Package 

Class DBLoadingUtils

  • All Implemented Interfaces:
    
public class DBLoadingUtils

    Common methods used by postgres and sqlite dbs for loading/retrieving data from the PHG dbs. This is the place encoding/decoding methods for table data should stored. Authors zrm22 and lcj34.

    • Constructor Detail

    • Method Detail

      • connection

         static Connection connection(boolean createNew)

        Creates a database connection from the TASSEL ParameterCache It is expected that only initial db loading methods will call this with "createNew" = true.

        Parameters:
        createNew - Indicates if the request is to connect to an existing db or to create a new one with the specified name.

      • connection

         static Connection connection(String propertiesFile, boolean createNew)

        Creates a database connection given a properties file It is expected that only initial db loading methods will call this with "createNew" = true.

        Parameters:
        propertiesFile - properties file
        createNew - Indicates if the request is to connect to an existing db or to create a new one with the specified name.

      • connection

         static Connection connection(String host, String user, String password, String dbName, String type, boolean createNew)

        Creates a new database connection or returns connection to existing db If createNew is FALSE then try to connect, and if db doesn't exist, return NULL NOTE: from postgres, User should never create a db that matches all lower case to an existing db. This will cause errors as our db check verifies based on all-lower case. To get a camel-case db name, the db must be created and accessed using This is likely to cause confusion, so this code defaults to postgres all-lowercase db names.

        Parameters:
        host - hostname
        user - user id
        password - password
        dbName - database name
        type - database type (sqlite or postgres)
        createNew - if true, delete old db if it exists; create new db from PHG schema

      • encodeHapCountsArrayFromMultiset

         static Array<byte> encodeHapCountsArrayFromMultiset(Multiset<HaplotypeNode> perfectHitSet, Multiset<HaplotypeNode> exclusionHitSet)

        THis method takes 2 multisets of HaplotypeNode objects: one indicating inclusion counts for a haplotype, the other indicating exclusion counts. These sets are on a per-taxon basis. The data will be written compressed to a byte array for storage in the PHG db haplotype_counts table. If indicated, the data will also be written to files.

      • createInitialAlleles

         static List<String> createInitialAlleles(int maxKmerLen)

        This method creates a list of allele strings based on the allele set of A,C,G,T,N The size of the set will be 5 + 5^2 + 5^3 + ... + 5^n where "n" is maxKmerLen passed in and "5^n" is 5 to the nth power. For example: if maxKmerLen = 3, size of initial Allele list is: 5 + 25 + 125 = 155; if maxKmerLen = 5, size of initial Allele list is: 5 + 25 + 125 + 625 + 3125 = 3905

      • formatMethodParamsToJSON

         static String formatMethodParamsToJSON(Map<String, String> parameterList)

        This method takes a Map of parameterName to parameterValue, and formats them into a JSON string. This string will be used by the calling method as the description entry for the PHG methods table.

      • parseMethodJsonParamsToString

         static Map<String, String> parseMethodJsonParamsToString(String methodDescription)

        Takes a passed method description string from a PHG dd methods table entry, and formats the JSON key/value pairs into a Mapfor the user. If the string does not parse to JSON, a single map entry of "notes":methodDescription will be created and returned.

      • createPathNodesForGameteGrp

         static List<Integer> createPathNodesForGameteGrp(String taxon, Connection conn, int gamete_grp_id)

        This method connects to a database, finds the haplotypes for a specific gamete group, and creates an ordered-by-ref-range list of haplotype ids. The intended use is for path creation for Assembly and WGS input.