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EMBOSS: dbxresource

dbxresource

Wiki

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Function

Index a data resource catalogue using b+tree indices

Description

dbxresource indexes the Data Resource Catalogue, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb.

These indexes allow access of flat files larger than 2Gb.

Usage

Here is a sample session with dbxresource


% dbxresource drcat 
Index a data resource catalogue using b+tree indices
Standard database name [drcat]: drcat
Resource name [drcatresource]: drcatresource
Database directory [.]: 
Wildcard database filename [DRCAT.dat]: DRCAT.dat
        id : ID
       acc : IDother
       nam : Name
       des : Description
       url : Server URL
       cat : Category name
     taxid : Taxon id
      edat : EDAM data term
      efmt : EDAM format term
       eid : EDAM data id term
      etpc : EDAM topic term
      xref : Link
      qout : Query output
      qfmt : Query output format
       qin : Query input parameters
      qurl : Query URL
      rest : Rest URL
      soap : SOAP URL
Index fields [*]: 
Compressed index files [Y]: 
General log output file [outfile.dbxresource]:

Go to the output files for this example

Command line arguments

Index a data resource catalogue using b+tree indices
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     [drcat] Basename for index files (Any string
                                  from 2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
  [-standardname]      string     [$(dbname)] Standard database name (Any
                                  string from 2 to 19 characters, matching
                                  regular expression /[A-z][A-z0-9_]+/)
  [-dbresource]        string     [drcatresource] Resource name (Any string
                                  from 2 to 19 characters, matching regular
                                  expression /[A-z][A-z0-9_]+/)
   -directory          directory  [.] Database directory
   -filenames          string     [DRCAT.dat] Wildcard database filename (Any
                                  string)
   -fields             menu       [*] Index fields (Values: id (ID); acc
                                  (IDother); nam (Name); des (Description);
                                  url (Server URL); cat (Category name); taxid
                                  (Taxon id); edat (EDAM data term); efmt
                                  (EDAM format term); eid (EDAM data id term);
                                  etpc (EDAM topic term); xref (Link); qout
                                  (Query output); qfmt (Query output format);
                                  qin (Query input parameters); qurl (Query
                                  URL); rest (Rest URL); soap (SOAP URL))
   -[no]compressed     boolean    [Y] Compressed index files
   -outfile            outfile    [*.dbxresource] General log output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -release            string     [0.0] Release number (Any string up to 9
                                  characters)
   -date               string     [00/00/00] Index date (Date string dd/mm/yy)
   -exclude            string     Wildcard filename(s) to exclude (Any string)
   -indexoutdir        outdir     [.] Index file output directory

   Associated qualifiers:

   "-directory" associated qualifiers
   -extension          string     Default file extension

   "-indexoutdir" associated qualifiers
   -extension          string     Default file extension

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier

Type

Description

Allowed values

Default

Standard (Mandatory) qualifiers

[-dbname]
(Parameter 1)

string

Basename for index files

Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/

drcat

[-standardname]
(Parameter 2)

string

Standard database name

Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/

$(dbname)

[-dbresource]
(Parameter 3)

string

Resource name

Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/

drcatresource

-directory

Input file format

dbxresource reads and indexes the Data Resource Catalogue DRCAT.dat file.

Output file format

dbxresource creates one summary file for the database and two files for each field indexed.

dbalias.ent is the master file containing the names of the files that have been indexed. It is an ASCII file. This file also contains the database release and date information.
dbalias.xid is the B+tree index file for the ID names. It is a binary file.

dbalias.pxid is an ASCII file containing information regarding the structure of the ID name index.

Output files for usage example

File: drcat.ent

# Number of files: 1
# Release: 0.0
# Date:    00/00/00
Single filename database
DRCAT.dat

File: drcat.pxac

Type      Identifier
Compress  Yes
Pages     3
Order     64
Fill      43
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     21
Fullcount 21
Kwlimit   18

File: drcat.pxcat

Type      Secondary
Compress  Yes
Pages     60
Order     37
Fill      29
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     19
Fullcount 72
Kwlimit   40

File: drcat.pxde

Type      Secondary
Compress  Yes
Pages     2539
Order     60
Fill      41
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     835
Fullcount 2001
Kwlimit   20

File: drcat.pxedat

Type      Secondary
Compress  Yes
Pages     198
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     65
Fullcount 150
Kwlimit   15

File: drcat.pxefmt

Type      Secondary
Compress  Yes
Pages     37
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     11
Fullcount 135
Kwlimit   15

File: drcat.pxeid

Type      Secondary
Compress  Yes
Pages     328
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     108
Fullcount 197
Kwlimit   15

File: drcat.pxetpc

Type      Secondary
Compress  Yes
Pages     204
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     67
Fullcount 204
Kwlimit   15

File: drcat.pxid

Type      Identifier
Compress  Yes
Pages     8
Order     44
Fill      33
Pagesize  2048
Level     0
Cachesize 100
Order2    99
Fill2     101
Count     110
Fullcount 110
Kwlimit   32

File: drcat.pxnm

Type      Secondary
Compress  Yes
Pages     1021
Order     60
Fill      41
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     335
Fullcount 659
Kwlimit   20

File: drcat.pxqfmt

Type      Secondary
Compress  Yes
Pages     52
Order     46
Fill      34
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     16
Fullcount 148
Kwlimit   30

File: drcat.pxqin

Type      Secondary
Compress  Yes
Pages     377
Order     25
Fill      21
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     122
Fullcount 204
Kwlimit   65

File: drcat.pxqout

Type      Secondary
Compress  Yes
Pages     391
Order     19
Fill      17
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     126
Fullcount 169
Kwlimit   90

File: drcat.pxqurl

Type      Secondary
Compress  Yes
Pages     2252
Order     46
Fill      34
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     737
Fullcount 2118
Kwlimit   30

File: drcat.pxrest

Type      Secondary
Compress  Yes
Pages     39
Order     60
Fill      41
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     12
Fullcount 43
Kwlimit   20

File: drcat.pxrf

Type      Secondary
Compress  Yes
Pages     15
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     4
Fullcount 87
Kwlimit   15

File: drcat.pxsoap

Type      Secondary
Compress  Yes
Pages     57
Order     71
Fill      46
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     18
Fullcount 23
Kwlimit   15

File: drcat.pxtaxid

Type      Secondary
Compress  Yes
Pages     82
Order     104
Fill      58
Pagesize  2048
Level     0
Cachesize 100
Order2    44
Fill2     54
Count     26
Fullcount 114
Kwlimit   6