Configuration tutorial

This short tutorial is divided into 4 parts: Requirements, Installation paths, Files glossary, Installation procedure.

The Requirements part details which version of SRS has been used and other requirements needed for the installation.
Please notice that this TP53 Database installation may vary using different SRS releases, refer to your SRS administrator manual for further information.

The Installation paths part explains where the files must be located; these paths may vary in relation to your SRS custom installation.

The File glossary is a short summary of all the files needed for the installation divided for typology.
Please notice that all these files can be freely copied into their destination paths apart from the System Configuration Files; these contain information pertinent to the specific SRS environment and to the related databases installed; since they vary from one installation to another, it is better to keep and update your files (e.g. cut and paste the information required from the Installation procedure)

The Installation procedure is the core of this tutorial.
Please notice that each time you have to modify one of the System Configuration Files, the needed code lines are provided.

1) Requirements
SRS 7.1 server
SRS Administrator System knowledge

2) Installation paths
../srs/data/ for the databases and DTD files
../srs/icarus/site/ for all the other files

3) Files Glossary
Databases Flatfile
p53_iarc flatfile for the TP53 Mutation Database
p53_iarc_ref.dat flatfilefor the Bibliographic Reference Database

DTD File
p53.dtd Document Text Definition file used for the XMLPrintMetaphor files generation (see page 450 of the SRS 7.1 Administrator Manual)

TP53 Database Configuration Files
p53_iarc.is Syntax file
p53_iarc.it Information file
p53_iarc.i Library structure file

Bibliographic References Database Configuration Files
p53_iarc_ref.is Syntax file
p53_iarc_ref.it Information file
p53_iarc_ref.i Library structure file

System Configuration Files
site.i
srsdb.i
loader.i
href.i
views.i

Icarus Layout Files
mutation.il
p53_mutation_view.il
p53_patient_view.il
p53_sample_view.il

SRS XMLPrintMetaphor Files (used for the generation of the XML output)
p53_iarc_printer.i
p53_iarc_mutation_printer.i
p53_iarc_patient_printer.i
p53_iarc_sample_printer.i

4) Installation Procedure
Data library implementation:
- copy in you Database Flatfiles and DTD File in your data directory
- copy the TP53 Databases Configuration Files and the Bibliographic References Database Configuration Files in your site directory
- Edit your srsdb file, add your data libraries:
# p53 databases for o2i added
$LibLoc:[$P53_IARC_DB enabled:y
includeFiles:{"SRSSITE:p53_iarc.i" "SRSSITE:p53_iarc.it"}
dir:"$dataRootOwn"
offDir:"$dataRootOwn"
]
$LibLoc:[$P53_IARC_REF_DB enabled:y
includeFiles:{"SRSSITE:p53_iarc_ref.i" "SRSSITE:p53_iarc_ref.it"}
dir:"$dataRootOwn"
offDir:"$dataRootOwn"
]

# P53 databases for o21
$LibId:[1204 lib:$P53_IARC_DB]
$LibId:[1205 lib:$P53_IARC_REF_DB]

Views implementation:
- edit your views.i file and add the following views:
$P53_Table_Loader_View=$View:[P53_Table_Loader_View
objLoader:$Mutation_Class
printEntryList:n
layout:@{
$FileDo:"($Env:SRSSITE)/mutation.il"
}
]
$P53_Mutation_View=$View:[P53_Mutation_View
objLoader:$P53_Mutation_View_Class
printEntryList:n
layout:@{
$FileDo:"($Env:SRSSITE)/p53_mutation_view.il"
}
]
$P53_Sample_View=$View:[P53_Sample_View
objLoader:$P53_Sample_View_Class
printEntryList:n
layout:@{
$FileDo:"($Env:SRSSITE)/p53_sample_view.il"
}
]
$P53_Patient_View=$View:[P53_Patient_View
objLoader:$P53_Patient_View_Class
printEntryList:n
layout:@{
$FileDo:"($Env:SRSSITE)/p53_patient_view.il"
}
]
$P53_Table_View=$View:[P53_Table_View
objLoader:$Mutation_Class
format:table
printEntryList:y
]

Loaders implementation:
Edit your loader file and add the following loaders:
# Loader for the P53_IARC databank
$XML_Mutation_Class=$LoadClass:[XML_Mutation
libs:{ $P53_IARC_DB }
attrs:{
$LoadAttr:[Mutation_id type:string load:$Tok:[field:$DF_Mutation_id]]
$LoadAttr:[Sample_id type:string load:$Tok:[field:$DF_Sample_id]]
$LoadAttr:[Ref_id type:string load:$Tok:[field:$DF_Ref_id]]
$LoadAttr:[Individual_id type:string load:$Tok:[field:$DF_Individual_id]]
$LoadAttr:[Tumor_origin type:string load:$Tok:[field:$DF_Tumor_origin]]
$LoadAttr:[Metastasis_localization type:string load:$Tok:[field:$DF_Metastasis_localization]]
$LoadAttr:[Exon type:string load:$Tok:[field:$DF_Exon]]
$LoadAttr:[Intron type:string load:$Tok:[field:$DF_Intron]]
$LoadAttr:[Codon_number type:string load:$Tok:[field:$DF_Codon_number]]
$LoadAttr:[Nucleotide type:string load:$Tok:[field:$DF_Nucleotide]]
$LoadAttr:[CpG_site type:string load:$Tok:[field:$DF_CpG_site]]
$LoadAttr:[Splice_site type:string load:$Tok:[field:$DF_Splice_site]]
$LoadAttr:[Type type:string load:$Tok:[field:$DF_Type]]
$LoadAttr:[Description type:string load:$Tok:[field:$DF_Description]]
$LoadAttr:[WT_codon type:string load:$Tok:[field:$DF_WT_codon]]
$LoadAttr:[Mutant_codon type:string load:$Tok:[field:$DF_Mutant_codon]]
$LoadAttr:[WT_AA type:string load:$Tok:[field:$DF_WT_AA]]
$LoadAttr:[Mutant_AA type:string load:$Tok:[field:$DF_Mutant_AA]]
$LoadAttr:[Protein_description type:string load:$Tok:[field:$DF_Protein_description]]
$LoadAttr:[Effect type:string load:$Tok:[field:$DF_Effect]]
$LoadAttr:[Putative_stop type:string load:$Tok:[field:$DF_Putative_stop]]
$LoadAttr:[Sample_name type:string load:$Tok:[field:$DF_Sample_name]]
$LoadAttr:[Sample_source type:string load:$Tok:[field:$DF_Sample_source]]
$LoadAttr:[Topography type:string load:$Tok:[field:$DF_Topography]]
$LoadAttr:[Short_topo type:string load:$Tok:[field:$DF_Short_topo]]
$LoadAttr:[Topo_code type:string load:$Tok:[field:$DF_Topo_code]]
$LoadAttr:[Sub_topography type:string load:$Tok:[field:$DF_Sub_topography]]
$LoadAttr:[Morphology type:string load:$Tok:[field:$DF_Morphology]]
$LoadAttr:[Morpho_code type:string load:$Tok:[field:$DF_Morpho_code]]
$LoadAttr:[Grade type:string load:$Tok:[field:$DF_Grade]]
$LoadAttr:[Stage type:string load:$Tok:[field:$DF_Stage]]
$LoadAttr:[TNM type:string load:$Tok:[field:$DF_TNM]]
$LoadAttr:[P53_IHC type:string load:$Tok:[field:$DF_P53_IHC]]
$LoadAttr:[Add_info type:string load:$Tok:[field:$DF_Add_info]]
$LoadAttr:[Sex type:string load:$Tok:[field:$DF_Sex]]
$LoadAttr:[Age type:string load:$Tok:[field:$DF_Age]]
$LoadAttr:[Ethnicity type:string load:$Tok:[field:$DF_Ethnicity]]
$LoadAttr:[Population type:string load:$Tok:[field:$DF_Population]]
$LoadAttr:[Country type:string load:$Tok:[field:$DF_Country]]
$LoadAttr:[Geo_area type:string load:$Tok:[field:$DF_Geo_area]]
$LoadAttr:[TP53_polymorphism type:string load:$Tok:[field:$DF_TP53_polymorphism]]
$LoadAttr:[Germline_mutation type:string load:$Tok:[field:$DF_Germline_mutation]]
$LoadAttr:[Family_history type:string load:$Tok:[field:$DF_Family_history]]
$LoadAttr:[Tobacco type:string load:$Tok:[field:$DF_Tobacco]]
$LoadAttr:[Alcohol type:string load:$Tok:[field:$DF_Alcohol]]
$LoadAttr:[Exposure type:string load:$Tok:[field:$DF_Exposure]]
$LoadAttr:[Infectious_agent type:string load:$Tok:[field:$DF_Infectious_agent]]
$LoadAttr:[PubMed_entry type:string load:$Tok:[field:$DF_PubMed_entry]]
}]

$P53_Mutation_View_Class=$LoadClass:[P53_Mutation_View_Class
libs:{ $P53_IARC_DB }
attrs:{
$LoadAttr:[Mutation_id type:string load:$Tok:[field:$DF_Mutation_id]]
$LoadAttr:[Ref_id type:string load:$Tok:[field:$DF_Ref_id]]
$LoadAttr:[Exon type:string load:$Tok:[field:$DF_Exon]]
$LoadAttr:[Intron type:string load:$Tok:[field:$DF_Intron]]
$LoadAttr:[Codon_number type:string load:$Tok:[field:$DF_Codon_number]]
$LoadAttr:[Nucleotide type:string load:$Tok:[field:$DF_Nucleotide]]
$LoadAttr:[CpG_site type:string load:$Tok:[field:$DF_CpG_site]]
$LoadAttr:[Splice_site type:string load:$Tok:[field:$DF_Splice_site]]
$LoadAttr:[Type type:string load:$Tok:[field:$DF_Type]]
$LoadAttr:[Description type:string load:$Tok:[field:$DF_Description]]
$LoadAttr:[WT_codon type:string load:$Tok:[field:$DF_WT_codon]]
$LoadAttr:[Mutant_codon type:string load:$Tok:[field:$DF_Mutant_codon]]
$LoadAttr:[WT_AA type:string load:$Tok:[field:$DF_WT_AA]]
$LoadAttr:[Mutant_AA type:string load:$Tok:[field:$DF_Mutant_AA]]
$LoadAttr:[Protein_description type:string load:$Tok:[field:$DF_Protein_description]]
$LoadAttr:[Effect type:string load:$Tok:[field:$DF_Effect]]
$LoadAttr:[Putative_stop type:string load:$Tok:[field:$DF_Putative_stop]]
$LoadAttr:[PubMed_entry type:string load:$Tok:[field:$DF_PubMed_entry]]
}]

$P53_Sample_View_Class=$LoadClass:[P53_Sample_View_Class
libs:{ $P53_IARC_DB }
attrs:{
$LoadAttr:[Mutation_id type:string load:$Tok:[field:$DF_Mutation_id]]
$LoadAttr:[Ref_id type:string load:$Tok:[field:$DF_Ref_id]]
$LoadAttr:[Sample_id type:string load:$Tok:[field:$DF_Sample_id]]
$LoadAttr:[Sample_name type:string load:$Tok:[field:$DF_Sample_name]]
$LoadAttr:[Sample_source type:string load:$Tok:[field:$DF_Sample_source]]
$LoadAttr:[Tumor_origin type:string load:$Tok:[field:$DF_Tumor_origin]]
$LoadAttr:[Metastasis_localization type:string load:$Tok:[field:$DF_Metastasis_localization]]
$LoadAttr:[Topography type:string load:$Tok:[field:$DF_Topography]]
$LoadAttr:[Short_topo type:string load:$Tok:[field:$DF_Short_topo]]
$LoadAttr:[Topo_code type:string load:$Tok:[field:$DF_Topo_code]]
$LoadAttr:[Sub_topography type:string load:$Tok:[field:$DF_Sub_topography]]
$LoadAttr:[Morphology type:string load:$Tok:[field:$DF_Morphology]]
$LoadAttr:[Morpho_code type:string load:$Tok:[field:$DF_Morpho_code]]
$LoadAttr:[Grade type:string load:$Tok:[field:$DF_Grade]]
$LoadAttr:[Stage type:string load:$Tok:[field:$DF_Stage]]
$LoadAttr:[TNM type:string load:$Tok:[field:$DF_TNM]]
$LoadAttr:[P53_IHC type:string load:$Tok:[field:$DF_P53_IHC]]
$LoadAttr:[Add_info type:string load:$Tok:[field:$DF_Add_info]]
}]

$P53_Patient_View_Class=$LoadClass:[P53_Patient_View_Class
libs:{ $P53_IARC_DB }
attrs:{
$LoadAttr:[Mutation_id type:string load:$Tok:[field:$DF_Mutation_id]]
$LoadAttr:[Ref_id type:string load:$Tok:[field:$DF_Ref_id]]
$LoadAttr:[Individual_id type:string load:$Tok:[field:$DF_Individual_id]]
$LoadAttr:[Sex type:string load:$Tok:[field:$DF_Sex]]
$LoadAttr:[Age type:string load:$Tok:[field:$DF_Age]]
$LoadAttr:[Ethnicity type:string load:$Tok:[field:$DF_Ethnicity]]
$LoadAttr:[Population type:string load:$Tok:[field:$DF_Population]]
$LoadAttr:[Country type:string load:$Tok:[field:$DF_Country]]
$LoadAttr:[Geo_area type:string load:$Tok:[field:$DF_Geo_area]]
$LoadAttr:[TP53_polymorphism type:string load:$Tok:[field:$DF_TP53_polymorphism]]
$LoadAttr:[Germline_mutation type:string load:$Tok:[field:$DF_Germline_mutation]]
$LoadAttr:[Family_history type:string load:$Tok:[field:$DF_Family_history]]
$LoadAttr:[Tobacco type:string load:$Tok:[field:$DF_Tobacco]]
$LoadAttr:[Alcohol type:string load:$Tok:[field:$DF_Alcohol]]
$LoadAttr:[Exposure type:string load:$Tok:[field:$DF_Exposure]]
$LoadAttr:[Infectious_agent type:string load:$Tok:[field:$DF_Infectious_agent]]
}]

$Mutation_Class=$LoadClass:[Mutation
libs:{ $P53_IARC_DB }
attrs:{
$LoadAttr:[Mutation_id type:string load:$Tok:[field:$DF_Mutation_id]]
$LoadAttr:[Sample_id type:string load:$Tok:[field:$DF_Sample_id]]
$LoadAttr:[Ref_id type:string load:$Tok:[field:$DF_Ref_id]]
$LoadAttr:[Individual_id type:string load:$Tok:[field:$DF_Individual_id]]
$LoadAttr:[Tumor_origin type:string load:$Tok:[field:$DF_Tumor_origin]]
$LoadAttr:[Metastasis_localization type:string load:$Tok:[field:$DF_Metastasis_localization]]
$LoadAttr:[Exon type:string load:$Tok:[field:$DF_Exon]]
$LoadAttr:[Intron type:string load:$Tok:[field:$DF_Intron]]
$LoadAttr:[Codon_number type:string load:$Tok:[field:$DF_Codon_number]]
$LoadAttr:[Nucleotide type:string load:$Tok:[field:$DF_Nucleotide]]
$LoadAttr:[CpG_site type:string load:$Tok:[field:$DF_CpG_site]]
$LoadAttr:[Splice_site type:string load:$Tok:[field:$DF_Splice_site]]
$LoadAttr:[Type type:string load:$Tok:[field:$DF_Type]]
$LoadAttr:[Description type:string load:$Tok:[field:$DF_Description]]
$LoadAttr:[WT_codon type:string load:$Tok:[field:$DF_WT_codon]]
$LoadAttr:[Mutant_codon type:string load:$Tok:[field:$DF_Mutant_codon]]
$LoadAttr:[WT_AA type:string load:$Tok:[field:$DF_WT_AA]]
$LoadAttr:[Mutant_AA type:string load:$Tok:[field:$DF_Mutant_AA]]
$LoadAttr:[Protein_description type:string load:$Tok:[field:$DF_Protein_description]]
$LoadAttr:[Effect type:string load:$Tok:[field:$DF_Effect]]
$LoadAttr:[Putative_stop type:string load:$Tok:[field:$DF_Putative_stop]]
$LoadAttr:[Sample_name type:string load:$Tok:[field:$DF_Sample_name]]
$LoadAttr:[Sample_source type:string load:$Tok:[field:$DF_Sample_source]]
$LoadAttr:[Topography type:string load:$Tok:[field:$DF_Topography]]
$LoadAttr:[Short_topo type:string load:$Tok:[field:$DF_Short_topo]]
$LoadAttr:[Topo_code type:string load:$Tok:[field:$DF_Topo_code]]
$LoadAttr:[Sub_topography type:string load:$Tok:[field:$DF_Sub_topography]]
$LoadAttr:[Morphology type:string load:$Tok:[field:$DF_Morphology]]
$LoadAttr:[Morpho_code type:string load:$Tok:[field:$DF_Morpho_code]]
$LoadAttr:[Grade type:string load:$Tok:[field:$DF_Grade]]
$LoadAttr:[Stage type:string load:$Tok:[field:$DF_Stage]]
$LoadAttr:[TNM type:string load:$Tok:[field:$DF_TNM]]
$LoadAttr:[P53_IHC type:string load:$Tok:[field:$DF_P53_IHC]]
$LoadAttr:[Add_info type:string load:$Tok:[field:$DF_Add_info]]
$LoadAttr:[Sex type:string load:$Tok:[field:$DF_Sex]]
$LoadAttr:[Age type:string load:$Tok:[field:$DF_Age]]
$LoadAttr:[Ethnicity type:string load:$Tok:[field:$DF_Ethnicity]]
$LoadAttr:[Population type:string load:$Tok:[field:$DF_Population]]
$LoadAttr:[Country type:string load:$Tok:[field:$DF_Country]]
$LoadAttr:[Geo_area type:string load:$Tok:[field:$DF_Geo_area]]
$LoadAttr:[TP53_polymorphism type:string load:$Tok:[field:$DF_TP53_polymorphism]]
$LoadAttr:[Germline_mutation type:string load:$Tok:[field:$DF_Germline_mutation]]
$LoadAttr:[Family_history type:string load:$Tok:[field:$DF_Family_history]]
$LoadAttr:[Tobacco type:string load:$Tok:[field:$DF_Tobacco]]
$LoadAttr:[Alcohol type:string load:$Tok:[field:$DF_Alcohol]]
$LoadAttr:[Exposure type:string load:$Tok:[field:$DF_Exposure]]
$LoadAttr:[Infectious_agent type:string load:$Tok:[field:$DF_Infectious_agent]]
$LoadAttr:[PubMed_entry type:string load:$Tok:[field:$DF_PubMed_entry]]
}]

Link implementation:
edit your site.i file and add the following lines:
$hrefs.merge:{
ExampleR:$Href:[$EXAMPLE_DB]
medlineR:$Href:[url:"<A HREF=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract6gt;%s</A>"]
}

SRS Icarus layout implementation:
- copy the Icarus Layout Files in your site directory

XML output implementation:
- copy all the SRS XMLPrintMetaphor files in your site directory
- edit your site.i file and add the following lines:
# 2004/04/01 Aggiunta P53_IARC_printer.i
file:"SRSSITE:p53_iarc_printer.i"
file:"SRSSITE:p53_iarc_mutation_printer.i"
file:"SRSSITE:p53_iarc_sample_printer.i"
file:"SRSSITE:p53_iarc_patient_printer.i"

Final steps:
Launch an SRS section
Index the databases
Enjoy you query!!!