Error and test planning

Planning error catching and testing python modules

Contents table

• Predicated errors and bugs in Python get_ncbi_genomes.py

Predicated errors and bugs in Python get_ncbi_genomes.py

Predicated bugs/errors

Solution to all IOerror: network error is to retry. Do this automatically by writing in the script to retry or
make the user manually restart the script? The later seems
like a better idea. Entrez already does a try of three, does this count for network errors? Could a retry system in the script be written so the retries
or spaced out by time, with default values in the script,
but the user can change the max number of tries and time
between the tries if they want?

1. Calling parse_input_file() Expected error type: ? Potential errors more likely to occur as a result of one of the functions
   being called within parse_line_file() encountering an area. Therefore,
   the error type will be very broad.

2. Calling collate_accession_numbers() Expected error type: ? Potential errors more likely to occur as a result of one of the functions
   being called within collate_accession_numbers() encountering an area.
   Therefore, the error type will be very broad.

3. Errors in parse_input_file() 3a. Calling the input file. Expected error: file not found Error message recieved: FileNotFoundError: [Errno 2] No such file or directory: '<filename>' Potential cause of error: file does not exist in cwd, or not in directory given by input
   or a typo in the input of filename and/or path.

3b. Calling get_genus_species_name()

i. Expected error: index error Error message recieved: IndexError: list index out of range Program terminates when trying to retrieve name from retrieved entrez record Potential cause of error: typo in species name leading to no entry from entrez containing
the information of a species being pulled down In error log, include which line was being processed to make it easier for use to double
check the probable cause.

ii. Expected error: IOError Cause of error: Network error when using Entrez to call to NCBI

3c. Calling get_tax_id()

i. Expected error: index error Error message recieved: IndexError: list index out of range Program terminates when trying to retrieve tax id from retrieved entrez record Potential cause of error: typo in species name or taxonomy id (so that taxonomy id it fails
taxonomy id check and script processes it as a species name), leading to no entry from entrez
containing the information of a species being pulled down In error log, include which line was being processed to make it easier for use to double
check the probable cause.

ii. Expected error: IOError Cause of error: Network error when using Entrez to call to NCBI

3d. Creating dataframe Potential error of empty entries if nothing was retrieved from the entrez call. Look up if pandas can be used to check for this

4. Errors in collate_accession_numbers() 4a. Calling get_accession_numbers() These areas will mainly arise from the Entrez calls

4ai. Using Entrez to retrieve assembly ids i. Error message recieved: IndexError: list index out of range Cause of error: If taxonomy ID is not recognised, terminates programme Edit so prints out taxonomy ID with the issue

ii. Expected error: IOError Cause of error: Network error

4aii. Using Entrez to post assembly ids i Expected error: RuntimeError(value) Error message: RuntimeError: cannot get document summary Cause of error: incorretly formated assembly ids into query, or too large post
try reducing total number of species Should I add an option for reduced speed, add it as an args question,
so that if yes, if statement checks it here and if yes adds a 1 sec
sleep timer, to prevent over demand of network that causes you to be
kicked off.

ii Expected error: IOError Cause of error: Network error

4aiii. Using Entrez to retrieve accession numbers per assembly id i. Expected error: RuntimeError(value) Error message: RuntimeError: cannot get document summary Cause of error: incorretly formated assembly ids into query, or too large post
try reducing total number of species, or too mant requests per second Should I add an option for reduced speed, add it as an args question,
so that if yes, if statement checks it here and if yes adds a 1 sec
sleep timer, to prevent over demand of network that causes you to be
kicked off.

ii. Expected error: IOError Cause of error: Network error when using Entrez to call to NCBI