mli.lib package

Submodules

mli.lib.config module

The module provides an interface for reading and editing the configuration file.

Classes:

ConfigProgram(sFilePath=’config.ini’)

Using:

There are two ways to use the class.

Foo = ConfigProgram()

or

Foo = ConfigProgram('my_config.ini')

Now you can read parameters from configfile and save to it.

Parameter = Foo.get_config_value(Section, Option)
class mli.lib.config.ConfigProgram(sPathApp, sFilePath='config.ini')[source]

Bases: ConfigParser

A class for working with a configuration file. Allows you to read from the configuration file and write there.

Using:
Foo = ConfigProgram()

# For reading.
Section = 'bar'
Options = 'baz'
Value = Foo.get_config_value(Section, Option)

# For writing.
Value = 'some_string'
Foo.set_config_value (Section, Option, Value)

If you only need to create a Section and an Option, you omit the Value.

get_config_value(sSection, sOption)[source]

The method allows reading from a configuration file.

Parameters

  • sSection (str) – The section in the configuration file to read from.

  • sOption (str) – The option in the configuration file to need reading.

Returns

The value of the specified parameter in the section.

Return type

str

set_config_value(sSection, sOption, sValue='')[source]

The method allows writing into a configuration file.

Parameters

  • sSection (str) – The section in the configuration file to write to.

  • sOption (str) – The option in the configuration file to write to.

  • sValue (str) – The value to write.

mli.lib.gbif_parser module

The module provides a means to get information from a taxon, as specified in gbif .

function:

gbif_get_children(sGBIF_id) gbif_get_id_from_gbif(sName, sLevel=’species’) gbif_get_id(oConnector, sName, sLevelEn) gbif_get_many(sURL, sGBIF_id) gbif_get_status_id(oConnector, sStatus) gbif_get_synonyms(sGBIF_id) gbif_get_taxon_info(sGBIF_id, sLevel=’species’) gbif_get_update(oConnector, iLevel) gbif_is_lichen(dTaxon) gbif_parser_name(sString) gbif_parser_taxon(dData) gbif_parsing_answer(oConnector, lAnswer, sType) gbif_parsing_species(oConnector, dAnswer) gbif_save_species(oConnector, dAnswer, iLevel) gbif_update(oConnector, dAnswer, iTaxonID)

mli.lib.gbif_parser.gbif_get_children(sGBIF_id)[source]
Generates an api link for obtaining children from the server and

returns a normalized response.

Parameters

sGBIF_id – A key ID of taxon in gbif.

Type

str

Returns

A normalized response.

Return type

list[dict[str, bool, str, str, str, str, str, int]|None]

mli.lib.gbif_parser.gbif_get_id(oConnector, sName, sLevelEn)[source]

Checks if the taxon’s id exists in the database, and if it doesn’t, it gets it from the site.

Parameters

  • oConnector (SQL) – An instance of the sqlite database api class.

  • sName (str) – A name of the taxon.

  • sLevelEn (str) – A name of the taxon rank in english language.

Returns

ID taxon in gbif.

Return type

int

mli.lib.gbif_parser.gbif_get_id_from_gbif(sName, sLevel='species')[source]

Looks up a taxon name in the gbif database.

Parameters

  • sName (str) – The name of a taxon.

  • sLevel (str) – The rank of a taxon.

Returns

Key ID of the taxon in gbif.

Return type

str

mli.lib.gbif_parser.gbif_get_many(sURL, sGBIF_id)[source]
Generates an api link for obtaining children from the server and

returns a normalized response.

Parameters

  • sURL (str) – An URL for sending to gbif server.

  • sGBIF_id – A key ID of taxon in gbif.

Type

str

Returns

A normalized response.

Return type

list[dict[str, bool, str, str, str, str, str, int]|None]

mli.lib.gbif_parser.gbif_get_status_id(oConnector, sStatus)[source]

Returns the status id from the database.

Parameters

  • oConnector (SQL) – An instance of the sqlite database api class.

  • sStatus (str) – The name of the status, as is customary in gbif.

Returns

the status ID.

Return type

int or bool

mli.lib.gbif_parser.gbif_get_synonyms(sGBIF_id)[source]
Generates an api link for obtaining synonyms from the server and

returns a normalized response.

Parameters

sGBIF_id – A key ID of taxon in gbif.

Type

str

Returns

A normalized response.

Return type

list[dict[str, bool, str, str, str, str, str, int]|None]

mli.lib.gbif_parser.gbif_get_taxon_info(sGBIF_id, sLevel='species')[source]

General information about the taxon by its ID.

Parameters

  • sGBIF_id – A key ID of taxon in gbif.

  • sLevel (str) – A level of the taxon.

Type

str

Returns

A normalized dictionary of taxon information.

Return type

dict[str, bool, str, str, str, str, str, int]|None

mli.lib.gbif_parser.gbif_get_update(oConnector, iLevel)[source]

Allows you to select all names from the database by level, start getting data from gbif and enter information into the database.

Parameters

  • oConnector (SQL) – An instance of the sqlite database api class.

  • iLevel (int) – ID of a rank in database.

Returns

None

mli.lib.gbif_parser.gbif_is_lichen(dTaxon)[source]

Checks if the taxon is a lichen.

Parameters

dTaxon (dict) – Filed ‘result’ of answer from gbif.

Returns

True if taxon is lichen, and False if opposite.

Return type

bool

mli.lib.gbif_parser.gbif_parser_name(sString)[source]

Parsing a name of the taxon separating the canonical name from the name of the author and year, if possible.

Parameters

sString (str) – A string with a name of the taxon.

Returns

A canonical name, an author name and a naming year of the taxon.

Return type

list[str, str, int]

mli.lib.gbif_parser.gbif_parser_taxon(dData)[source]
Selects from the server response the information necessary for further

processing.

Parameters

dData (dict) – An answer of server.

Returns

Selection from the server response with the necessary information.

Return type

dict[str, bool, str, str, str, str, str, int]|None

mli.lib.gbif_parser.gbif_parsing_answer(oConnector, lAnswer, sType)[source]

Parses the response a list of dictionaries with taxon information.

Parameters

  • oConnector (SQL) – An instance of the sqlite database api class.

  • lAnswer (list[dict[str, bool, str, str, str, str, str, int]|None]) – A list of dictionaries with taxon information.

  • sType (str) – The first word to output to the string. It makes sense to indicate either ‘Synonym’ or ‘Children’.

Returns

None

mli.lib.gbif_parser.gbif_parsing_species(oConnector, dAnswer)[source]

Specifies whether to make changes to the database.

Parameters

  • oConnector (SQL) – An instance of the sqlite database api class.

  • dAnswer (dict[str, bool, str, str, str, str, str, int]) – A dictionary with information about the taxon.

Returns

None

mli.lib.gbif_parser.gbif_save_species(oConnector, dAnswer, iLevel)[source]

Saving information about the taxon in database.

Parameters

  • oConnector (SQL) – An instance of the sqlite database api class.

  • dAnswer (dict[str, bool, str, str, str, str, str, int]) – A dictionary with information about the taxon.

  • iLevel (int) – The level’s ID in database.

Returns

The taxon’s ID in database.

Return type

int or bool

mli.lib.gbif_parser.gbif_update(oConnector, dAnswer, iTaxonID)[source]

Updates information in the database about the author and naming year.

Parameters

  • oConnector (SQL) – An instance of the sqlite database api class.

  • dAnswer (dict[str, bool, str, str, str, str, str, int]) – A dictionary with information about the taxon.

  • iTaxonID (int) – The taxon’s ID in database.

Returns

None

mli.lib.log module

mli.lib.log.start_logging()[source]

mli.lib.sql module

The module provides an API for working with the database. It creates a multi-level API that can be used in other modules to create requests using a minimum of transmitted data.

Function:

get_columns(sColumns, sConj=’AND’)

Class:

SQL

Using:

Foo = SQL(_DataBaseFile_)

class mli.lib.sql.SQL(sFileDB)[source]

Bases: object

Provides interface for working with database from others scripts.

Methods
# Standard methods.

  • __init__ – Method initializes a cursor of sqlite database.

  • __del__ – Method closes the cursor of sqlite database.

# Low level methods.

  • export_db – Method exports from db to sql script.

  • execute_script – Method imports from slq script to db.

  • execute_query – Method execute sql_search query.

  • insert_row – Method inserts a record in the database table.

  • delete_row – Method deletes a row from the table.

  • update – Method updates value(s) in record of the database table.

  • select – Method does selection from the table.

# Average level API.

  • sql_get_id: Finds id of the row by value(s) of table column(s).

  • sql_get_all: Method gets all records in database table.

  • sql_count: Method counts number of records in database table.

  • sql_table_clean: Method cleans up the table.

del_garbage(sSource='GBIF')[source]
delete_row(sTable, sColumns=None, tValues=None)[source]

Deletes row in the database table by value(s).

Parameters

  • sTable (str or None) – A table as string in where need to delete row.

  • sColumns (str or None) – Column(s) where the value(s) will be found. (by default, None).

  • tValues (tuple or list) – value(s) as tuple for search of rows. (by default, None).

Returns

True if the deletion is successful, otherwise False.

Return type

bool

execute_query(sSQL, tValues=None)[source]

Method executes sql script.

Parameters

  • sSQL (str) – SQL query.

  • tValues (tuple or list or None) – value(s) that need to safe inserting into query (by default, None).

Returns

Cursor or bool – True if script execution is successful, otherwise False.

execute_script(sSQL)[source]

Method executes sql script.

The main difference from the method is the ability to execute several commands at the same time. For example, using this method, you can restore the database from sql dump.

Parameters

sSQL (str) – SQL Script as string.

Returns

True if script execution is successful, otherwise False.

Return type

bool

export_db()[source]

Method exports from db to sql script.

get_all_by_rank(iRank)[source]
get_color_id(sColumn, sValue)[source]
get_full_taxon_list()[source]
get_garbage()[source]
get_id_by_name_author(tValue, sTable='Taxa')[source]
get_id_by_name_status(tValue)[source]
get_main_taxon(iTaxonID)[source]
get_name_author(aValue)[source]
get_rank_id(sColumns, sValues)[source]
get_rank_name(sColumns, iValues)[source]
get_source_id(sValue)[source]
get_status_id(sValue, sColumn='statusLocalName')[source]
get_status_taxon(sSciName)[source]
get_statuses()[source]
get_substrate_id(sValue)[source]
get_synonym_id(sSciName)[source]
get_synonyms(iValue)[source]
get_taxon_children(iID, sStatus)[source]
get_taxon_id(sSciName, sAuthor='')[source]
get_taxon_info(sName)[source]
get_taxon_list(sStatus)[source]
get_taxon_rank(sSciName)[source]
insert_row(sTable, sColumns, tValues)[source]

Inserts a record in the database table.

Parameters

  • sTable (str) – Table name as string.

  • sColumns (str) – Columns names of the table by where needs inserting.

  • tValues (tuple or list) – Value(s) as tuple for inserting.

Returns

ID of an inserted row if the insert was successful. Otherwise, False.

Return type

str or bool

insert_taxon(sName, sAuthor, iYear, PublishedIn, iRank, iMainTax, iStatus)[source]
select(sTable, sGet, sWhere='', tValues='', sConj='', sFunc='')[source]

Looks for row by value(s) in table column(s).

Parameters

  • sTable (str) – Table name as string.

  • sGet (str) – Name of the column of the table, which will be returned.

  • sWhere (str or None) – Names of columns of the table, by which to search (by default, empty).

  • sConj (str or None) – The one from ‘AND’ or ‘OR’ operator condition. By default, is used ‘AND’.

  • tValues (tuple or list or None) – Value(s) as tuple for search (by default, empty).

  • sFunc (str or None) – Function name of sqlite, which need to apply (by default, empty). Note: Now, you can use only two sqlite functions: Count and DISTINCT.

Returns

Cursor or bool – Cursor object within rows that was found, or False, if the row not found.

sql_count(sTable)[source]

Counts number of records in database table.

Parameters

sTable (str) – Table name as string where records should be count.

Returns

Number of found records.

Return type

int or bool

sql_get_all(sTable)[source]

Gets all records in database table.

Parameters

sTable (str) – Table name as string where records should be received.

Returns

Tuple of all rows of table.

Return type

tuple or bool

sql_get_id(sTable, sID, sWhere, tValues, sConj='')[source]
sql_get_values(sTable, sID, sWhere, tValues, sConj='')[source]

Looks for ID of the row by value(s) of table column(s).

Parameters

  • sTable (str) – Table name as string.

  • sID (str) – Name of the column of the table by which to search.

  • sWhere (str) – Names of columns of the table by which to search.

  • tValues (tuple or list) – Value(s) as tuple for search.

  • sConj (str or None) – The one from ‘AND’ or ‘OR’ operator condition. By default, is used ‘AND’.

Returns

ID as Number in the row cell, or 0, if the row not found.

Return type

list or bool

sql_table_clean(lTable)[source]

Cleans up the table.

Parameters

lTable (tuple or list) – Table names as list or tuple of string, or table name as string where cleaning is need to do.

Returns

True, if execution is successful. Otherwise, False. Note: False is returned even if cleaning the last table in the tuple was not successful.

Return type

bool

update(sTable, sSetUpdate, sWhereUpdate, tValues)[source]

Updates value(s) in the record of the database table.

Parameters

  • sTable (str) – A Table as string where update is need to do.

  • sSetUpdate (str) – Column(s) where the value are writen.

  • sWhereUpdate (str) – A column where values correspond to the required.

  • tValues (tuple or list) – value(s) as tuple for search corresponding rows.

Returns

True if the insert was successful, otherwise False.

Return type

bool

mli.lib.sql.check_connect_db(oConnector, sBasePath, sDBDir)[source]
Checks for the existence of a database and if it does not find it, then

creates it with default values.

Parameters

  • oConnector (SQL) – Instance attribute of SQL.

  • sBasePath (str) – A path of the executed script.

  • sDBDir (str) – A dir when database is by default.

Returns

None

mli.lib.sql.get_columns(sColumns, sConj='AND')[source]

The function of parsing a string, accepts a list of table columns separated by commas and returns this list with ‘=? AND’ or ‘=? OR’ as separator.

Parameters

  • sColumns (str) – A string with a list of table columns separated by commas.

  • sConj (str or None) – The one from ‘AND’ or ‘OR’ operator condition. By default, is used ‘AND’.

Returns

The string with a list of table columns separated by ‘=? AND’ or ‘=? OR’.

Return type

str

mli.lib.sql.get_increase_value(sColumns, tValues)[source]
Checks counting elements of values, and if them fewer,

then makes them equal.

Note:

In the rison that tuple can’t be multiplied on flot, the process of increasing the tuple becomes somewhat resource-intensive. So, tValues should be consisting of one element.

Parameters

  • sColumns (str) – Colum(s) in query.

  • tValues (tuple or list) – Values should be specified in the request.

Returns

A tuple with values, which equal to sColumns.

Return type

list

mli.lib.str module

The module contains a collection of functions for solving routine tasks with strings.

class mli.lib.str.HTMLDoc[source]

Bases: object

get_doc()[source]
set_is_synonym(sName, sAuthor, sMainName, sMainAuthor)[source]
set_no_data(sNoData)[source]
set_rang_name(sRank, sName, sAuthor)[source]
set_string(String)[source]
set_title_chart(sTitle)[source]
set_title_doc(sRank, sName, sAuthor)[source]
mli.lib.str.str_get_file_patch(sDir, sFile)[source]

Concatenates file path and file name based on OS rules.

Parameters

  • sDir – String with a patch to a file.

  • sFile – String with a filename.

Returns

Patch to file based on OS rules.

mli.lib.str.str_get_html_name(sCanonicalName, sAuthor='')[source]
Inserts html tags into the taxon scientific name so that the canonical

name is written in italics.

Parameters

  • sCanonicalName (str) – A canonical name of the taxon.

  • sAuthor (str) – Author(s) of the taxon.

Returns

Formatted string.

Return type

str

mli.lib.str.str_get_path(sFullFile)[source]

Splits a path to path and file name.

Parameters

sFullFile (str) – Path with filename.

Returns

The path to file.

Return type

str

mli.lib.str.str_sep_comma(sString)[source]

Separates a string by comma to list.

Parameters

sString (str) – A string that needs to separate.

Returns

A separated string by comma.

Return type

list or None

mli.lib.str.str_sep_dot(sString)[source]

Separates a string by dot to list.

Parameters

sString (str) – A string that needs to separate.

Returns

A separated string by dot.

Return type

list or None

mli.lib.str.str_sep_name_taxon(sString)[source]
Splits the string into taxon name and author, taking a string of the

form ‘(rank) Taxon_name, authors’. It is permissible to indicate authors separated by commas, in brackets, using the ‘&’ symbol.

Parameters

sString (str) – A string that needed to separate.

Returns

A canonical form of taxon name and a string with the authors. Returns empty instead of author if no author was specified in the string.

Return type

list[str, str|None]

mli.lib.str.str_text_to_list(sString)[source]

Module contents