JorgeVB/code_unlearning_dataset · Data Studio

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Downloads multiple accounts from Gitkit server. Args: next_page_token: string, pagination token. max_results: pagination size. Returns: An array of accounts. def DownloadAccount(self, next_page_token=None, max_results=None): """Downloads multiple accounts from Gitkit server. Args: ...
Uploads multiple accounts to Gitkit server. Args: hash_algorithm: string, algorithm to hash password. hash_key: string, base64-encoded key of the algorithm. accounts: array of accounts to be uploaded. Returns: Response of the API. def UploadAccount(self, hash_algorithm, hash_key, acco...
Download Gitkit public cert. Returns: dict of public certs. def GetPublicCert(self): """Download Gitkit public cert. Returns: dict of public certs. """ cert_url = self.google_api_url + 'publicKeys' resp, content = self.http.request(cert_url) if resp.status == 200: retu...
Invokes Gitkit API, with optional access token for service account. Args: method: string, the api method name. params: dict of optional parameters for the API. need_service_account: false if service account is not needed. Raises: GitkitClientError: if the request is bad. GitkitSe...
Gets oauth2 access token for Gitkit API using service account. Returns: string, oauth2 access token. def _GetAccessToken(self): """Gets oauth2 access token for Gitkit API using service account. Returns: string, oauth2 access token. """ d = { 'assertion': self._GenerateAssertio...
Generates the signed assertion that will be used in the request. Returns: string, signed Json Web Token (JWT) assertion. def _GenerateAssertion(self): """Generates the signed assertion that will be used in the request. Returns: string, signed Json Web Token (JWT) assertion. """ now = ...
Raises error if API invocation failed. Args: raw_response: string, the http response. Raises: GitkitClientError: if the error code is 4xx. GitkitServerError: if the response if malformed. Returns: Successful response as dict. def _CheckGitkitError(self, raw_response): """Rais...
Initializes from user specified dictionary. Args: dictionary: dict of user specified attributes Returns: GitkitUser object def FromDictionary(cls, dictionary): """Initializes from user specified dictionary. Args: dictionary: dict of user specified attributes Returns: Gitki...
Converts to gitkit api request parameter dict. Returns: Dict, containing non-empty user attributes. def ToRequest(self): """Converts to gitkit api request parameter dict. Returns: Dict, containing non-empty user attributes. """ param = {} if self.email: param['email'] = self...
Verifies a Gitkit token string. Args: jwt: string, the token to be checked Returns: GitkitUser, if the token is valid. None otherwise. def VerifyGitkitToken(self, jwt): """Verifies a Gitkit token string. Args: jwt: string, the token to be checked Returns: GitkitUser, if ...
Gets user info by email. Args: email: string, the user email. Returns: GitkitUser, containing the user info. def GetUserByEmail(self, email): """Gets user info by email. Args: email: string, the user email. Returns: GitkitUser, containing the user info. """ user ...
Gets user info by id. Args: local_id: string, the user id at Gitkit server. Returns: GitkitUser, containing the user info. def GetUserById(self, local_id): """Gets user info by id. Args: local_id: string, the user id at Gitkit server. Returns: GitkitUser, containing the ...
Uploads multiple users to Gitkit server. Args: hash_algorithm: string, the hash algorithm. hash_key: array, raw key of the hash algorithm. accounts: list of GitkitUser. Returns: A dict of failed accounts. The key is the index of the 'accounts' list, starting from 0. def Uplo...
Gets all user info from Gitkit server. Args: pagination_size: int, how many users should be returned per request. The account info are retrieved in pagination. Yields: A generator to iterate all users. def GetAllUsers(self, pagination_size=10): """Gets all user info from Gitkit serv...
Gets out-of-band code for ResetPassword/ChangeEmail request. Args: param: dict of HTTP POST params user_ip: string, end user's IP address gitkit_token: string, the gitkit token if user logged in Returns: A dict of { email: user email who initializes the request new_emai...
Builds out-of-band URL. Gitkit API GetOobCode() is called and the returning code is combined with Gitkit widget URL to building the out-of-band url. Args: param: dict of request. mode: string, Gitkit widget mode to handle the oob action after user clicks the oob url in the email. ...
command is the command to run, as a string. runs a subprocess, returns stdout and stderr from the subprocess as strings. def run_subprocess(command): """ command is the command to run, as a string. runs a subprocess, returns stdout and stderr from the subprocess as strings. """ x = Popen(comman...
Given a set of kwargs, turns them into a string which can then be passed to a command. :param kwargs: kwargs from a function call. :return: outstr: A string, which is '' if no kwargs were given, and the kwargs in string format otherwise. def kwargs_to_string(kwargs): """ Given a set of kwargs, turns th...
:param result_file: Tab-delimited result file generated by mash dist. :return: mash_results: A list with each entry in the result file as an entry, with attributes reference, query, distance, pvalue, and matching_hash def read_mash_output(result_file): """ :param result_file: Tab-delimited result file ...
:param screen_result: Tab-delimited result file generated by mash screen. :return: results: A list with each line in the result file as an entry, with attributes identity, shared_hashes, median_multiplicity, pvalue, and query_id def read_mash_screen(screen_result): """ :param screen_result: Tab-delimit...
Runs a command using subprocess, and returns both the stdout and stderr from that command If exit code from command is non-zero, raises subproess.CalledProcessError :param cmd: command to run as a string, as it would be called on the command line :return: out, err: Strings that are the stdout and stderr fro...
Writes stdout, stderr, and a command to a logfile :param logfile: Path to file to write output to. :param out: Stdout of program called, as a string :param err: Stderr of program called, as a string :param cmd: command that was used def write_to_logfile(logfile, out, err, cmd): """ Writes stdou...
Looks at a directory to try to find paired fastq files. Should be able to find anything fastq. :param fastq_directory: Complete path to directory containing fastq files. :param forward_id: Identifier for forward reads. Default R1. :param reverse_id: Identifier for reverse reads. Default R2. :return: Lis...
Looks at a directory to find unpaired fastq files. :param fastq_directory: Complete path to directory containing fastq files. :param forward_id: Identifier for forward reads. Default _R1. :param reverse_id: Identifier for forward reads. Default _R2. :param find_fasta: If False, will look for fastq files...
A new way of making our specific databases: Make our profiles file have lists of every gene/allele present for each genus instead of just excluding a few genes for each. This way, should have much smaller databases while managing to make ConFindr a decent bit faster (maybe) :param profiles_file: Path to pro...
Since some genera have some rMLST genes missing, or two copies of some genes, genus-specific databases are needed. This will take only the alleles known to be part of each genus and write them to a genus-specific file. :param database_folder: Path to folder where rMLST_combined is stored. :param fasta_file:...
Given a pair of reads and an rMLST database, will extract reads that contain sequence from the database. :param pair: List containing path to forward reads at index 0 and path to reverse reads at index 1. :param database: Path to rMLST database, in FASTA format. :param forward_out: :param reverse_out: ...
Usese mash to find out whether or not a sample has more than one genus present, indicating cross-contamination. :param databases: A databases folder, which must contain refseq.msh, a mash sketch that has one representative per genus from refseq. :param tmpdir: Temporary directory to store mash result files ...
Finds if a site has at least two bases of high quality, enough that it can be considered fairly safe to say that base is actually there. :param high_quality_base_count: Dictionary of count of HQ bases at a position where key is base and values is the count of that base. :param base_count_cutoff: Number of ...
Finds if a position in a pileup has more than one base present. :param column: A pileupColumn generated by pysam :param quality_cutoff: Desired minimum phred quality for a base in order to be counted towards a multi-allelic column :param base_cutoff: Minimum number of bases needed to support presence of a b...
Gets contig names from a fasta file using SeqIO. :param fasta_file: Full path to uncompressed, fasta-formatted file :return: List of contig names. def get_contig_names(fasta_file): """ Gets contig names from a fasta file using SeqIO. :param fasta_file: Full path to uncompressed, fasta-formatted fil...
Examines a contig to find if there are positions where more than one base is present. :param contig_name: Name of contig as a string. :param bamfile_name: Full path to bamfile. Must be sorted/indexed :param reference_fasta: Full path to fasta file that was used to generate the bamfile. :param report_fil...
Uses a report generated by KMA to determine what allele is present for each rMLST gene. :param kma_report: The .res report generated by KMA. :param rmlst_report: rMLST report file to write information to. :return: a sorted list of loci present, in format gene_allele def find_rmlst_type(kma_report, rmlst_re...
Converts a dictionary to a string. {'C': 12, 'A':4} gets converted to C:12;A:4 :param base_dict: Dictionary of bases and counts created by find_if_multibase :return: String representing that dictionary. def base_dict_to_string(base_dict): """ Converts a dictionary to a string. {'C': 12, 'A':4} gets con...
Totals up number of bases in a fasta file. :param fasta_file: Path to an uncompressed, fasta-formatted file. :return: Number of total bases in file, as an int. def find_total_sequence_length(fasta_file): """ Totals up number of bases in a fasta file. :param fasta_file: Path to an uncompressed, fast...
Estimates the percent contamination of a sample (and standard deviation). :param contamination_report_file: File created by read_contig, :return: Estimated percent contamination and standard deviation. def estimate_percent_contamination(contamination_report_file): """ Estimates the percent contaminatio...
This needs some documentation fairly badly, so here we go. :param pair: This has become a misnomer. If the input reads are actually paired, needs to be a list with the full filepath to forward reads at index 0 and full path to reverse reads at index 1. If reads are unpaired, should be a list of length 1 wit...
Function that writes the output generated by ConFindr to a report file. Appends to a file that already exists, or creates the file if it doesn't already exist. :param output_report: Path to CSV output report file. Should have headers SampleName,Genus,NumContamSNVs, ContamStatus,PercentContam, and PercentCon...
BBTools can have their memory set manually. This will check that the memory setting is actually valid :param xmx_string: The users requested XMX, as a string. :return: True if the Xmx string will be accepted by BBTools, otherwise false. def check_acceptable_xmx(xmx_string): """ BBTools can have their m...
Character set code field. :param name: name for the field :return: an instance of the Character set code field rules def char_code(columns, name=None): """ Character set code field. :param name: name for the field :return: an instance of the Character set code field rules """ if name ...
Returns a callable that accepts the choices provided. Choices should be provided as a list of 2-tuples, where the first element is a string that should match user input (the key); the second being the value associated with the key. The callable by default will match, upon complete match the first ...
Prompt user for question, maybe choices, and get answer. Arguments: question The question to prompt. It will only be prompted once. validator Defaults to None. Must be a callable that takes in a value. The callable should raise ValueError when the value leads to an error,...
Prompt end user with a diff of original and new json that may overwrite the file at the target_path. This function only displays a confirmation prompt and it is up to the caller to implement the actual functionality. Optionally, a custom json.dumps method can also be passed in for output generation. ...
Locate a single npm package to return its browser or main entry. def locate_package_entry_file(working_dir, package_name): """ Locate a single npm package to return its browser or main entry. """ basedir = join(working_dir, 'node_modules', package_name) package_json = join(basedir, 'package.json')...
Template tag to render a list of pictures. def render_pictures(context, selection='recent', amount=3): """Template tag to render a list of pictures.""" pictures = Image.objects.filter( folder__id__in=Gallery.objects.filter(is_published=True).values_list( 'folder__pk', flat=True)) if sel...
Parses the VCF Header field and returns the number of samples in the VCF file def add_header(self, entry): """Parses the VCF Header field and returns the number of samples in the VCF file""" info = entry.split('\t') self.n_individuals = len(info)-9 for i,v in enumerate(info[9:]): ...
Parse an individual VCF entry and return a VCFEntry which contains information about the call (such as alternative allele, zygosity, etc.) def parse_entry(self, row): """Parse an individual VCF entry and return a VCFEntry which contains information about the call (such as alternative allele, zy...
This will parse the VCF entry and also store it within the VCFFile. It will also return the VCFEntry as well. def add_entry(self, row): """This will parse the VCF entry and also store it within the VCFFile. It will also return the VCFEntry as well. """ var_call = VCFEntry(self....
Returns the vcf header def get_header(self, individual=-1): """Returns the vcf header """ type_map = dict([(val,key) for key,val in self.meta.type_map.iteritems()]) extra = '\n'.join(['##{0}'.format(i) for i in self.meta.extra]) info = '\n'.join(['##INFO=<ID={0},Number={1},Type...
Parse and store the info field def add_info(self, entry): """Parse and store the info field""" entry = entry[8:-1] info = entry.split(',') if len(info) < 4: return False for v in info: key, value = v.split('=', 1) if key == 'ID': ...
Parse and store the filter field def add_filter(self, entry): """Parse and store the filter field""" entry = entry[10:-1] info = entry.split(',') if len(info) < 2: return False for v in info: key, value = v.split('=', 1) if key == 'ID': ...
Parse and store the alternative allele field def add_alt(self, entry): """Parse and store the alternative allele field""" entry = entry[7:-1] info = entry.split(',') if len(info) < 2: return False for v in info: key, value = v.split('=', 1) if...
Returns the VCF entry as it appears in the vcf file def sample_string(self, individual=-1): """Returns the VCF entry as it appears in the vcf file""" base = str(self) extra = self.get_sample_info(individual=individual) extra = [':'.join([str(j) for j in i]) for i in zip(*extra.values())...
Returns the sample info of a given sample or all by default def get_sample_info(self, individual=-1): """Returns the sample info of a given sample or all by default """ if isinstance(individual, str): individual = self.individuals[individual] extra = OrderedDict() f...
This will give a boolean list corresponding to whether each individual is homozygous for the alternative allele. def is_homozygous(self, individual=None): """This will give a boolean list corresponding to whether each individual is homozygous for the alternative allele. """ if ...
Returns the alternative alleles of the individual as a list def get_alt(self, individual=0, nucleotides_only=True): """Returns the alternative alleles of the individual as a list""" #not i.startswith(',') is put in to handle cases like <DEL:ME:ALU> where we have no alternate allele #but some re...
Returns the number of basepairs of each alternative allele def get_alt_length(self, individual=0): """Returns the number of basepairs of each alternative allele""" if isinstance(individual, str): individual = self.individuals[individual] return [len(self.alt[i-1].replace('.','')) fo...
Returns the longest length of the variant. For deletions, return is negative, SNPs return 0, and insertions are +. None return corresponds to no variant in interval for specified individual def get_alt_lengths(self): """Returns the longest length of the variant. For deletions, return is negativ...
Returns a boolean list of SNP status, ordered by samples def has_snp(self, individual=0): """Returns a boolean list of SNP status, ordered by samples""" if isinstance(individual, str): individual = self.individuals[individual] alts = self.get_alt(individual=individual) if al...
This parses a VCF row and stores the relevant information def parse_entry(self, entry): """This parses a VCF row and stores the relevant information""" entry = entry.split('\t') self.chrom, self.pos, self.id, self.ref, alt_, self.qual, filter_, info, self.format = entry[:9] self.samples...
Children are GFFFeatures and are defined when added. This is done to avoid memory overheads that may be incurred by GFF files that have millions of rows. def add_child(self, child): """Children are GFFFeatures and are defined when added. This is done to avoid memory overheads that may be incurr...
Transforms an object into it's ISO format, if possible. If the object can't be transformed, then an error is raised for the JSON parser. This is meant to be used on datetime instances, but will work with any object having a method called isoformat. :param obj: object to transform into it's ISO fo...
Inner encoding and try return string from entity dictionary :param field_encoders: :param entity_dict: :return: def try_encode(field_encoders, entity_dict): """ Inner encoding and try return string from entity dictionary :param field_encoders: :param entity_dict:...
Generate string of cwr format for all possible combinations of fields, accumulate and then elect the best. The best string it is who used most of all fields :param entity: :return: def encode(self, entity): """ Generate string of cwr format for all possible combinations of field...
For setting up the argparser for this instance. def argparser(self): """ For setting up the argparser for this instance. """ if self.__argparser is None: self.__argparser = self.argparser_factory() self.init_argparser(self.__argparser) return self.__argp...
Produces argparser for this type of Runtime. def argparser_factory(self): """ Produces argparser for this type of Runtime. """ return ArgumentParser( prog=self.prog, description=self.__doc__, add_help=False, )
This should not be called with an external argparser as it will corrupt tracking data if forced. def init_argparser(self, argparser): """ This should not be called with an external argparser as it will corrupt tracking data if forced. """ def prepare_argparser(): ...
This exists because argparser is dumb and naive and doesn't fail unrecognized arguments early. def unrecognized_arguments_error(self, args, parsed, extras): """ This exists because argparser is dumb and naive and doesn't fail unrecognized arguments early. """ # loop var...
This was used as part of the original non-recursive lookup for the target parser. def error(self, argparser, target, message): """ This was used as part of the original non-recursive lookup for the target parser. """ warnings.warn( 'Runtime.error is deprecat...
Subclass could override this by providing alternative keyword arguments and call this as its super. It should not reimplement this completely. Example: def init_argparser_export_target(self, argparser): super(MyToolchainRuntime, self).init_argparser_export_target( ...
Subclass could an extra expanation on how this is used. Arguments explanation Explanation text for the default help template help_template A standard help message for this option. def init_argparser_working_dir( self, argparser, explanation='', ...
For setting up build directory def init_argparser_build_dir( self, argparser, help=( 'the build directory, where all sources will be copied to ' 'as part of the build process; if left unspecified, the ' 'default behavior is to create a new temporary directory...
For setting up optional advice. def init_argparser_optional_advice( self, argparser, default=[], help=( 'a comma separated list of packages to retrieve optional ' 'advice from; the provided packages should have registered ' 'the appropriate entry points for s...
Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here for a subcommand. def init_argparser(self, argparser): """ Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here fo...
Prepare a spec for usage with the generic ToolchainRuntime. Subclasses should avoid overriding this; override create_spec instead. def prepare_spec(self, spec, **kwargs): """ Prepare a spec for usage with the generic ToolchainRuntime. Subclasses should avoid overriding this; o...
Turn the provided kwargs into arguments ready for toolchain. def kwargs_to_spec(self, kwargs): """ Turn the provided kwargs into arguments ready for toolchain. """ spec = self.create_spec(kwargs) self.prepare_spec(spec, **kwargs) return spec
Default helper for setting up the package_names option. This is separate so that subclasses are not assumed for the purposes of artifact creation; they should consider modifying the default help message to reflect the fact. def init_argparser_package_names(self, argparser, help=( ...
For setting up the source registry flag. def init_argparser_source_registry( self, argparser, default=None, help=( 'comma separated list of registries to use for gathering ' 'JavaScript sources from the given Python packages' )): """ For setting u...
Default helper for setting up the loaderplugin registries flags. Note that this is NOT part of the init_argparser due to implementation specific requirements. Subclasses should consider modifying the default value help message to cater to the toolchain it encapsulates. def init_argpar...
Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here for a subcommand. def init_argparser(self, argparser): """ Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here fo...
Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here for a subcommand. def init_argparser(self, argparser): """ Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here fo...
Creates the grammar for an Alphanumeric (A) field, accepting only the specified number of characters. By default Alphanumeric fields accept only ASCII characters, excluding lowercases. If the extended flag is set to True, then non-ASCII characters are allowed, but the no ASCII lowercase constraint is k...
Checks that the string is not empty. If it is empty an exception is raised, stopping the validation. This is used for compulsory alphanumeric fields. :param string: the field value def _check_not_empty(string): """ Checks that the string is not empty. If it is empty an exception is raised, ...
Creates the grammar for a Numeric (N) field, accepting only the specified number of characters. This version only allows integers. :param columns: number of columns for this field :param name: name for the field :return: grammar for the integer numeric field def numeric(columns, name=None): "...
Creates the grammar for a Numeric (N) field, accepting only the specified number of characters. This version only allows floats. As nothing in the string itself indicates how many of the characters are for the integer and the decimal sections, this should be specified with the nums_int parameter. ...
Transforms a string into a float. The nums_int parameter indicates the number of characters, starting from the left, to be used for the integer value. All the remaining ones will be used for the decimal value. :param number: string with the number :param nums_int: characters, counting from the lef...
Checks that the number parsed from the string is above a minimum. This is used on compulsory numeric fields. If the value is not above the minimum an exception is thrown. :param string: the field value :param minimum: minimum value def _check_above_value_float(string, minimum): """ Checks th...
Creates the grammar for a Boolean (B) field, accepting only 'Y' or 'N' :param name: name for the field :return: grammar for the flag field def boolean(name=None): """ Creates the grammar for a Boolean (B) field, accepting only 'Y' or 'N' :param name: name for the field :return: grammar for th...
Transforms a string into a boolean value. If a value which is not 'Y' or 'N' is received, a ParseException is thrown. :param: string: the string to transform :return: True if the string is 'Y', False if it is 'N' def _to_boolean(string): """ Transforms a string into a boolean value. If a val...
Creates the grammar for a Flag (F) field, accepting only 'Y', 'N' or 'U'. :param name: name for the field :return: grammar for the flag field def flag(name=None): """ Creates the grammar for a Flag (F) field, accepting only 'Y', 'N' or 'U'. :param name: name for the field :return: grammar for...
Creates the grammar for a Date (D) field, accepting only numbers in a certain pattern. :param name: name for the field :return: grammar for the date field def date(name=None): """ Creates the grammar for a Date (D) field, accepting only numbers in a certain pattern. :param name: name for ...
Creates the grammar for a Time or Duration (T) field, accepting only numbers in a certain pattern. :param name: name for the field :return: grammar for the date field def time(name=None): """ Creates the grammar for a Time or Duration (T) field, accepting only numbers in a certain pattern. ...
Creates the grammar for a Lookup (L) field, accepting only values from a list. Like in the Alphanumeric field, the result will be stripped of all heading and trailing whitespaces. :param values: values allowed :param name: name for the field :return: grammar for the lookup field def lookup(va...
Creates the grammar for a blank field. These are for constant empty strings which should be ignored, as they are used just as fillers. :param columns: number of columns, which is the required number of whitespaces :param name: name for the field :return: grammar for the blank field def blank(...
This returns a list of GFF objects (or GFF Features) with the given attribute and if supplied, those attributes with the specified value :param attribute: The 'info' field attribute we are querying :param value: Optional keyword, only return attributes equal to this value :param feature...
This returns a list of GFF objects which cover a specified location. :param seqid: The landmark identifier (usually a chromosome) :param start: The 1-based position of the start of the range we are querying :param end: The 1-based position of the end of the range we are querying :param ...
This returns a list of VCFEntry objects which cover a specified location. :param chrom: The landmark identifier (usually a chromosome) :param start: The 1-based position of the start of the range we are querying :param end: The 1-based position of the end of the range we are querying :p...
Remove a list of variants from the positions we are scanning def remove_variants(self, variants): """Remove a list of variants from the positions we are scanning""" chroms = set([i.chrom for i in variants]) for chrom in chroms: if self.append_chromosome: chrom = 'chr...
The default implementation is a recursive lookup method, which subclasses may make use of. Subclasses must implement this to return a mapping of modnames the the absolute path of the desired sourcefiles. Example: return { 'text': '/tmp/src/example_module/text/index.js', ...
Attempt to locate the plugin source; returns a mapping of modnames to the absolute path of the located sources. def generate_handler_sourcepath( self, toolchain, spec, loaderplugin_sourcepath): """ Attempt to locate the plugin source; returns a mapping of modnames to the abs...

Downloads multiple accounts from Gitkit server. Args: next_page_token: string, pagination token. max_results: pagination size. Returns: An array of accounts. def DownloadAccount(self, next_page_token=None, max_results=None): """Downloads multiple accounts from Gitkit server. Args: ...

Uploads multiple accounts to Gitkit server. Args: hash_algorithm: string, algorithm to hash password. hash_key: string, base64-encoded key of the algorithm. accounts: array of accounts to be uploaded. Returns: Response of the API. def UploadAccount(self, hash_algorithm, hash_key, acco...

Download Gitkit public cert. Returns: dict of public certs. def GetPublicCert(self): """Download Gitkit public cert. Returns: dict of public certs. """ cert_url = self.google_api_url + 'publicKeys' resp, content = self.http.request(cert_url) if resp.status == 200: retu...

Invokes Gitkit API, with optional access token for service account. Args: method: string, the api method name. params: dict of optional parameters for the API. need_service_account: false if service account is not needed. Raises: GitkitClientError: if the request is bad. GitkitSe...

Gets oauth2 access token for Gitkit API using service account. Returns: string, oauth2 access token. def _GetAccessToken(self): """Gets oauth2 access token for Gitkit API using service account. Returns: string, oauth2 access token. """ d = { 'assertion': self._GenerateAssertio...

Generates the signed assertion that will be used in the request. Returns: string, signed Json Web Token (JWT) assertion. def _GenerateAssertion(self): """Generates the signed assertion that will be used in the request. Returns: string, signed Json Web Token (JWT) assertion. """ now = ...

Raises error if API invocation failed. Args: raw_response: string, the http response. Raises: GitkitClientError: if the error code is 4xx. GitkitServerError: if the response if malformed. Returns: Successful response as dict. def _CheckGitkitError(self, raw_response): """Rais...

Initializes from user specified dictionary. Args: dictionary: dict of user specified attributes Returns: GitkitUser object def FromDictionary(cls, dictionary): """Initializes from user specified dictionary. Args: dictionary: dict of user specified attributes Returns: Gitki...

Converts to gitkit api request parameter dict. Returns: Dict, containing non-empty user attributes. def ToRequest(self): """Converts to gitkit api request parameter dict. Returns: Dict, containing non-empty user attributes. """ param = {} if self.email: param['email'] = self...

Verifies a Gitkit token string. Args: jwt: string, the token to be checked Returns: GitkitUser, if the token is valid. None otherwise. def VerifyGitkitToken(self, jwt): """Verifies a Gitkit token string. Args: jwt: string, the token to be checked Returns: GitkitUser, if ...

Gets user info by email. Args: email: string, the user email. Returns: GitkitUser, containing the user info. def GetUserByEmail(self, email): """Gets user info by email. Args: email: string, the user email. Returns: GitkitUser, containing the user info. """ user ...

Gets user info by id. Args: local_id: string, the user id at Gitkit server. Returns: GitkitUser, containing the user info. def GetUserById(self, local_id): """Gets user info by id. Args: local_id: string, the user id at Gitkit server. Returns: GitkitUser, containing the ...

Uploads multiple users to Gitkit server. Args: hash_algorithm: string, the hash algorithm. hash_key: array, raw key of the hash algorithm. accounts: list of GitkitUser. Returns: A dict of failed accounts. The key is the index of the 'accounts' list, starting from 0. def Uplo...

Gets all user info from Gitkit server. Args: pagination_size: int, how many users should be returned per request. The account info are retrieved in pagination. Yields: A generator to iterate all users. def GetAllUsers(self, pagination_size=10): """Gets all user info from Gitkit serv...

Gets out-of-band code for ResetPassword/ChangeEmail request. Args: param: dict of HTTP POST params user_ip: string, end user's IP address gitkit_token: string, the gitkit token if user logged in Returns: A dict of { email: user email who initializes the request new_emai...

Builds out-of-band URL. Gitkit API GetOobCode() is called and the returning code is combined with Gitkit widget URL to building the out-of-band url. Args: param: dict of request. mode: string, Gitkit widget mode to handle the oob action after user clicks the oob url in the email. ...

command is the command to run, as a string. runs a subprocess, returns stdout and stderr from the subprocess as strings. def run_subprocess(command): """ command is the command to run, as a string. runs a subprocess, returns stdout and stderr from the subprocess as strings. """ x = Popen(comman...

Given a set of kwargs, turns them into a string which can then be passed to a command. :param kwargs: kwargs from a function call. :return: outstr: A string, which is '' if no kwargs were given, and the kwargs in string format otherwise. def kwargs_to_string(kwargs): """ Given a set of kwargs, turns th...

:param result_file: Tab-delimited result file generated by mash dist. :return: mash_results: A list with each entry in the result file as an entry, with attributes reference, query, distance, pvalue, and matching_hash def read_mash_output(result_file): """ :param result_file: Tab-delimited result file ...

:param screen_result: Tab-delimited result file generated by mash screen. :return: results: A list with each line in the result file as an entry, with attributes identity, shared_hashes, median_multiplicity, pvalue, and query_id def read_mash_screen(screen_result): """ :param screen_result: Tab-delimit...

Runs a command using subprocess, and returns both the stdout and stderr from that command If exit code from command is non-zero, raises subproess.CalledProcessError :param cmd: command to run as a string, as it would be called on the command line :return: out, err: Strings that are the stdout and stderr fro...

Writes stdout, stderr, and a command to a logfile :param logfile: Path to file to write output to. :param out: Stdout of program called, as a string :param err: Stderr of program called, as a string :param cmd: command that was used def write_to_logfile(logfile, out, err, cmd): """ Writes stdou...

Looks at a directory to try to find paired fastq files. Should be able to find anything fastq. :param fastq_directory: Complete path to directory containing fastq files. :param forward_id: Identifier for forward reads. Default R1. :param reverse_id: Identifier for reverse reads. Default R2. :return: Lis...

Looks at a directory to find unpaired fastq files. :param fastq_directory: Complete path to directory containing fastq files. :param forward_id: Identifier for forward reads. Default _R1. :param reverse_id: Identifier for forward reads. Default _R2. :param find_fasta: If False, will look for fastq files...

A new way of making our specific databases: Make our profiles file have lists of every gene/allele present for each genus instead of just excluding a few genes for each. This way, should have much smaller databases while managing to make ConFindr a decent bit faster (maybe) :param profiles_file: Path to pro...

Since some genera have some rMLST genes missing, or two copies of some genes, genus-specific databases are needed. This will take only the alleles known to be part of each genus and write them to a genus-specific file. :param database_folder: Path to folder where rMLST_combined is stored. :param fasta_file:...

Given a pair of reads and an rMLST database, will extract reads that contain sequence from the database. :param pair: List containing path to forward reads at index 0 and path to reverse reads at index 1. :param database: Path to rMLST database, in FASTA format. :param forward_out: :param reverse_out: ...

Usese mash to find out whether or not a sample has more than one genus present, indicating cross-contamination. :param databases: A databases folder, which must contain refseq.msh, a mash sketch that has one representative per genus from refseq. :param tmpdir: Temporary directory to store mash result files ...

Finds if a site has at least two bases of high quality, enough that it can be considered fairly safe to say that base is actually there. :param high_quality_base_count: Dictionary of count of HQ bases at a position where key is base and values is the count of that base. :param base_count_cutoff: Number of ...

Finds if a position in a pileup has more than one base present. :param column: A pileupColumn generated by pysam :param quality_cutoff: Desired minimum phred quality for a base in order to be counted towards a multi-allelic column :param base_cutoff: Minimum number of bases needed to support presence of a b...

Gets contig names from a fasta file using SeqIO. :param fasta_file: Full path to uncompressed, fasta-formatted file :return: List of contig names. def get_contig_names(fasta_file): """ Gets contig names from a fasta file using SeqIO. :param fasta_file: Full path to uncompressed, fasta-formatted fil...

Examines a contig to find if there are positions where more than one base is present. :param contig_name: Name of contig as a string. :param bamfile_name: Full path to bamfile. Must be sorted/indexed :param reference_fasta: Full path to fasta file that was used to generate the bamfile. :param report_fil...

Uses a report generated by KMA to determine what allele is present for each rMLST gene. :param kma_report: The .res report generated by KMA. :param rmlst_report: rMLST report file to write information to. :return: a sorted list of loci present, in format gene_allele def find_rmlst_type(kma_report, rmlst_re...

Converts a dictionary to a string. {'C': 12, 'A':4} gets converted to C:12;A:4 :param base_dict: Dictionary of bases and counts created by find_if_multibase :return: String representing that dictionary. def base_dict_to_string(base_dict): """ Converts a dictionary to a string. {'C': 12, 'A':4} gets con...

Totals up number of bases in a fasta file. :param fasta_file: Path to an uncompressed, fasta-formatted file. :return: Number of total bases in file, as an int. def find_total_sequence_length(fasta_file): """ Totals up number of bases in a fasta file. :param fasta_file: Path to an uncompressed, fast...

Estimates the percent contamination of a sample (and standard deviation). :param contamination_report_file: File created by read_contig, :return: Estimated percent contamination and standard deviation. def estimate_percent_contamination(contamination_report_file): """ Estimates the percent contaminatio...

This needs some documentation fairly badly, so here we go. :param pair: This has become a misnomer. If the input reads are actually paired, needs to be a list with the full filepath to forward reads at index 0 and full path to reverse reads at index 1. If reads are unpaired, should be a list of length 1 wit...

Function that writes the output generated by ConFindr to a report file. Appends to a file that already exists, or creates the file if it doesn't already exist. :param output_report: Path to CSV output report file. Should have headers SampleName,Genus,NumContamSNVs, ContamStatus,PercentContam, and PercentCon...

BBTools can have their memory set manually. This will check that the memory setting is actually valid :param xmx_string: The users requested XMX, as a string. :return: True if the Xmx string will be accepted by BBTools, otherwise false. def check_acceptable_xmx(xmx_string): """ BBTools can have their m...

Character set code field. :param name: name for the field :return: an instance of the Character set code field rules def char_code(columns, name=None): """ Character set code field. :param name: name for the field :return: an instance of the Character set code field rules """ if name ...

Returns a callable that accepts the choices provided. Choices should be provided as a list of 2-tuples, where the first element is a string that should match user input (the key); the second being the value associated with the key. The callable by default will match, upon complete match the first ...

Prompt user for question, maybe choices, and get answer. Arguments: question The question to prompt. It will only be prompted once. validator Defaults to None. Must be a callable that takes in a value. The callable should raise ValueError when the value leads to an error,...

Prompt end user with a diff of original and new json that may overwrite the file at the target_path. This function only displays a confirmation prompt and it is up to the caller to implement the actual functionality. Optionally, a custom json.dumps method can also be passed in for output generation. ...

Locate a single npm package to return its browser or main entry. def locate_package_entry_file(working_dir, package_name): """ Locate a single npm package to return its browser or main entry. """ basedir = join(working_dir, 'node_modules', package_name) package_json = join(basedir, 'package.json')...

Template tag to render a list of pictures. def render_pictures(context, selection='recent', amount=3): """Template tag to render a list of pictures.""" pictures = Image.objects.filter( folder__id__in=Gallery.objects.filter(is_published=True).values_list( 'folder__pk', flat=True)) if sel...

Parses the VCF Header field and returns the number of samples in the VCF file def add_header(self, entry): """Parses the VCF Header field and returns the number of samples in the VCF file""" info = entry.split('\t') self.n_individuals = len(info)-9 for i,v in enumerate(info[9:]): ...

Parse an individual VCF entry and return a VCFEntry which contains information about the call (such as alternative allele, zygosity, etc.) def parse_entry(self, row): """Parse an individual VCF entry and return a VCFEntry which contains information about the call (such as alternative allele, zy...

This will parse the VCF entry and also store it within the VCFFile. It will also return the VCFEntry as well. def add_entry(self, row): """This will parse the VCF entry and also store it within the VCFFile. It will also return the VCFEntry as well. """ var_call = VCFEntry(self....

Returns the vcf header def get_header(self, individual=-1): """Returns the vcf header """ type_map = dict([(val,key) for key,val in self.meta.type_map.iteritems()]) extra = '\n'.join(['##{0}'.format(i) for i in self.meta.extra]) info = '\n'.join(['##INFO=<ID={0},Number={1},Type...

Parse and store the info field def add_info(self, entry): """Parse and store the info field""" entry = entry[8:-1] info = entry.split(',') if len(info) < 4: return False for v in info: key, value = v.split('=', 1) if key == 'ID': ...

Parse and store the filter field def add_filter(self, entry): """Parse and store the filter field""" entry = entry[10:-1] info = entry.split(',') if len(info) < 2: return False for v in info: key, value = v.split('=', 1) if key == 'ID': ...

Parse and store the alternative allele field def add_alt(self, entry): """Parse and store the alternative allele field""" entry = entry[7:-1] info = entry.split(',') if len(info) < 2: return False for v in info: key, value = v.split('=', 1) if...

Returns the VCF entry as it appears in the vcf file def sample_string(self, individual=-1): """Returns the VCF entry as it appears in the vcf file""" base = str(self) extra = self.get_sample_info(individual=individual) extra = [':'.join([str(j) for j in i]) for i in zip(*extra.values())...

Returns the sample info of a given sample or all by default def get_sample_info(self, individual=-1): """Returns the sample info of a given sample or all by default """ if isinstance(individual, str): individual = self.individuals[individual] extra = OrderedDict() f...

This will give a boolean list corresponding to whether each individual is homozygous for the alternative allele. def is_homozygous(self, individual=None): """This will give a boolean list corresponding to whether each individual is homozygous for the alternative allele. """ if ...

Returns the alternative alleles of the individual as a list def get_alt(self, individual=0, nucleotides_only=True): """Returns the alternative alleles of the individual as a list""" #not i.startswith(',') is put in to handle cases like <DEL:ME:ALU> where we have no alternate allele #but some re...

Returns the number of basepairs of each alternative allele def get_alt_length(self, individual=0): """Returns the number of basepairs of each alternative allele""" if isinstance(individual, str): individual = self.individuals[individual] return [len(self.alt[i-1].replace('.','')) fo...

Returns the longest length of the variant. For deletions, return is negative, SNPs return 0, and insertions are +. None return corresponds to no variant in interval for specified individual def get_alt_lengths(self): """Returns the longest length of the variant. For deletions, return is negativ...

Returns a boolean list of SNP status, ordered by samples def has_snp(self, individual=0): """Returns a boolean list of SNP status, ordered by samples""" if isinstance(individual, str): individual = self.individuals[individual] alts = self.get_alt(individual=individual) if al...

This parses a VCF row and stores the relevant information def parse_entry(self, entry): """This parses a VCF row and stores the relevant information""" entry = entry.split('\t') self.chrom, self.pos, self.id, self.ref, alt_, self.qual, filter_, info, self.format = entry[:9] self.samples...

Children are GFFFeatures and are defined when added. This is done to avoid memory overheads that may be incurred by GFF files that have millions of rows. def add_child(self, child): """Children are GFFFeatures and are defined when added. This is done to avoid memory overheads that may be incurr...

Transforms an object into it's ISO format, if possible. If the object can't be transformed, then an error is raised for the JSON parser. This is meant to be used on datetime instances, but will work with any object having a method called isoformat. :param obj: object to transform into it's ISO fo...

Inner encoding and try return string from entity dictionary :param field_encoders: :param entity_dict: :return: def try_encode(field_encoders, entity_dict): """ Inner encoding and try return string from entity dictionary :param field_encoders: :param entity_dict:...

Generate string of cwr format for all possible combinations of fields, accumulate and then elect the best. The best string it is who used most of all fields :param entity: :return: def encode(self, entity): """ Generate string of cwr format for all possible combinations of field...

For setting up the argparser for this instance. def argparser(self): """ For setting up the argparser for this instance. """ if self.__argparser is None: self.__argparser = self.argparser_factory() self.init_argparser(self.__argparser) return self.__argp...

Produces argparser for this type of Runtime. def argparser_factory(self): """ Produces argparser for this type of Runtime. """ return ArgumentParser( prog=self.prog, description=self.__doc__, add_help=False, )

This should not be called with an external argparser as it will corrupt tracking data if forced. def init_argparser(self, argparser): """ This should not be called with an external argparser as it will corrupt tracking data if forced. """ def prepare_argparser(): ...

This exists because argparser is dumb and naive and doesn't fail unrecognized arguments early. def unrecognized_arguments_error(self, args, parsed, extras): """ This exists because argparser is dumb and naive and doesn't fail unrecognized arguments early. """ # loop var...

This was used as part of the original non-recursive lookup for the target parser. def error(self, argparser, target, message): """ This was used as part of the original non-recursive lookup for the target parser. """ warnings.warn( 'Runtime.error is deprecat...

Subclass could override this by providing alternative keyword arguments and call this as its super. It should not reimplement this completely. Example: def init_argparser_export_target(self, argparser): super(MyToolchainRuntime, self).init_argparser_export_target( ...

Subclass could an extra expanation on how this is used. Arguments explanation Explanation text for the default help template help_template A standard help message for this option. def init_argparser_working_dir( self, argparser, explanation='', ...

For setting up build directory def init_argparser_build_dir( self, argparser, help=( 'the build directory, where all sources will be copied to ' 'as part of the build process; if left unspecified, the ' 'default behavior is to create a new temporary directory...

For setting up optional advice. def init_argparser_optional_advice( self, argparser, default=[], help=( 'a comma separated list of packages to retrieve optional ' 'advice from; the provided packages should have registered ' 'the appropriate entry points for s...

Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here for a subcommand. def init_argparser(self, argparser): """ Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here fo...

Prepare a spec for usage with the generic ToolchainRuntime. Subclasses should avoid overriding this; override create_spec instead. def prepare_spec(self, spec, **kwargs): """ Prepare a spec for usage with the generic ToolchainRuntime. Subclasses should avoid overriding this; o...

Turn the provided kwargs into arguments ready for toolchain. def kwargs_to_spec(self, **kwargs): """ Turn the provided kwargs into arguments ready for toolchain. """ spec = self.create_spec(**kwargs) self.prepare_spec(spec, **kwargs) return spec

Default helper for setting up the package_names option. This is separate so that subclasses are not assumed for the purposes of artifact creation; they should consider modifying the default help message to reflect the fact. def init_argparser_package_names(self, argparser, help=( ...

For setting up the source registry flag. def init_argparser_source_registry( self, argparser, default=None, help=( 'comma separated list of registries to use for gathering ' 'JavaScript sources from the given Python packages' )): """ For setting u...

Default helper for setting up the loaderplugin registries flags. Note that this is NOT part of the init_argparser due to implementation specific requirements. Subclasses should consider modifying the default value help message to cater to the toolchain it encapsulates. def init_argpar...

Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here for a subcommand. def init_argparser(self, argparser): """ Other runtimes (or users of ArgumentParser) can pass their subparser into here to collect the arguments here fo...

Creates the grammar for an Alphanumeric (A) field, accepting only the specified number of characters. By default Alphanumeric fields accept only ASCII characters, excluding lowercases. If the extended flag is set to True, then non-ASCII characters are allowed, but the no ASCII lowercase constraint is k...

Checks that the string is not empty. If it is empty an exception is raised, stopping the validation. This is used for compulsory alphanumeric fields. :param string: the field value def _check_not_empty(string): """ Checks that the string is not empty. If it is empty an exception is raised, ...

Creates the grammar for a Numeric (N) field, accepting only the specified number of characters. This version only allows integers. :param columns: number of columns for this field :param name: name for the field :return: grammar for the integer numeric field def numeric(columns, name=None): "...

Creates the grammar for a Numeric (N) field, accepting only the specified number of characters. This version only allows floats. As nothing in the string itself indicates how many of the characters are for the integer and the decimal sections, this should be specified with the nums_int parameter. ...

Transforms a string into a float. The nums_int parameter indicates the number of characters, starting from the left, to be used for the integer value. All the remaining ones will be used for the decimal value. :param number: string with the number :param nums_int: characters, counting from the lef...

Checks that the number parsed from the string is above a minimum. This is used on compulsory numeric fields. If the value is not above the minimum an exception is thrown. :param string: the field value :param minimum: minimum value def _check_above_value_float(string, minimum): """ Checks th...

Creates the grammar for a Boolean (B) field, accepting only 'Y' or 'N' :param name: name for the field :return: grammar for the flag field def boolean(name=None): """ Creates the grammar for a Boolean (B) field, accepting only 'Y' or 'N' :param name: name for the field :return: grammar for th...

Transforms a string into a boolean value. If a value which is not 'Y' or 'N' is received, a ParseException is thrown. :param: string: the string to transform :return: True if the string is 'Y', False if it is 'N' def _to_boolean(string): """ Transforms a string into a boolean value. If a val...

Creates the grammar for a Flag (F) field, accepting only 'Y', 'N' or 'U'. :param name: name for the field :return: grammar for the flag field def flag(name=None): """ Creates the grammar for a Flag (F) field, accepting only 'Y', 'N' or 'U'. :param name: name for the field :return: grammar for...

Creates the grammar for a Date (D) field, accepting only numbers in a certain pattern. :param name: name for the field :return: grammar for the date field def date(name=None): """ Creates the grammar for a Date (D) field, accepting only numbers in a certain pattern. :param name: name for ...

Creates the grammar for a Time or Duration (T) field, accepting only numbers in a certain pattern. :param name: name for the field :return: grammar for the date field def time(name=None): """ Creates the grammar for a Time or Duration (T) field, accepting only numbers in a certain pattern. ...

Creates the grammar for a Lookup (L) field, accepting only values from a list. Like in the Alphanumeric field, the result will be stripped of all heading and trailing whitespaces. :param values: values allowed :param name: name for the field :return: grammar for the lookup field def lookup(va...

Creates the grammar for a blank field. These are for constant empty strings which should be ignored, as they are used just as fillers. :param columns: number of columns, which is the required number of whitespaces :param name: name for the field :return: grammar for the blank field def blank(...

This returns a list of GFF objects (or GFF Features) with the given attribute and if supplied, those attributes with the specified value :param attribute: The 'info' field attribute we are querying :param value: Optional keyword, only return attributes equal to this value :param feature...

This returns a list of GFF objects which cover a specified location. :param seqid: The landmark identifier (usually a chromosome) :param start: The 1-based position of the start of the range we are querying :param end: The 1-based position of the end of the range we are querying :param ...

This returns a list of VCFEntry objects which cover a specified location. :param chrom: The landmark identifier (usually a chromosome) :param start: The 1-based position of the start of the range we are querying :param end: The 1-based position of the end of the range we are querying :p...

Remove a list of variants from the positions we are scanning def remove_variants(self, variants): """Remove a list of variants from the positions we are scanning""" chroms = set([i.chrom for i in variants]) for chrom in chroms: if self.append_chromosome: chrom = 'chr...

The default implementation is a recursive lookup method, which subclasses may make use of. Subclasses must implement this to return a mapping of modnames the the absolute path of the desired sourcefiles. Example: return { 'text': '/tmp/src/example_module/text/index.js', ...

Attempt to locate the plugin source; returns a mapping of modnames to the absolute path of the located sources. def generate_handler_sourcepath( self, toolchain, spec, loaderplugin_sourcepath): """ Attempt to locate the plugin source; returns a mapping of modnames to the abs...