ERL2DB(1) ERL2DB(1)
NAME
erl2db - ERL download format to DBase import format con-
version program.
SYNOPSIS
erl2db [-ahdDeirRsSvV] [-E editor-path] [-o output-file]
[--] [file...]
DESCRIPTION
erl2db is a program to convert an Electronic Reference
Library (ERL) download file to a DBase ASCII import file.
The download file should be created with WinSPIRS and con-
tain all fields, each field on a single line (see subsec-
tion Example ERL datarecord). Abbreviated fieldidentifiers
must be used (TI:, AU: etc.). The outputfile contains all
fields of one record on a single line. It is suited to be
read by DBase.
This section is divided into the following subsections:
Initialization, Options, Processing, Example ERL
datarecord, Example erl2db output record, Example profile,
Syntax of profile, Semantics of profile and Program exit
status.
Initialization
When erl2db is run, it starts scanning the commandline
parameters. Then erl2db looks for a profile in the current
directory. If no profile is found there, erl2db looks for
the system-wide profile in the directory where the program
resides. If no profile has been found, erl2db issues a
warning message: without a profile that contains an output
definition, no output records are generated. erl2db pro-
cesses the datafile(s) specified and outputs the converted
records and statistic information. When no files are spec-
ified, erl2db behaves as a filter program.
Options
erl2db can be executed with the following options:
-a author,
-h overview of options,
-D print debug information on stderr,
-d print debug information on stdout,
-e edit address when it contains too many fields,
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-ee force edit of addressfields,
-i select files specified on commandline interac-
tively,
-R print number of record last processed (stderr),
-r print number of record last processed (stdout),
-S print statistic message (grand total, on stderr),
-s print statistic message (grand total, on stdout),
-ss print also statistic message for each record,
-V print informative messages (filename, on stderr),
-v print informative messages (filename, on stdout),
-vv print also number of record ([d]) for each record
processed,
-vvv print also ERL fieldname ([ll]) for each field
processed,
-vvvv print also contents ([contents]) for each field
processed,
-- end option section,
-E editor-path
specify name or path of editor (implies -e),
-o output-file
specify name of outputfile.
A %s in the argument for option -E can be used to specify
the position of the name of the file with the address that
is to be edited.
Processing
erl2db processes one record at a time. First it scans the
various fields and does fieldspecific inputprocessing,
like case conversion and word substitutution, as specified
by the [Capitalize], [Title] etc. sections in the profile.
Then it writes the output record as specified by the pro-
file [Output] section and the record statistics as speci-
fied by the profile [Statistics] section.
Following are the most notable inputprocessing steps.
Title
The titleline is split into separate words. The words are
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lookup-up in the dictionary filled with entries from the
profile [Title] section and replaced when found. Finally
words not present in the dictionary are capitalized if so
specified in the profile [Capitalize] section. Words are
separated by the following characters: space, tab and
".,:;/'!?*()[]{}<>.
When the titleline is too long according to the corre-
sponding output definition, it is truncated and ends with
an ellipsis (...).
Authors
The format of the author fields is changed from e.g BOSCH-
MK to Bosch,M.K.. The names are capitalized as specified
in the profile [Capitalize] section.
The author names can be retrieved in an alternate output
format with the Authors_lt [Output] definition as: MK
Bosch.
In some instances, -(Reprint-Author) is appended to the
name of an author. This name can be retrieved with the
ReprintAuthor [Output] definition as: MK Bosch. If there
is no such indication, ReprintAuthor yields the name of
the first author.
Address
The address field is scanned upto the phrase (Reprint
Address). The words are lookup-up in the dictionary filled
with entries from the profile [Address] section and
replaced when found. Finally words not present in the dic-
tionary that are longer than two characters are capital-
ized if so specified in the profile [Capitalize] section.
Words are separated by, and do not contain the following
characters: space, comma and semicolon.
Journal
The journalname is obtained from the ERL SO: field. It is
changed from e.g. BIOCHEMISTRY-MOSCOW to Biochemistry
Moscow. The words are lookup-up in the dictionary filled
with entries from the profile [Journal] section and
replaced when found. Finally words not present in the dic-
tionary are capitalized if so specified in the profile
[Capitalize] section. Words are separated by, and do not
contain the following characters: dash and dot.
Keywords
The keywords are obtained from the ERL KW:, KA: and KP:
fields. The words are lookup-up in the dictionary filled
with entries from the profile [Keywords] section and
replaced when found. Finally words not present in the dic-
tionary are capitalized if so specified in the profile
[Capitalize] section. Words are separated by, and do not
contain the following characters: space and semicolon.
Abstract
The abstractline is split into words, separated by a
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space. When the abstract is too long according to the cor-
responding output definition, it is truncated and ends
with an ellipsis (...).
CC-Edition
The format of the Current Contents edition is changed from
e.g. CC-Life-Sciences to Life Sciences. The words of the
Current Contents edition are capitalized if so specified
in the profile [Capitalize] section. Words are separated
by, and do not contain the following characters: space and
dash.
Example ERL datarecord
An example of an ERL datarecord is shown below.
AN: RX893-16 See Table of Contents
TI: LACK OF BINDING COMPETITION BETWEEN DIURON AND PERFLUOROISOPROPYLDINITROBENZENE DERIVATIVES, NOVEL...
AU: ZHARMUKHAMEDOV-SK; KLIMOV-VV; ALLAKHVERDIEV-SI
AD: RUSSIAN ACAD SCI, INST SOIL SCI & PHOTOSYNTH, PUSHCHINO 142292 RUSSIA (Reprint Address)
SO: BIOCHEMISTRY-MOSCOW. JUN 1995; 60 (6) : 723-728.
PT: Article-Citation
PY: 1995
IS: 0006-2979
LA: ENGLISH
KA: PHOTOSYSTEM II; LIGHT INDUCED ELECTRON TRANSFER; ELECTRON TRANSFER INHIBITORS; DIURON; COMPETITIVE...
KP: THYLAKOID MEMBRANE; HERBICIDE BINDING; REACTION CENTERS; FLUORESCENCE; PLASTOQUINONE; CHLOROPLASTS;...
AB: Binding competition between Diuron and perfluoroisopropyldinitrobenzene (PFIPDNB)(3) derivatives, novel...
JS: BIOCHEMISTRY-AND-BIOPHYSICS
CC: CC-Life-Sciences
RF: 32 REFS
GA: RX893
UD: 9603
Example erl2db output record
Here is the erl2db output record for the ERL datarecord
shown above, when erl2db is used with the profile as shown
in subsection Example profile below. Note that all infor-
mation is contained in one line.
"Zharmukhamedov","S.K.","Klimov","V.V.","Allakhverdiev","S.I.","","","","","","",
"PHOTOSYSTEM II","LIGHT INDUCED ELECTRON TRANSFE","ELECTRON TRANSFER INHIBITORS",
"DIURON","COMPETITIVE BINDING","THYLAKOID MEMBRANE","HERBICIDE BINDING",
"REACTION CENTERS","FLUORESCENCE","PLASTOQUINONE",
"Lack Of Binding Competition Between Diuron And Perfluoroisopropyldinitrobenzene
Derivatives, Novel Inhibitors Of Electron Transfer In Photosystem II",
"Biochemistry Moscow","English","J","60","723","728",
"SK Zharmukhamedov",
"Russian Acad Sci","Inst Soil Sci & Photosynth","Pushchino 142292 Russia","","","","",
"1995",
"Binding competition between Diuron and perfluoroisopropyldinitrobenzene
(PFIPDNB)(3) derivatives, novel inhibitors of photosystem II (PS II), was
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ERL2DB(1) ERL2DB(1)
investigated by studying their effect on the electron transfer reactions in
PS II. The inhibition of PS ","II reactions by the PFIPDNB derivatives was
insensitive to Diuron at concentrations that exceed that of sdthe PFIPDNB
derivatives by two orders of magnitude. The lack of the functional
competition between these substances indicates that the binding sit","e for
the PFIPDNB derivatives is different from that for Diuron, a known inhibitor
of electron transfer in PS II.","","","","","","","","9603"
Example erl2db log-messages
Here is an example of the erl2db log-messages, obtained
with option -vvv.
[AN][TI][AU][AD][SO][PT][PY][IS][LA][KA][KP][AB][JS][CC][RF][GA][UD][2]
Record #2:
title complete
abstract complete
journal complete
volume complete
publication year complete
begin page complete
end page complete
language complete
3 authors, 0 truncated, 0 skipped
15 keyword fields, 1 truncated, 5 skipped
3 address fields, 0 truncated, 0 skipped, not edited
...
Grand total of:
1 file processed
72 records processed
0 titles truncated
2 abstracts truncated
0 journal names truncated
0 volume fields truncated
0 publication years truncated
0 begin pages truncated
0 end pages truncated
1 language field truncated
273 authors, 0 truncated, 3 skipped
810 keyword fields, 26 truncated, 162 skipped
305 address fields, 6 truncated, 0 skipped, 0 addresses edited
Example profile
The profile contains information on which fields must
undergo case conversion (be capitalized), the specific
spelling and case of words in title, keyword, journal and
address fields, the specification of the format of the
output record and the specification of the statistic
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information that is to be printed (see also subsection
Syntax of profile).
Here is an example erl2db profile.
#
# bin/erl2db.pro - system wide profile for ERL to Dbase conversion program.
#
#
# Capitalization of the following fields:
#
[Capitalize]
Authors
Title
Journal
Language
Address
#
# Word spelling and capitalization, as used in title translation:
#
[Title]
"II" = "II" # as in Photosystem II
"EPR" = "EPR" # abbreviation
#
# Word spelling and capitalization, as used in journal translation:
#
[Journal]
"AND" = "and"
"ET" = "et"
"THE" = "the"
"OF" = "of"
#
# Word spelling and capitalization, as used in address translation:
#
[Address]
"POB" = "POB" # as in POB 9504
"USA" = "USA" # as in NY 10032 USA
#
# output field format:
#
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[Output]
Authors = "30, 10, 10" # nameWidth, initWidth, #
Number = " " # authorArtn = "5"
Keywords = "30, 10" # width, #
Title = "250, 1" # width, #
Journal = "100" # width
Language = "7" # width ( 3? )
String = "J" # default Journal
Volume = "8" # width
BeginPage = "6" # width
EndPage = "6" # width
ReprintAuthor = "30" # width
Address = "30, 7" # width, #
PublicationYear = "4" # width
Abstract = "250, 10" # width, #
UpdateCode = "4" # width
#
# statistic fields to print:
#
[Statistics]
File
Record
Title
Abstract
Journal
Volume
PublicationYear
BeginPage
EndPage
Language
Authors
Keywords
Address
#
# End of file
#
Syntax of profile
The syntax of the profile is shown below. The contents of
the profile are divided into sections. The definitions of
these sections are case-sensitive. Comments are intro-
duced by a # and extend to the end of the line. Comments
and whitespace are ignored.
To simplify the syntax of the profile, a single set of
reserved words is used for all sections, though not all
reserved words are meaningful in each section (e.g.
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PublicationYear in section [Capitalize]). In these circum-
stances, the use of a reserved word is silently ignored.
Use of an invalid word in a section is signalled as an
error though.
definition ::= section*
section ::= capitalize-section
| title-section
| keywords-section
| journal-section
| address-section
| output-section
| statistics-section
capitalize-section ::= '[Capitalize]' enumeration-entry*
title-section ::= '[Title]' dictionary-entry*
keywords-section ::= '[Keywords]' dictionary-entry*
journal-section ::= '[Journal]' dictionary-entry*
address-section ::= '[Address]' dictionary-entry*
output-section ::= '[Output]' definition-entry*
statistics-section ::= '[Statistics]' enumeration-entry*
enumeration-entry ::= reserved-word
dictionary-entry ::= string '=' string
definition-entry ::= reserved-word '=' string
string ::= '"' [printable]* '"'
reserved-word ::= 'Abstract'
| 'Address'
| 'Authors'
| 'Authors_lt'
| 'BeginPage'
| 'CC-Edition'
| 'EndPage'
| 'File'
| 'GenuineArticle'
| 'ISSN'
| 'Journal'
| 'JournalSubject'
| 'Keywords'
| 'Language'
| 'Number'
| 'PublicationType'
| 'PublicationYear'
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| 'RecordType'
| 'Record'
| 'References'
| 'ReprintAuthor'
| 'String'
| 'Title'
| 'UpdateCode'
| 'Volume'
Semantics of profile
The strings at the left side of the assignment in dictio-
nary entries should be single words in accordance with the
word-splitting mechanism for that dictionary section.
The output format definitionstrings in the [Output] sec-
tion come in three versions:
"fieldwidth, fieldwidth, number-of-fields"
Authors (name,
initials).
"fieldwidth, number-of-fields" Abstract,
Authors_lt, Key-
words, Title.
"fieldwidth" all other output-
fields
The Number and String output definitions can be used to
insert static numerical and string fields into the output
record (see subsection Example profile).
The File and Record reserved words are normally used in
the [Statistics] section only. However, they also can be
used in the [Output] section to provide the name of the
file being processed and the number of the record respec-
tively.
Meaningful and correct statistic information can only be
gathered for fields that are included in the [Output] sec-
tion, except for the fields File and Record. Because it is
checked if a field for which statistic information is
requested is included in the [Output] section, the [Out-
put] section should precede the [Statistics] section.
Program exit status
When a file cannot be found, or the file cannot be prop-
erly processed, the program stops and issues an error mes-
sage. The failure to process a file is reflected in the
programs exit status (see DIAGNOSTICS below).
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ERL2DB(1) ERL2DB(1)
ENVIRONMENT
COMSPEC command interpreter used to run the editor
for address-editing.
FILES
erl2db.pro profile in current directory,
bin\erl2db.pro system-wide profile, in same directory as
erl2db.exe.
DIAGNOSTICS
erl2db can return the following exit values:
0 success: program execution has been successfully com-
pleted,
1 commandline error: an invalid option is specified,
2 processing error: a file could not be opened or closed,
an error occurred while writing to an output file,
3 interruption: the user interrupted the program,
4 internal error: an unexpected situation in program
behaviour occurred.
SEE ALSO
mkdb(1), mkdbfix(1),
EXAMPLE
erl2db -RssvvvE "c:\bin\e %s 2" -o erl2db.out erl2db.inp >
erl2db.log
BUGS
(to be determined.)
AUTHOR
M.J. Moene
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