minsci package

Subpackages

• minsci.deepdict package
  • Submodules
  • minsci.deepdict.deepdict module
  • Module contents
• minsci.geobots package
  • Submodules
  • minsci.geobots.containers module
  • minsci.geobots.geobots module
  • minsci.geobots.plss module
  • Module contents
• minsci.geotaxa package
  • Subpackages
    • minsci.geotaxa.containers package
      • Submodules
      • minsci.geotaxa.containers.minscitaxon module
      • Module contents
  • Submodules
  • minsci.geotaxa.geotaxa module
  • minsci.geotaxa.updater module
  • Module contents
• minsci.xmu package
  • Subpackages
    • minsci.xmu.containers package
      • Submodules
      • minsci.xmu.containers.auditrecord module
      • minsci.xmu.containers.bibliorecord module
      • minsci.xmu.containers.mediarecord module
      • minsci.xmu.containers.minscirecord module
      • minsci.xmu.containers.taxonrecord module
      • minsci.xmu.containers.xmurecord module
      • Module contents
    • minsci.xmu.tools package
      • Subpackages
        • minsci.xmu.tools.biblio package
          • Submodules
          • minsci.xmu.tools.biblio.bibbot module
          • minsci.xmu.tools.biblio.bibcheck module
          • minsci.xmu.tools.biblio.doi module
          • minsci.xmu.tools.biblio.ris module
          • Module contents
        • minsci.xmu.tools.multimedia package
          • Submodules
          • minsci.xmu.tools.multimedia.cataloger module
          • minsci.xmu.tools.multimedia.embedder module
          • minsci.xmu.tools.multimedia.hasher module
          • Module contents
      • Submodules
      • minsci.xmu.tools.audits module
      • minsci.xmu.tools.describer module
      • minsci.xmu.tools.groups module
      • minsci.xmu.tools.legacy module
      • minsci.xmu.tools.mapper module
      • minsci.xmu.tools.matcher module
      • minsci.xmu.tools.operations module
      • Module contents
  • Submodules
  • minsci.xmu.fields module
  • minsci.xmu.xmu module
  • minsci.xmu.xmungo module
  • Module contents

Submodules

minsci.exceptions module

Custom exceptions for minsci module

exception minsci.exceptions.MinSciException

Bases: exceptions.Exception

Root exception. Used only to except any error, never raised.

exception minsci.exceptions.PathError

Bases: minsci.exceptions.MinSciException

Called when pull request on DeepDict fails to resolve

exception minsci.exceptions.RowMismatch

Bases: minsci.exceptions.MinSciException

Called when columns in table have different numbers of rows

exception minsci.exceptions.TaxonNotFound

Bases: minsci.exceptions.MinSciException

Called when columns in table have different numbers of rows

minsci.helpers module

Helper functions used throughout the minsci module

minsci.helpers.add_article(val)

Prepend the appropriate indefinite article to a string

Parameters:val (str) – string to which to add a/an Returns:String with indefinite article prepended

minsci.helpers.base2int(i, base)

Converts integer in specified base to base 10

minsci.helpers.catnum_keyer(catnum)

Create sortable key for a catalog number by zero-padding each component

Parameters:catnum (str or dict) – the catalog number to key Returns:Sortable catalog number

minsci.helpers.cprint(obj, show=True)

Conditionally pretty print an object

Parameters:

• obj (mixed) – the object to print
• show (bool) – print the object if true

minsci.helpers.dedupe(lst, lower=True)

Dedupes a list while maintaining order and case

Parameters:list (list) – a list of strings Returns:Deduplicated copy of the original list

minsci.helpers.dict_from_odbc(cursor, tbl, row_id=None, cols=None, where=None, encoding='cp1252')

Creates a :param cursor: :type cursor: pyodbc.Cursor :param tbl: name of table to query. For Excel, table name must be

formatted as [tbl$].

Parameters:

• row_id (list) – name of field(s) to use as key for dictionary
• col (list) – list of columns to return. If None, will return all.
• where (str) – formatted where clause
• encoding (str) – encoding of source file

Returns:

Dictionary keyed to row_id

minsci.helpers.format_catnum(parsed, code=True, div=False)

Formats parsed catalog number to a string

Parameters:

• parsed (dict) – parsed catalog number
• code (bool) – include museum code in catnum if True
• div (bool) – include div abbreviation in catnum if True

Returns:

Catalog number formatted as a string, like ‘G3551-00’. Use format_catnums to process a list of parsed catalog numbers.

minsci.helpers.format_catnums(parsed, code=True, div=False)

Converts a list of parsed catalog numbers into strings

Parameters:

• parsed (list) – list of dicts containing parsed catnums
• code (bool) – include museum code in catnum if True
• div (bool) – include div abbreviation in catnum if True

Returns:

[‘G3551-00’]

Return type:

List of catalog numbers formatted as strings

minsci.helpers.fxrange(start, stop, step)

Mimics functionality of xrange for floats

From http://stackoverflow.com/questions/477486/

Parameters:

• start (int or float) – first value in range (inclusive)
• stop (int or float) – last value in range (exclusive)
• step (float) – value by which to increment start

minsci.helpers.init_odbc(fn)

Opens ODBC connection based on database type

Parameters:fn (string) – filename (or path) Returns:pyodbc.Connection object

minsci.helpers.int2base(i, base)

Converts base 10 integer to specified base

minsci.helpers.lcfirst(val)

Lowercase first letter of string while leaving the rest alone

Parameters:val (str) – string to capitalize Returns:Capitalized string

minsci.helpers.localize_datetime(timestamp, timezone_id='US/Eastern', mask='%Y-%m-%dT%H:%M:%S')

Loclize timestamp to specified timezone

Returns:Localize datetime as string formatted according to the mask

minsci.helpers.oxford_comma(lst, lowercase=False)

Formats list as comma-delimited string

Parameters:

• lst (list) – list of strings
• lowercase (bool) – if true, convert the first letter in each value in the list to lowercase

Returns:

Comma-delimited string

minsci.helpers.parse_catnum(val, attrs=None, default_suffix='', min_suffix_length=0, strip_suffix=False, prefixed_only=False)

Find and parse catalog numbers in a string

Parameters:

• s (str) – string containing catalog numbers or range
• attrs (dict) – additional parameters keyed to EMu field
• default_suffix (str) – default suffix to add if none present
• strip_suffx (bool) – strip leading zeroes from suffix if True
• prefixed_only (bool) – find only those catalog numbers that are prefixed by a valid museum code (NMNH or USNM)

Returns:

List of dicts containing catalog numbers parsed into prefix, number, and suffix: {‘CatPrefix’: ‘G’, ‘CatNumber’: ‘3551’, ‘CatSuffix’: 00}. Pass to format_catnums to convert to strings.

minsci.helpers.parse_catnums(vals, **kwargs)

Parse a list of strings containing catalog numbers

See parse_catnums() for a description of the available arguments.

Returns:A list of parsed catnums

minsci.helpers.parse_names(name_string, last_name_first=False)

Parses name strings into components using nameparser

minsci.helpers.plural(val)

Converts string to plural

Parameters:s (str) – a string Returns:The plural form of the original string

minsci.helpers.prompt(text, validator, confirm=False, helptext='No help text provided', errortext='Invalid response!')

Prompts for and validates user input

Parameters:

• text (str) – the prompt to present to the user
• validator (mixed) – the dict, list, or string used to validate the repsonse
• confirm (bool) – if true, user will be prompted to confirm value
• helptext (str) – text to show if user response is “?”
• errortext (str) – text to return if user response does not validate

Returns:

Validated response to prompt

minsci.helpers.read_file(path, success, error=None)

Process file at given path using success callback

minsci.helpers.read_unicode_text(fp, encoding='utf-16', skiplines=0)

Read a unicode text file generated by Excel

minsci.helpers.rprint(obj, show=True)

Pretty print object, then pause execution

Parameters:

• obj (mixed) – the object to print
• show (bool) – print the object if true

minsci.helpers.singular(val)

Converts string to singular

Parameters:s (str) – a string Returns:The singular form of the original string

minsci.helpers.sort_by_reference(lst, order)

Reorder list to match order of another list

minsci.helpers.sort_catnums(catnums)

Sort a list of catalog numbers

Parameters:catnums (list) – list of catalog numbers, either as strings or parsed into dicts Returns:Sorted list of catalog numebrs. Catalog numbers are formatted in the same way as they were in the original list.

minsci.helpers.std(val, aggressive=False)

Standardizes the given value for string comparisons

Parameters:aggressive (bool) – if True, strips everything except letters and numbers Returns:Standardized value as unicode

minsci.helpers.ucfirst(val)

Capitalize first letter of string while leaving the rest alone

Parameters:val (str) – string to capitalize Returns:Capitalized string

minsci.helpers.utflatten(val)

Converts diacritcs in string to their to an ascii equivalents

Modified to use the unidecode module, but kept alias so older scripts will still work.

minsci.helpers.write_emu_search(mask, catnums, output='search.txt')

Module contents

Provides helper functions used throughout the minsci module