:value-of select="Entnahmedatum"/></Entnahmedatum></xsl:if>
<xsl:if test="Patienten_mit_Biomaterial='ja' or Patienten_mit_Biomaterial='Ja' or Patienten_mit_Biomaterial='true'"><Patienten_mit_Biomaterial>true</Patienten_mit_Biomaterial></xsl:if>
<xsl:if test="Patienten_mit_Biomaterial='nein' or Patienten_mit_Biomaterial='Nein' or Patienten_mit_Biomaterial='false'"><Patienten_mit_Biomaterial>false</Patienten_mit_Biomaterial></xsl:if>
<Fixierungsart><xsl:value-of select="Fixierungsart"/></Fixierungsart>
<Probentyp><xsl:value-of select="Probentyp"/></Probentyp>
<Probenart><xsl:value-of select="Probenart"/></Probenart>
<xsl:if test="Fixierungsart"><Fixierungsart><xsl:value-of select="Fixierungsart"/></Fixierungsart></xsl:if>
<xsl:if test="Probentyp"><Probentyp><xsl:value-of select="Probentyp"/></Probentyp></xsl:if>
<xsl:if test="Probenart"><Probenart><xsl:value-of select="Probenart"/></Probenart></xsl:if>
</Sample>
</xsl:template>

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166 changes: 84 additions & 82 deletions src/main/resources/MDS2FHIR.xsl
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Expand Up @@ -178,102 +178,104 @@
<xsl:template match="Sample" mode="sample">
<xsl:param name="Patient_ID" select="../@Patient_ID" />
<xsl:variable name="Sample_ID" select="@Sample_ID" />
<entry>
<fullUrl value="http://example.com/Specimen/{$Sample_ID}"/>
<resource>
<Specimen>
<id value="{$Sample_ID}"/>
<meta>
<profile value="https://fhir.bbmri.de/StructureDefinition/Specimen"/>
</meta>
<type>
<coding>
<system value="https://fhir.bbmri.de/CodeSystem/SampleMaterialType"/>
<code>
<xsl:choose>
<xsl:when test="./Probentyp='Gewebeprobe'">
<xsl:if test="./Probentyp and (./Fixierungsart or ./Probenart)">
<entry>
<fullUrl value="http://example.com/Specimen/{$Sample_ID}"/>
<resource>
<Specimen>
<id value="{$Sample_ID}"/>
<meta>
<profile value="https://fhir.bbmri.de/StructureDefinition/Specimen"/>
</meta>
<type>
<coding>
<system value="https://fhir.bbmri.de/CodeSystem/SampleMaterialType"/>
<code>
<xsl:choose>
<xsl:when test="./Fixierungsart='Kryo/Frisch (FF)'">
<xsl:when test="./Probentyp='Gewebeprobe'">
<xsl:choose>
<xsl:when test="./Probenart='Tumorgewebe'">
<xsl:attribute name="value">tumor-tissue-frozen</xsl:attribute>
<xsl:when test="./Fixierungsart='Kryo/Frisch (FF)'">
<xsl:choose>
<xsl:when test="./Probenart='Tumorgewebe'">
<xsl:attribute name="value">tumor-tissue-frozen</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Normalgewebe'">
<xsl:attribute name="value">normal-tissue-frozen</xsl:attribute>
</xsl:when>
<xsl:otherwise>
<xsl:attribute name="value">other-tissue-frozen</xsl:attribute>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:when test="./Probenart='Normalgewebe'">
<xsl:attribute name="value">normal-tissue-frozen</xsl:attribute>
<xsl:when test="./Fixierungsart='Paraffin (FFPE)'">
<xsl:choose>
<xsl:when test="./Probenart='Tumorgewebe'">
<xsl:attribute name="value">tumor-tissue-ffpe</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Normalgewebe'">
<xsl:attribute name="value">normal-tissue-ffpe</xsl:attribute>
</xsl:when>
<xsl:otherwise>
<xsl:attribute name="value">other-tissue-ffpe</xsl:attribute>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:otherwise>
<xsl:attribute name="value">other-tissue-frozen</xsl:attribute>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:when test="./Fixierungsart='Paraffin (FFPE)'">
<xsl:when test="./Probentyp='Flüssigprobe'">
<xsl:choose>
<xsl:when test="./Probenart='Tumorgewebe'">
<xsl:attribute name="value">tumor-tissue-ffpe</xsl:attribute>
<xsl:when test="./Probenart='Vollblut'">
<xsl:attribute name="value">whole-blood</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Serum'">
<xsl:attribute name="value">blood-serum</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Plasma'">
<xsl:attribute name="value">blood-plasma</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Urin'">
<xsl:attribute name="value">urine</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Liquor'">
<xsl:attribute name="value">csf-liquor</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Knochenmark'">
<xsl:attribute name="value">bone-marrow</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='DNA'">
<xsl:attribute name="value">dna</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='RNA'">
<xsl:attribute name="value">rna</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Normalgewebe'">
<xsl:attribute name="value">normal-tissue-ffpe</xsl:attribute>
<xsl:when test="./Probenart='Protein'">
<xsl:attribute name="value">derivative-other</xsl:attribute>
</xsl:when>
<xsl:otherwise>
<xsl:attribute name="value">other-tissue-ffpe</xsl:attribute>
<xsl:attribute name="value">liquid-other</xsl:attribute>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
</xsl:choose>
</xsl:when>
<xsl:when test="./Probentyp='Flüssigprobe'">
<xsl:choose>
<xsl:when test="./Probenart='Vollblut'">
<xsl:attribute name="value">whole-blood</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Serum'">
<xsl:attribute name="value">blood-serum</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Plasma'">
<xsl:attribute name="value">blood-plasma</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Urin'">
<xsl:attribute name="value">urine</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Liquor'">
<xsl:attribute name="value">csf-liquor</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Knochenmark'">
<xsl:attribute name="value">bone-marrow</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='DNA'">
<xsl:attribute name="value">dna</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='RNA'">
<xsl:attribute name="value">rna</xsl:attribute>
</xsl:when>
<xsl:when test="./Probenart='Protein'">
<xsl:attribute name="value">derivative-other</xsl:attribute>
</xsl:when>
<xsl:otherwise>
<xsl:attribute name="value">liquid-other</xsl:attribute>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
</xsl:choose>
</code>
</coding>
</type>
<subject>
<reference value="Patient/{$Patient_ID}"/>
</subject>
<xsl:if test="./Entnahmedatum">
<collection>
<collectedDateTime value="{mds2fhir:transformDate(./Entnahmedatum)}"/>
</collection>
</xsl:if>
</Specimen>
</resource>
<request>
<method value="PUT"/>
<url value="Specimen/{$Sample_ID}"/>
</request>
</entry>
</code>
</coding>
</type>
<subject>
<reference value="Patient/{$Patient_ID}"/>
</subject>
<xsl:if test="./Entnahmedatum">
<collection>
<collectedDateTime value="{mds2fhir:transformDate(./Entnahmedatum)}"/>
</collection>
</xsl:if>
</Specimen>
</resource>
<request>
<method value="PUT"/>
<url value="Specimen/{$Sample_ID}"/>
</request>
</entry>
</xsl:if>
</xsl:template>
<xsl:template match="Diagnosis" mode="diagnosis">
<xsl:param name="Patient_ID" select="../@Patient_ID" />
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