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IBP banding data system: Internal maintenance specification

Table of Contents

1. Overview

1.1. How to get this publication
1.2. Files generated from this document

2. Installation

2.1. Unix installation from a .zip archive
2.2. Unix installation from the Web

3. Object architecture

3.1. Architecture of the data compilers
3.2. Encounter (output) objects
3.3. Station authority files
3.4. Species authority files

4. baseclasses.py: Prologue

5. Manifest constants

5.1. Constants for species authority files
5.2. Constants related to encounter records
5.3. Encounter codes
5.4. Encounter record attribute names
5.5. Band number constants

6. scanFieldList(): A utility routine for flat-file scanning

7. scanFieldItems(): Parse a sequence of FieldItem objects

8. class BaseStationSet: Base class for station authority objects

8.1. BaseStationSet.locationLookup()
8.2. BaseStationSet.stationNoLookup()
8.3. BaseStationSet.__init__(): Constructor
8.4. BaseStationSet.readLine(): Read one station line
8.5. BaseStationSet.addStation(): Add a new station

9. class Location: Represents a group of stations

9.1. Location.__init__(): Constructor
9.2. Location.addStation(): Add a new station to a location
9.3. Location.lookupStaCode()
9.4. Location.__str__()

10. class Station: Represents one station

10.1. Station.__init__(): Constructor
10.2. Station.__str__()

11. class MapsStationSet: Station set object

11.1. MapsStationSet.__init__()
11.2. MapsStationSet.readline()

12. class MawsStationSet: Station set object

12.1. MawsStationSet.__init__()

13. class BaseSpeciesSet: Base class for species authority objects

13.1. BaseSpeciesSet.lookupSpec4()
13.2. BaseSpeciesSet.lookupSpec6()
13.3. BaseSpeciesSet.engRe(): Search English names
13.4. BaseSpeciesSet.__init__(): Constructor
13.5. BaseSpeciesSet.readLine()
13.6. BaseSpeciesSet.addSpecies(): Add a new species line

14. class Maps2004SpeciesSet

14.1. Maps2004SpeciesSet.__init__()
14.2. Maps2004SpeciesSet.readLine()

15. class Maps1998SpeciesSet

16. class Maws2002SpeciesSet

17. class SpeciesSearcher: Logic for the species code search scripts

17.1. SpeciesSearcher: Manifest constants
17.2. SpeciesSearcher.__init__()
17.3. SpeciesSearcher.run(): Execute a search
17.4. SpeciesSearcher.run4(): Four-letter code search
17.5. SpeciesSearcher.run6()
17.6. SpeciesSearcher.runEng()

18. class Species: Definition of a species code

18.1. Species.__init__(): Constructor
18.2. Species.__str__()

19. class BaseCompiler: Base class for banding data compilers

19.1. class BaseCompiler: The interface
19.2. Internal state of the BaseCompiler class
19.3. BaseCompiler.__init__(): Constructor
19.4. BaseCompiler.parseFileName(): Parse the batch file name
19.5. BaseCompiler.parseFileLocality(): Find the location or station code in a batch file name
19.6. BaseCompiler.checkForLocation()
19.7. BaseCompiler.checkForStation()
19.8. BaseCompiler.scanCallback(): Error localization string
19.9. BaseCompiler.__iter__(): Iterator
19.10. BaseCompiler.classify(): Which kind of line is it?
19.11. BaseCompiler.scanPageHeader(): Process a page header line
19.12. BaseCompiler.scanPrefix(): Process a band prefiix line
19.13. BaseCompiler.scanEncounter(): Process an encounter line

20. class Maps2006Compiler: Compiler for MAPS 2006 files

21. class Maps2004Compiler: Compiler for MAPS 2004 protocol

21.1. Maps2004Compiler.scanEncounter()

22. class Maws2007Compiler: MAWS 2007 compiler

22.1. Maws2007Compiler.scanEncounter()

23. class Maws2004Compiler: MAWS compiler

23.1. Maws2004Compiler.scanEncounter()

24. class PageHeader: Page header line object

24.1. PageHeader.__init__(): Constructor
24.2. PageHeader.scanLine(): Scan a page header line
24.3. PageHeader.checkSite(): Verify correct location or station

25. class Prefix: Band number prefix line

25.1. Prefix.__init__(): Constructor
25.2. Prefix.scanLine(): Scan a band prefix line

26. class FieldItem: Base class for encounter record fields

27. class SingleField: Generic single-character field

27.1. SingleField.scanField()
27.2. SingleField.flatten(): Flatten single-character field

28. class PageNoField: Page number field

28.1. PageNoField.flatten()

29. class BandSizeField: Band size field

29.1. BandSizeField.flatten()

30. class LocationField: Location code field

30.1. LocationField.flatten()

31. class CaptureCodeField: Encounter record type code

31.1. CaptureCodeField.flatten()

32. class BandNoField: Band number field

32.1. BandNoField.prefix(): Extract band number prefix
32.2. BandNoField.suffix(): Extract band number suffix
32.3. BandNoField.incrementPrefix(): Increment a prefix with rollover
32.4. BandNoField.scanField()
32.5. BandNoField.flatten()
32.6. BandNoField.attachSuffix(): Join a band prefix and suffix

33. class BandNoSuffix: Short band number

33.1. BandNoSuffix.scanField()

34. class Spec4Field: Four-letter species code

34.1. Spec4Field.scanField()
34.2. Spec4Field.flatten()

35. class Spec6Field: Six-letter MAWS species code

35.1. Spec6Field.scanField()
35.2. Spec6Field.flatten()

36. class AgeCodeField: Age code

36.1. AgeCodeField.scanField()

37. class HowGroupField: How-code group

37.1. HowGroupField.scanField(): Scan a group of how-codes
37.2. HowGroupField.flatten()

38. class SexCodeField: Sex code

38.1. SexCodeField.scanField()

39. class SkullField: Skull ossification

39.1. SkullField.scanField()

40. class CloacalField: Cloacal protuberance

41. class BroodField: Brood patch

42. class FatField: Fat class

43. class BodyMoltField: Body molt

44. class FlightMoltField: Flight feather molt

45. class FlightWearField: Flight feather wear

46. class JuvenalField: Juvenal plumage

47. class MicroAgingField: Base class for microaging fields

48. class MicroPPCField: Primary coverts micro-aging field

49. class MicroSSCField: Secondary coverts micro-aging field

50. class MicroPPFField: Primaries micro-aging field

51. class MicroSSFField: Secondaries micro-aging field

52. class MicroTTField: Tertials micro-aging field

53. class MicroRRField: Rectrices micro-aging field

54. class MicroHDField

55. class MicroUPPField

56. class MicroUNPField

57. class MicroBPLField: Body plumage micro-aging field

58. class MicroNFField: Non-feather micro-aging field

59. class WingField: Wing length

59.1. WingField.scanField(): Scan a wing length field
59.2. WingField.flatten()

60. class MassField: Body mass

60.1. MassField.scanField()
60.2. MassField.flatten()

61. class StatusField: Release status code

61.1. StatusField.scanField()
61.2. StatusField.flatten()

62. class DateField: Date field

62.1. DateField.scanField()
62.2. DateField.flatten()

63. class MawsDateField: MAWS date field

63.1. MawsDateField.scanField()

64. class HHMField: Time of day

64.1. HHMField.scanField()
64.2. HHMField.flatten()

65. class StationCodeField: Station code

65.1. StationCodeField.scanField()
65.2. StationCodeField.flatten()

66. class Net2Field: Two-character net code

66.1. Net2Field.scanField()
66.2. Net2Field.flatten()

67. class Net4Field: Four-character net code

67.1. Net4Field.scanField()
67.2. Net4Field.flatten()

68. class DispositionField

68.1. DispositionField.scanField()

69. class NoteField: Note number

69.1. NoteField.scanField()
69.2. NoteField.flatten()

70. class PulledField: Feather-pulled code

71. class ColorBandsField: Color-band sequence

71.1. ColorBandsField.scanField()
71.2. ColorBandsField.flatten()

72. class SwabField: Cloacal swab code

72.1. SwabField.scanField()

73. class BaseEncounter: General output record

73.1. Design notes for the BaseEncounter class
73.2. BaseEncounter.OUT_FIELD_LIST: Definition of the output format
73.3. BaseEncounter.__init__(): Constructor
73.4. BaseEncounter.__getattr__(): Handle references to undefined attributes
73.5. BaseEncounter.flatten(): Convert to a flat-file record
73.6. BaseEncounter.scanLine(): Scan a raw encounter record
73.7. BaseEncounter.scanShort(): Scan lost or destroyed encounter line
73.8. BaseEncounter.scanUnbanded(): Scan unbanded encounter line
73.9. BaseEncounter.scanNewBand(): Scan short new-band line
73.10. BaseEncounter.scanLongNew(): Scan long new-band line
73.11. BaseEncounter.scanRecap(): Scan recapture encounter line
73.12. BaseEncounter.dispatchMap: Encounter record routing dictionary
73.13. BaseEncounter.scanBody(): Scan encounter line body and tail sections
73.14. BaseEncounter.scanTail(): Scan tail fields
73.15. BaseEncounter.scanTailField(): Scan one free-form tail field
73.16. BaseEncounter.tailColor(): Scan color-band tail
73.17. BaseEncounter.tailDisposition(): Scan disposition code tail field
73.18. BaseEncounter.tailPulled(): Scan feather-pulled tail field
73.19. BaseEncounter.tailNote(): Scan note tail field
73.20. BaseEncounter.tailSwab(): Scan swab tail field
73.21. BaseEncounter.tailDispatch: Tail field routing dictionary
73.22. BaseEncounter.copyDitto(): Implement single-column ditto

74. class Maps2004Encounter

74.1. Maps2004Encounter.OUT_FIELD_LIST: Output format definition
74.2. Maps2004Encounter.scanBody()
74.3. Maps2004Encounter.scanTail()
74.4. Maps2004Encounter.scanOldAlign(): Scan old alignment or feather-pulled field
74.5. Maps2004Encounter.scanLongTail()

75. class Maws2007Encounter

75.1. Maws2007Encounter.BODY_FIELD_LIST
75.2. Maws2007Encounter.scanBody(): Scan encounter line body and tail sections

76. class Maws2004Encounter

76.1. Maws2004Encounter.OUT_FIELD_LIST: Output record format table
76.2. Maws2004Encounter.BODY_FIELD_LIST

77. iband7: Current MAPS data compiler

77.1. Prologue
77.2. Imports
77.3. Manifest constants
77.4. iband7 main()
77.5. Epilogue
77.6. Test files for iband7

78. maps2004: MAPS data compiler for 2004 protocol

78.1. Prologue
78.2. Imports
78.3. Manifest constants
78.4. maps2004 main()
78.5. Epilogue

79. maps1998: MAPS data compiler for 1998 protocol

80. imaws2007: Current MAWS data compiler

80.1. Prologue
80.2. Imports
80.3. Manifest constants
80.4. imaws2007 main()
80.5. Epilogue

81. imaws2004: MAWS 2004 data compiler

81.1. Prologue
81.2. Imports
81.3. Manifest constants
81.4. imaws2004 main()
81.5. Epilogue

82. showstas: Look up MAPS station and location codes

82.1. showstas: Prologue
82.2. showstas: Imports
82.3. showstas: main
82.4. showstas: Epilogue

83. showmaws: Look up MAWS station and location codes

83.1. showmaws: Prologue
83.2. showmaws: Imports
83.3. showmaws: Manifest constants
83.4. showmaws: main
83.5. showmaws: Epilogue

84. spec2004, spec2002, and spec1998

84.1. spec2004 prologue
84.2. spec2004: Main
84.3. spec2004: Epilogue
84.4. spec2002
84.5. spec1998

85. dbfstruct: Display the structure of a dBASE V file

85.1. Prologue
85.2. main()
85.3. headerReport(): General information
85.4. fieldReport(): Report on field definitions
85.5. Epilogue

86. dbflatten: Convert a dBASE V file to flat format

86.1. Prologue
86.2. main()
86.3. flattenRecord(): Flatten one record
86.4. flattenField(): Flatten one field
86.5. Epilogue

87. The dbfpy package for reading dBASE V files

87.1. Dbf: Database object
87.2. DbfHeader: Database header object
87.3. DbfFieldDef: Field definition object
87.4. DbfRecord: Record object

1. Overview

This document describes the implementation of the system specified by iband7: IBP banding data entry system.

The actual code for several applications is contained in this document, document in literate style. For more information, see the author's lightweight literate programming page.

1.1. How to get this publication

This publication is available in Web form and also as a PDF document. Please forward any comments to john@nmt.edu.

1.2. Files generated from this document

This document is an exposition of the source code using lightweight literate programming practice: the source code is extracted from this document, so what you see here is the actual code. For more information on this practice, see the author's Lightweight Literate Programming page.

Here are links to all the files generated by extraction from this documentation's source file:

These files are not extracted from the source file, but are necessary or useful:

ibandims.xml: DocBook source file for this document, including all extracted source files.
Makefile: Used by the make utility to build HTML and PDF documentation and extract source code.
cset.py: A module from the author's standard Python library to represent sets of characters.
dump2006: A quick-and-dirty script to display output files in the MAPS 2006 protocol, used in testing iband7.
log.py: A module from the author's standard Python library that does error logging.
scan.py: A module from the author's standard Python library that manages reading an input stream and reporting errors on it.
README: Manifest of most of the files in this directory and what they do.

To execute some of these programs, you will need the public-domain, external dbf.py module; see Section 87, “The dbfpy package for reading dBASE V files”, which has links to the download page, and all the files from that module currently in use.

Next: 2. Installation

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John W. Shipman

Comments welcome: john@nmt.edu

Last updated: 2009-10-20 14:16

URL: http://infohost.nmt.edu