query
stringlengths 5
1.23k
| positive
stringlengths 53
15.2k
| id_
int64 0
252k
| task_name
stringlengths 87
242
| negative
sequencelengths 20
553
|
|---|---|---|---|---|
add index to id to make it unique wrt ids | def append_index_id ( id , ids ) : index = 1 mod = '%s_%s' % ( id , index ) while mod in ids : index += 1 mod = '%s_%s' % ( id , index ) ids . append ( mod ) return mod , ids | 200 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/nr_fasta.py#L11-L21 | [
"def",
"_parseDelayImportDirectory",
"(",
"self",
",",
"rva",
",",
"size",
",",
"magic",
"=",
"consts",
".",
"PE32",
")",
":",
"return",
"self",
".",
"getDataAtRva",
"(",
"rva",
",",
"size",
")"
] |
de - replicate fastas based on sequence names | def de_rep ( fastas , append_index , return_original = False ) : ids = [ ] for fasta in fastas : for seq in parse_fasta ( fasta ) : header = seq [ 0 ] . split ( '>' ) [ 1 ] . split ( ) id = header [ 0 ] if id not in ids : ids . append ( id ) if return_original is True : yield [ header , seq ] else : yield seq elif append_index == True : new , ids = append_index_id ( id , ids ) if return_original is True : yield [ header , [ '>%s %s' % ( new , ' ' . join ( header [ 1 : : ] ) ) , seq [ 1 ] ] ] else : yield [ '>%s %s' % ( new , ' ' . join ( header [ 1 : : ] ) ) , seq [ 1 ] ] | 201 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/nr_fasta.py#L23-L43 | [
"def",
"open",
"(",
"self",
")",
":",
"sess_id",
"=",
"self",
".",
"_get_sess_id",
"(",
")",
"if",
"sess_id",
":",
"self",
".",
"application",
".",
"pc",
".",
"websockets",
"[",
"self",
".",
"_get_sess_id",
"(",
")",
"]",
"=",
"self",
"self",
".",
"write_message",
"(",
"json",
".",
"dumps",
"(",
"{",
"\"cmd\"",
":",
"\"status\"",
",",
"\"status\"",
":",
"\"open\"",
"}",
")",
")",
"else",
":",
"self",
".",
"write_message",
"(",
"json",
".",
"dumps",
"(",
"{",
"\"cmd\"",
":",
"\"error\"",
",",
"\"error\"",
":",
"\"Please login\"",
",",
"\"code\"",
":",
"401",
"}",
")",
")"
] |
Request data associated with postcode . | def get ( postcode ) : postcode = quote ( postcode . replace ( ' ' , '' ) ) url = '%s/postcode/%s.json' % ( END_POINT , postcode ) return _get_json_resp ( url ) | 202 | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L22-L34 | [
"def",
"_randomize_subject_list",
"(",
"data_list",
",",
"random",
")",
":",
"if",
"random",
"==",
"RandomType",
".",
"REPRODUCIBLE",
":",
"for",
"i",
"in",
"range",
"(",
"len",
"(",
"data_list",
")",
")",
":",
"_randomize_single_subject",
"(",
"data_list",
"[",
"i",
"]",
",",
"seed",
"=",
"i",
")",
"elif",
"random",
"==",
"RandomType",
".",
"UNREPRODUCIBLE",
":",
"for",
"data",
"in",
"data_list",
":",
"_randomize_single_subject",
"(",
"data",
")"
] |
Request all postcode data within distance miles of postcode . | def get_from_postcode ( postcode , distance ) : postcode = quote ( postcode . replace ( ' ' , '' ) ) return _get_from ( distance , 'postcode=%s' % postcode ) | 203 | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L56-L69 | [
"def",
"load_config",
"(",
"logdir",
")",
":",
"# pylint: disable=missing-raises-doc",
"config_path",
"=",
"logdir",
"and",
"os",
".",
"path",
".",
"join",
"(",
"logdir",
",",
"'config.yaml'",
")",
"if",
"not",
"config_path",
"or",
"not",
"tf",
".",
"gfile",
".",
"Exists",
"(",
"config_path",
")",
":",
"message",
"=",
"(",
"'Cannot resume an existing run since the logging directory does not '",
"'contain a configuration file.'",
")",
"raise",
"IOError",
"(",
"message",
")",
"with",
"tf",
".",
"gfile",
".",
"FastGFile",
"(",
"config_path",
",",
"'r'",
")",
"as",
"file_",
":",
"config",
"=",
"yaml",
".",
"load",
"(",
"file_",
",",
"Loader",
"=",
"yaml",
".",
"Loader",
")",
"message",
"=",
"'Resume run and write summaries and checkpoints to {}.'",
"tf",
".",
"logging",
".",
"info",
"(",
"message",
".",
"format",
"(",
"config",
".",
"logdir",
")",
")",
"return",
"config"
] |
Checks if latitude and longitude correct | def _check_point ( self , lat , lng ) : if abs ( lat ) > 90 or abs ( lng ) > 180 : msg = "Illegal lat and/or lng, (%s, %s) provided." % ( lat , lng ) raise IllegalPointException ( msg ) | 204 | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L123-L127 | [
"def",
"_parse_materials",
"(",
"header",
",",
"views",
")",
":",
"try",
":",
"import",
"PIL",
".",
"Image",
"except",
"ImportError",
":",
"log",
".",
"warning",
"(",
"\"unable to load textures without pillow!\"",
")",
"return",
"None",
"# load any images",
"images",
"=",
"None",
"if",
"\"images\"",
"in",
"header",
":",
"# images are referenced by index",
"images",
"=",
"[",
"None",
"]",
"*",
"len",
"(",
"header",
"[",
"\"images\"",
"]",
")",
"# loop through images",
"for",
"i",
",",
"img",
"in",
"enumerate",
"(",
"header",
"[",
"\"images\"",
"]",
")",
":",
"# get the bytes representing an image",
"blob",
"=",
"views",
"[",
"img",
"[",
"\"bufferView\"",
"]",
"]",
"# i.e. 'image/jpeg'",
"# mime = img['mimeType']",
"try",
":",
"# load the buffer into a PIL image",
"images",
"[",
"i",
"]",
"=",
"PIL",
".",
"Image",
".",
"open",
"(",
"util",
".",
"wrap_as_stream",
"(",
"blob",
")",
")",
"except",
"BaseException",
":",
"log",
".",
"error",
"(",
"\"failed to load image!\"",
",",
"exc_info",
"=",
"True",
")",
"# store materials which reference images",
"materials",
"=",
"[",
"]",
"if",
"\"materials\"",
"in",
"header",
":",
"for",
"mat",
"in",
"header",
"[",
"\"materials\"",
"]",
":",
"# flatten key structure so we can loop it",
"loopable",
"=",
"mat",
".",
"copy",
"(",
")",
"# this key stores another dict of crap",
"if",
"\"pbrMetallicRoughness\"",
"in",
"loopable",
":",
"# add keys of keys to top level dict",
"loopable",
".",
"update",
"(",
"loopable",
".",
"pop",
"(",
"\"pbrMetallicRoughness\"",
")",
")",
"# save flattened keys we can use for kwargs",
"pbr",
"=",
"{",
"}",
"for",
"k",
",",
"v",
"in",
"loopable",
".",
"items",
"(",
")",
":",
"if",
"not",
"isinstance",
"(",
"v",
",",
"dict",
")",
":",
"pbr",
"[",
"k",
"]",
"=",
"v",
"elif",
"\"index\"",
"in",
"v",
":",
"# get the index of image for texture",
"idx",
"=",
"header",
"[",
"\"textures\"",
"]",
"[",
"v",
"[",
"\"index\"",
"]",
"]",
"[",
"\"source\"",
"]",
"# store the actual image as the value",
"pbr",
"[",
"k",
"]",
"=",
"images",
"[",
"idx",
"]",
"# create a PBR material object for the GLTF material",
"materials",
".",
"append",
"(",
"visual",
".",
"texture",
".",
"PBRMaterial",
"(",
"*",
"*",
"pbr",
")",
")",
"return",
"materials"
] |
Checks for cached responses before requesting from web - service | def _lookup ( self , skip_cache , fun , * args , * * kwargs ) : if args not in self . cache or skip_cache : self . cache [ args ] = fun ( * args , * * kwargs ) return self . cache [ args ] | 205 | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L129-L136 | [
"def",
"get_fptr",
"(",
"self",
")",
":",
"cmpfunc",
"=",
"ctypes",
".",
"CFUNCTYPE",
"(",
"ctypes",
".",
"c_int",
",",
"WPARAM",
",",
"LPARAM",
",",
"ctypes",
".",
"POINTER",
"(",
"KBDLLHookStruct",
")",
")",
"return",
"cmpfunc",
"(",
"self",
".",
"handle_input",
")"
] |
Calls postcodes . get_nearest but checks correctness of lat and long and by default utilises a local cache . | def get_nearest ( self , lat , lng , skip_cache = False ) : lat , lng = float ( lat ) , float ( lng ) self . _check_point ( lat , lng ) return self . _lookup ( skip_cache , get_nearest , lat , lng ) | 206 | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L152-L167 | [
"def",
"update_task_redundancy",
"(",
"config",
",",
"task_id",
",",
"redundancy",
")",
":",
"if",
"task_id",
"is",
"None",
":",
"msg",
"=",
"(",
"\"Are you sure you want to update all the tasks redundancy?\"",
")",
"if",
"click",
".",
"confirm",
"(",
"msg",
")",
":",
"res",
"=",
"_update_tasks_redundancy",
"(",
"config",
",",
"task_id",
",",
"redundancy",
")",
"click",
".",
"echo",
"(",
"res",
")",
"else",
":",
"click",
".",
"echo",
"(",
"\"Aborting.\"",
")",
"else",
":",
"res",
"=",
"_update_tasks_redundancy",
"(",
"config",
",",
"task_id",
",",
"redundancy",
")",
"click",
".",
"echo",
"(",
"res",
")"
] |
Calls postcodes . get_from_postcode but checks correctness of distance and by default utilises a local cache . | def get_from_postcode ( self , postcode , distance , skip_cache = False ) : distance = float ( distance ) if distance < 0 : raise IllegalDistanceException ( "Distance must not be negative" ) # remove spaces and change case here due to caching postcode = postcode . lower ( ) . replace ( ' ' , '' ) return self . _lookup ( skip_cache , get_from_postcode , postcode , float ( distance ) ) | 207 | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L169-L189 | [
"def",
"rewind",
"(",
"self",
")",
":",
"if",
"self",
".",
"mode",
"!=",
"READ",
":",
"raise",
"OSError",
"(",
"\"Can't rewind in write mode\"",
")",
"self",
".",
"fileobj",
".",
"seek",
"(",
"0",
")",
"self",
".",
"_new_member",
"=",
"True",
"self",
".",
"extrabuf",
"=",
"b\"\"",
"self",
".",
"extrasize",
"=",
"0",
"self",
".",
"extrastart",
"=",
"0",
"self",
".",
"offset",
"=",
"0"
] |
Calls postcodes . get_from_geo but checks the correctness of all arguments and by default utilises a local cache . | def get_from_geo ( self , lat , lng , distance , skip_cache = False ) : # remove spaces and change case here due to caching lat , lng , distance = float ( lat ) , float ( lng ) , float ( distance ) if distance < 0 : raise IllegalDistanceException ( "Distance must not be negative" ) self . _check_point ( lat , lng ) return self . _lookup ( skip_cache , get_from_geo , lat , lng , distance ) | 208 | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L191-L210 | [
"def",
"toggle",
"(",
"self",
",",
"rows",
")",
":",
"for",
"r",
"in",
"Progress",
"(",
"rows",
",",
"'toggling'",
",",
"total",
"=",
"len",
"(",
"self",
".",
"rows",
")",
")",
":",
"if",
"not",
"self",
".",
"unselectRow",
"(",
"r",
")",
":",
"self",
".",
"selectRow",
"(",
"r",
")"
] |
get coordinates of insertions from insertion - masked sequence | def insertions_from_masked ( seq ) : insertions = [ ] prev = True for i , base in enumerate ( seq ) : if base . isupper ( ) and prev is True : insertions . append ( [ ] ) prev = False elif base . islower ( ) : insertions [ - 1 ] . append ( i ) prev = True return [ [ min ( i ) , max ( i ) ] for i in insertions if i != [ ] ] | 209 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L15-L28 | [
"def",
"remove_server",
"(",
"self",
",",
"server_id",
")",
":",
"# Validate server_id",
"server",
"=",
"self",
".",
"_get_server",
"(",
"server_id",
")",
"# Delete any instances we recorded to be cleaned up",
"if",
"server_id",
"in",
"self",
".",
"_owned_subscriptions",
":",
"inst_list",
"=",
"self",
".",
"_owned_subscriptions",
"[",
"server_id",
"]",
"# We iterate backwards because we change the list",
"for",
"i",
"in",
"six",
".",
"moves",
".",
"range",
"(",
"len",
"(",
"inst_list",
")",
"-",
"1",
",",
"-",
"1",
",",
"-",
"1",
")",
":",
"inst",
"=",
"inst_list",
"[",
"i",
"]",
"server",
".",
"conn",
".",
"DeleteInstance",
"(",
"inst",
".",
"path",
")",
"del",
"inst_list",
"[",
"i",
"]",
"del",
"self",
".",
"_owned_subscriptions",
"[",
"server_id",
"]",
"if",
"server_id",
"in",
"self",
".",
"_owned_filters",
":",
"inst_list",
"=",
"self",
".",
"_owned_filters",
"[",
"server_id",
"]",
"# We iterate backwards because we change the list",
"for",
"i",
"in",
"six",
".",
"moves",
".",
"range",
"(",
"len",
"(",
"inst_list",
")",
"-",
"1",
",",
"-",
"1",
",",
"-",
"1",
")",
":",
"inst",
"=",
"inst_list",
"[",
"i",
"]",
"server",
".",
"conn",
".",
"DeleteInstance",
"(",
"inst",
".",
"path",
")",
"del",
"inst_list",
"[",
"i",
"]",
"del",
"self",
".",
"_owned_filters",
"[",
"server_id",
"]",
"if",
"server_id",
"in",
"self",
".",
"_owned_destinations",
":",
"inst_list",
"=",
"self",
".",
"_owned_destinations",
"[",
"server_id",
"]",
"# We iterate backwards because we change the list",
"for",
"i",
"in",
"six",
".",
"moves",
".",
"range",
"(",
"len",
"(",
"inst_list",
")",
"-",
"1",
",",
"-",
"1",
",",
"-",
"1",
")",
":",
"inst",
"=",
"inst_list",
"[",
"i",
"]",
"server",
".",
"conn",
".",
"DeleteInstance",
"(",
"inst",
".",
"path",
")",
"del",
"inst_list",
"[",
"i",
"]",
"del",
"self",
".",
"_owned_destinations",
"[",
"server_id",
"]",
"# Remove server from this listener",
"del",
"self",
".",
"_servers",
"[",
"server_id",
"]"
] |
get insertion information from header | def seq_info ( names , id2names , insertions , sequences ) : seqs = { } # seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]] for name in names : id = id2names [ name ] gene = name . split ( 'fromHMM::' , 1 ) [ 0 ] . rsplit ( ' ' , 1 ) [ 1 ] model = name . split ( 'fromHMM::' , 1 ) [ 1 ] . split ( '=' , 1 ) [ 1 ] . split ( ) [ 0 ] i_gene_pos = insertions [ id ] # coordinates of each insertion wrt gene i_model_pos = name . split ( 'fromHMM::' , 1 ) [ 1 ] . split ( 'model-pos(ins-len)=' ) [ 1 ] . split ( ) [ 0 ] . split ( ';' ) # model overlap i_info = [ ] for i , ins in enumerate ( i_gene_pos ) : model_pos = i_model_pos [ i ] . split ( '-' ) [ 1 ] . split ( '(' ) [ 0 ] length = i_model_pos [ i ] . split ( '(' ) [ 1 ] . split ( ')' ) [ 0 ] iheader = '>%s_%s insertion::seq=%s type=insertion strand=n/a gene-pos=%s-%s model-pos=%s' % ( id , ( i + 1 ) , ( i + 1 ) , ins [ 0 ] , ins [ 1 ] , model_pos ) iseq = sequences [ id ] [ 1 ] [ ins [ 0 ] : ( ins [ 1 ] + 1 ) ] iseq = [ iheader , iseq ] info = [ ins , model_pos , length , iseq , [ ] , [ ] ] i_info . append ( info ) seqs [ id ] = [ gene , model , i_info ] return seqs | 210 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L64-L86 | [
"def",
"remove_matching_braces",
"(",
"latex",
")",
":",
"if",
"latex",
".",
"startswith",
"(",
"'{'",
")",
"and",
"latex",
".",
"endswith",
"(",
"'}'",
")",
":",
"opened",
"=",
"1",
"matches",
"=",
"True",
"for",
"char",
"in",
"latex",
"[",
"1",
":",
"-",
"1",
"]",
":",
"if",
"char",
"==",
"'{'",
":",
"opened",
"+=",
"1",
"elif",
"char",
"==",
"'}'",
":",
"opened",
"-=",
"1",
"if",
"opened",
"==",
"0",
":",
"matches",
"=",
"False",
"if",
"matches",
":",
"latex",
"=",
"latex",
"[",
"1",
":",
"-",
"1",
"]",
"return",
"latex"
] |
make sure thresh % feature is contained within insertion | def check_overlap ( pos , ins , thresh ) : ins_pos = ins [ 0 ] ins_len = ins [ 2 ] ol = overlap ( ins_pos , pos ) feat_len = pos [ 1 ] - pos [ 0 ] + 1 # print float(ol) / float(feat_len) if float ( ol ) / float ( feat_len ) >= thresh : return True return False | 211 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L91-L102 | [
"def",
"list_configs",
"(",
")",
":",
"try",
":",
"configs",
"=",
"snapper",
".",
"ListConfigs",
"(",
")",
"return",
"dict",
"(",
"(",
"config",
"[",
"0",
"]",
",",
"config",
"[",
"2",
"]",
")",
"for",
"config",
"in",
"configs",
")",
"except",
"dbus",
".",
"DBusException",
"as",
"exc",
":",
"raise",
"CommandExecutionError",
"(",
"'Error encountered while listing configurations: {0}'",
".",
"format",
"(",
"_dbus_exception_to_reason",
"(",
"exc",
",",
"locals",
"(",
")",
")",
")",
")"
] |
length of largest insertion | def max_insertion ( seqs , gene , domain ) : seqs = [ i [ 2 ] for i in list ( seqs . values ( ) ) if i [ 2 ] != [ ] and i [ 0 ] == gene and i [ 1 ] == domain ] lengths = [ ] for seq in seqs : for ins in seq : lengths . append ( int ( ins [ 2 ] ) ) if lengths == [ ] : return 100 return max ( lengths ) | 212 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L305-L316 | [
"def",
"status",
"(",
"sec",
")",
":",
"if",
"_meta_",
".",
"prg_bar",
"in",
"[",
"\"on\"",
",",
"\"ON\"",
"]",
":",
"syms",
"=",
"[",
"\"|\"",
",",
"\"/\"",
",",
"\"-\"",
",",
"\"\\\\\"",
"]",
"for",
"sym",
"in",
"syms",
":",
"sys",
".",
"stdout",
".",
"write",
"(",
"\"\\b{0}{1}{2}\"",
".",
"format",
"(",
"_meta_",
".",
"color",
"[",
"\"GREY\"",
"]",
",",
"sym",
",",
"_meta_",
".",
"color",
"[",
"\"ENDC\"",
"]",
")",
")",
"sys",
".",
"stdout",
".",
"flush",
"(",
")",
"time",
".",
"sleep",
"(",
"float",
"(",
"sec",
")",
")"
] |
get length of model | def model_length ( gene , domain ) : if gene == '16S' : domain2max = { 'E_coli_K12' : int ( 1538 ) , 'bacteria' : int ( 1689 ) , 'archaea' : int ( 1563 ) , 'eukarya' : int ( 2652 ) } return domain2max [ domain ] elif gene == '23S' : domain2max = { 'E_coli_K12' : int ( 2903 ) , 'bacteria' : int ( 3146 ) , 'archaea' : int ( 3774 ) , 'eukarya' : int ( 9079 ) } return domain2max [ domain ] else : print ( sys . stderr , '# length unknown for gene: %s, domain: %s' % ( gene , domain ) ) exit ( ) | 213 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L318-L330 | [
"def",
"_do_http",
"(",
"opts",
",",
"profile",
"=",
"'default'",
")",
":",
"ret",
"=",
"{",
"}",
"url",
"=",
"__salt__",
"[",
"'config.get'",
"]",
"(",
"'modjk:{0}:url'",
".",
"format",
"(",
"profile",
")",
",",
"''",
")",
"user",
"=",
"__salt__",
"[",
"'config.get'",
"]",
"(",
"'modjk:{0}:user'",
".",
"format",
"(",
"profile",
")",
",",
"''",
")",
"passwd",
"=",
"__salt__",
"[",
"'config.get'",
"]",
"(",
"'modjk:{0}:pass'",
".",
"format",
"(",
"profile",
")",
",",
"''",
")",
"realm",
"=",
"__salt__",
"[",
"'config.get'",
"]",
"(",
"'modjk:{0}:realm'",
".",
"format",
"(",
"profile",
")",
",",
"''",
")",
"timeout",
"=",
"__salt__",
"[",
"'config.get'",
"]",
"(",
"'modjk:{0}:timeout'",
".",
"format",
"(",
"profile",
")",
",",
"''",
")",
"if",
"not",
"url",
":",
"raise",
"Exception",
"(",
"'missing url in profile {0}'",
".",
"format",
"(",
"profile",
")",
")",
"if",
"user",
"and",
"passwd",
":",
"auth",
"=",
"_auth",
"(",
"url",
"=",
"url",
",",
"realm",
"=",
"realm",
",",
"user",
"=",
"user",
",",
"passwd",
"=",
"passwd",
")",
"_install_opener",
"(",
"auth",
")",
"url",
"+=",
"'?{0}'",
".",
"format",
"(",
"_urlencode",
"(",
"opts",
")",
")",
"for",
"line",
"in",
"_urlopen",
"(",
"url",
",",
"timeout",
"=",
"timeout",
")",
".",
"read",
"(",
")",
".",
"splitlines",
"(",
")",
":",
"splt",
"=",
"line",
".",
"split",
"(",
"'='",
",",
"1",
")",
"if",
"splt",
"[",
"0",
"]",
"in",
"ret",
":",
"ret",
"[",
"splt",
"[",
"0",
"]",
"]",
"+=",
"',{0}'",
".",
"format",
"(",
"splt",
"[",
"1",
"]",
")",
"else",
":",
"ret",
"[",
"splt",
"[",
"0",
"]",
"]",
"=",
"splt",
"[",
"1",
"]",
"return",
"ret"
] |
setup unique marker for every orf annotation - change size if necessary | def setup_markers ( seqs ) : family2marker = { } # family2marker[family] = [marker, size] markers = cycle ( [ '^' , 'p' , '*' , '+' , 'x' , 'd' , '|' , 'v' , '>' , '<' , '8' ] ) size = 60 families = [ ] for seq in list ( seqs . values ( ) ) : for insertion in seq [ 2 ] : for family in list ( insertion [ - 1 ] . values ( ) ) : if family not in families : families . append ( family ) for family in families : marker = next ( markers ) if marker == '^' : size = size * 0.5 family2marker [ family ] = [ marker , size ] return family2marker | 214 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L332-L351 | [
"def",
"on_end_validation",
"(",
"self",
",",
"event",
")",
":",
"self",
".",
"Enable",
"(",
")",
"self",
".",
"Show",
"(",
")",
"self",
".",
"magic_gui_frame",
".",
"Destroy",
"(",
")"
] |
plot insertions for each gene and domain | def plot_by_gene_and_domain ( name , seqs , tax , id2name ) : for gene in set ( [ seq [ 0 ] for seq in list ( seqs . values ( ) ) ] ) : for domain in set ( [ seq [ 1 ] for seq in list ( seqs . values ( ) ) ] ) : plot_insertions ( name , seqs , gene , domain , tax , id2name ) | 215 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L551-L557 | [
"def",
"configure_logger",
"(",
"self",
",",
"tc_config_log_filename",
"=",
"None",
",",
"tc_output_log_filename",
"=",
"None",
")",
":",
"# Get config logger filename",
"config_log_filename",
"=",
"DriverWrappersPool",
".",
"get_configured_value",
"(",
"'Config_log_filename'",
",",
"tc_config_log_filename",
",",
"'logging.conf'",
")",
"config_log_filename",
"=",
"os",
".",
"path",
".",
"join",
"(",
"DriverWrappersPool",
".",
"config_directory",
",",
"config_log_filename",
")",
"# Configure logger only if logging filename has changed",
"if",
"self",
".",
"config_log_filename",
"!=",
"config_log_filename",
":",
"# Get output logger filename",
"output_log_filename",
"=",
"DriverWrappersPool",
".",
"get_configured_value",
"(",
"'Output_log_filename'",
",",
"tc_output_log_filename",
",",
"'toolium.log'",
")",
"output_log_filename",
"=",
"os",
".",
"path",
".",
"join",
"(",
"DriverWrappersPool",
".",
"output_directory",
",",
"output_log_filename",
")",
"output_log_filename",
"=",
"output_log_filename",
".",
"replace",
"(",
"'\\\\'",
",",
"'\\\\\\\\'",
")",
"try",
":",
"logging",
".",
"config",
".",
"fileConfig",
"(",
"config_log_filename",
",",
"{",
"'logfilename'",
":",
"output_log_filename",
"}",
",",
"False",
")",
"except",
"Exception",
"as",
"exc",
":",
"print",
"(",
"\"[WARN] Error reading logging config file '{}': {}\"",
".",
"format",
"(",
"config_log_filename",
",",
"exc",
")",
")",
"self",
".",
"config_log_filename",
"=",
"config_log_filename",
"self",
".",
"output_log_filename",
"=",
"output_log_filename",
"self",
".",
"logger",
"=",
"logging",
".",
"getLogger",
"(",
"__name__",
")"
] |
get the description for each ORF | def get_descriptions ( fastas ) : id2desc = { } for fasta in fastas : for seq in parse_fasta ( fasta ) : header = seq [ 0 ] . split ( '>' ) [ 1 ] . split ( ' ' ) id = header [ 0 ] if len ( header ) > 1 : desc = ' ' . join ( header [ 1 : ] ) else : desc = 'n/a' length = float ( len ( [ i for i in seq [ 1 ] . strip ( ) if i != '*' ] ) ) id2desc [ id ] = [ fasta , desc , length ] return id2desc | 216 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L37-L52 | [
"def",
"parse_setup",
"(",
"filepath",
")",
":",
"# TODO: Need to parse setup.cfg and merge with the data from below",
"# Monkey patch setuptools.setup to capture keyword arguments",
"setup_kwargs",
"=",
"{",
"}",
"def",
"setup_interceptor",
"(",
"*",
"*",
"kwargs",
")",
":",
"setup_kwargs",
".",
"update",
"(",
"kwargs",
")",
"import",
"setuptools",
"setuptools_setup",
"=",
"setuptools",
".",
"setup",
"setuptools",
".",
"setup",
"=",
"setup_interceptor",
"# Manually compile setup.py",
"with",
"open",
"(",
"filepath",
",",
"'r'",
")",
"as",
"f",
":",
"code",
"=",
"compile",
"(",
"f",
".",
"read",
"(",
")",
",",
"''",
",",
"'exec'",
")",
"setup",
"=",
"ModuleType",
"(",
"'setup'",
")",
"exec",
"(",
"code",
",",
"setup",
".",
"__dict__",
")",
"# Remove monkey patch",
"setuptools",
".",
"setup",
"=",
"setuptools_setup",
"return",
"setup_kwargs"
] |
optimize later? slow ... should combine with calculate_threshold module | def print_genome_matrix ( hits , fastas , id2desc , file_name ) : out = open ( file_name , 'w' ) fastas = sorted ( fastas ) print ( '## percent identity between genomes' , file = out ) print ( '# - \t %s' % ( '\t' . join ( fastas ) ) , file = out ) for fasta in fastas : line = [ fasta ] for other in fastas : if other == fasta : average = '-' else : average = numpy . average ( [ hits [ fasta ] [ other ] [ i ] [ 3 ] for i in hits [ fasta ] [ other ] ] ) line . append ( str ( average ) ) print ( '\t' . join ( line ) , file = out ) print ( '' , file = out ) print ( '## percent of orfs that are orthologous between genomes' , file = out ) print ( '# - \t %s' % ( '\t' . join ( fastas ) ) , file = out ) for fasta in fastas : line = [ fasta ] for other in fastas : if other == fasta : percent = '-' else : orthologs = float ( len ( hits [ fasta ] [ other ] ) ) orfs = float ( len ( [ i for i in id2desc if id2desc [ i ] [ 0 ] == fasta ] ) ) percent = float ( orthologs / orfs ) * 100 line . append ( str ( percent ) ) print ( '\t' . join ( line ) , file = out ) | 217 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L140-L171 | [
"def",
"from_non_aligned_residue_IDs",
"(",
"Chain",
",",
"StartResidueID",
",",
"EndResidueID",
",",
"Sequence",
"=",
"None",
")",
":",
"return",
"PDBSection",
"(",
"Chain",
",",
"PDB",
".",
"ResidueID2String",
"(",
"StartResidueID",
")",
",",
"PDB",
".",
"ResidueID2String",
"(",
"EndResidueID",
")",
",",
"Sequence",
"=",
"Sequence",
")"
] |
compare genome to self to get the best possible bit score for each ORF | def self_compare ( fastas , id2desc , algorithm ) : for fasta in fastas : blast = open ( search ( fasta , fasta , method = algorithm , alignment = 'local' ) ) for hit in best_blast ( blast , 1 ) : id , bit = hit [ 0 ] . split ( ) [ 0 ] , float ( hit [ - 1 ] ) id2desc [ id ] . append ( bit ) return id2desc | 218 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L240-L249 | [
"def",
"_is_accepted_input",
"(",
"self",
",",
"input_string",
")",
":",
"ret",
"=",
"False",
"accept_filter",
"=",
"(",
"self",
".",
"volume_string",
",",
"\"http stream debug: \"",
")",
"reject_filter",
"=",
"(",
")",
"for",
"n",
"in",
"accept_filter",
":",
"if",
"n",
"in",
"input_string",
":",
"ret",
"=",
"True",
"break",
"if",
"ret",
":",
"for",
"n",
"in",
"reject_filter",
":",
"if",
"n",
"in",
"input_string",
":",
"ret",
"=",
"False",
"break",
"return",
"ret"
] |
if thresholds are not specififed calculate based on the distribution of normalized bit scores | def calc_thresholds ( rbh , file_name , thresholds = [ False , False , False , False ] , stdevs = 2 ) : calc_threshold = thresholds [ - 1 ] norm_threshold = { } for pair in itertools . permutations ( [ i for i in rbh ] , 2 ) : if pair [ 0 ] not in norm_threshold : norm_threshold [ pair [ 0 ] ] = { } norm_threshold [ pair [ 0 ] ] [ pair [ 1 ] ] = { } out = open ( file_name , 'w' ) print ( '#### summary of rbh comparisons\n' , file = out ) comparisons = [ ] for genome in rbh : for compare in rbh [ genome ] : pair = '' . join ( sorted ( [ genome , compare ] ) ) if pair in comparisons : continue comparisons . append ( pair ) scores = { 'percent identity' : [ ] , 'e-value' : [ ] , 'bit score' : [ ] , 'normalized bit score' : [ ] , 'alignment length fraction' : [ ] } print ( '### blast between %s and %s\n' % ( genome , compare ) , file = out ) for id in rbh [ genome ] [ compare ] : pident , length_fraction , e , bit , norm_bit = rbh [ genome ] [ compare ] [ id ] [ 3 : ] scores [ 'percent identity' ] . append ( pident ) scores [ 'alignment length fraction' ] . append ( length_fraction ) scores [ 'e-value' ] . append ( e ) scores [ 'bit score' ] . append ( bit ) scores [ 'normalized bit score' ] . append ( norm_bit ) if calc_threshold is True : norms = scores [ 'normalized bit score' ] average = numpy . average ( norms ) std = numpy . std ( norms ) normal_thresh = average - ( std * stdevs ) print ( '## average normalized bit score: %s' % average , file = out ) print ( '## standard deviation of normalized bit scores: %s' % std , file = out ) print ( '## normalized bit score threshold set to: %s\n' % ( normal_thresh ) , file = out ) norm_threshold [ genome ] [ compare ] , norm_threshold [ compare ] [ genome ] = normal_thresh , normal_thresh for score in scores : print ( '## %s' % ( score ) , file = out ) if len ( scores [ score ] ) > 0 : print ( '## average: %s' % numpy . average ( scores [ score ] ) , file = out ) # hist = histogram(scores[score], []) # for line in hist: # print >> out, line print ( '' , file = out ) out . close ( ) if calc_threshold is True : return thresholds [ 0 : - 1 ] + [ norm_threshold ] else : return thresholds | 219 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L303-L352 | [
"def",
"start_transmit",
"(",
"self",
",",
"blocking",
"=",
"False",
",",
"start_packet_groups",
"=",
"True",
",",
"*",
"ports",
")",
":",
"port_list",
"=",
"self",
".",
"set_ports_list",
"(",
"*",
"ports",
")",
"if",
"start_packet_groups",
":",
"port_list_for_packet_groups",
"=",
"self",
".",
"ports",
".",
"values",
"(",
")",
"port_list_for_packet_groups",
"=",
"self",
".",
"set_ports_list",
"(",
"*",
"port_list_for_packet_groups",
")",
"self",
".",
"api",
".",
"call_rc",
"(",
"'ixClearTimeStamp {}'",
".",
"format",
"(",
"port_list_for_packet_groups",
")",
")",
"self",
".",
"api",
".",
"call_rc",
"(",
"'ixStartPacketGroups {}'",
".",
"format",
"(",
"port_list_for_packet_groups",
")",
")",
"self",
".",
"api",
".",
"call_rc",
"(",
"'ixStartTransmit {}'",
".",
"format",
"(",
"port_list",
")",
")",
"time",
".",
"sleep",
"(",
"0.2",
")",
"if",
"blocking",
":",
"self",
".",
"wait_transmit",
"(",
"*",
"ports",
")"
] |
make and split a rbh network | def neto ( fastas , algorithm = 'usearch' , e = 0.01 , bit = 40 , length = .65 , norm_bit = False ) : thresholds = [ e , bit , length , norm_bit ] id2desc = get_descriptions ( fastas ) # get [fasta, description, length] for ORF id id2desc = self_compare ( fastas , id2desc , algorithm ) # get best possible bit score for each ORF # (comparing with itself) [fasta, description, length, bestbit] hits = compare_genomes ( fastas , id2desc , algorithm ) # pair wise genome comparisons {genome: {id: [match_type = 'rbh' or 'fbh', scores]}} calc_thresholds ( hits , file_name = 'fbh.scores.summary.txt' ) rbh_network ( id2desc , hits , file_name = 'fbh.network.edges.txt' ) hits , rbh = find_rbh ( hits , id2desc ) # remove hits that are not reciprocal best blast hits thresholds = calc_thresholds ( rbh , 'rbh.scores.summary.txt' , thresholds ) # print rbh score summary to rbh_score_summary.txt and # calculate normalized bit score cutoff for each pair of # genomes, if desired g = rbh_network ( id2desc , rbh , file_name = 'rbh.network.edges.txt' ) filtered_g , filtered_rbh = rbh_network ( id2desc , rbh , 'rbh.filtered.network.edges.txt' , thresholds ) calc_thresholds ( filtered_rbh , file_name = 'rbh.filtered.scores.summary.txt' ) print_summary ( filtered_g , fastas , id2desc , file_name = 'rbh.filtered.network.nodes.txt' ) print_network_matrix ( filtered_g , fastas , id2desc , file_name = 'rbh.filtered.network.matrix.txt' ) print_genome_matrix ( filtered_rbh , fastas , id2desc , file_name = 'rbh.filtered.network.genome_matrix.txt' ) split_g = split_network ( filtered_g , id2desc , file_name = 'rbh.filtered.split.network.edges.txt' ) print_summary ( split_g , fastas , id2desc , file_name = 'rbh.filtered.split.network.nodes.txt' ) print_network_matrix ( split_g , fastas , id2desc , file_name = 'rbh.filtered.split.network.matrix.txt' ) return split_g | 220 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L416-L445 | [
"def",
"feeds",
"(",
"self",
")",
":",
"url",
"=",
"self",
".",
"_build_url",
"(",
"'feeds'",
")",
"json",
"=",
"self",
".",
"_json",
"(",
"self",
".",
"_get",
"(",
"url",
")",
",",
"200",
")",
"del",
"json",
"[",
"'ETag'",
"]",
"del",
"json",
"[",
"'Last-Modified'",
"]",
"urls",
"=",
"[",
"'timeline_url'",
",",
"'user_url'",
",",
"'current_user_public_url'",
",",
"'current_user_url'",
",",
"'current_user_actor_url'",
",",
"'current_user_organization_url'",
",",
"]",
"for",
"url",
"in",
"urls",
":",
"json",
"[",
"url",
"]",
"=",
"URITemplate",
"(",
"json",
"[",
"url",
"]",
")",
"links",
"=",
"json",
".",
"get",
"(",
"'_links'",
",",
"{",
"}",
")",
"for",
"d",
"in",
"links",
".",
"values",
"(",
")",
":",
"d",
"[",
"'href'",
"]",
"=",
"URITemplate",
"(",
"d",
"[",
"'href'",
"]",
")",
"return",
"json"
] |
Collapses multiple dimensions into a single raster_info complex struct | def _parse_raster_info ( self , prop = RASTER_INFO ) : raster_info = { } . fromkeys ( _iso_definitions [ prop ] , u'' ) # Ensure conversion of lists to newlines is in place raster_info [ 'dimensions' ] = get_default_for_complex_sub ( prop = prop , subprop = 'dimensions' , value = parse_property ( self . _xml_tree , None , self . _data_map , '_ri_num_dims' ) , xpath = self . _data_map [ '_ri_num_dims' ] ) xpath_root = self . _get_xroot_for ( prop ) xpath_map = self . _data_structures [ prop ] for dimension in parse_complex_list ( self . _xml_tree , xpath_root , xpath_map , RASTER_DIMS ) : dimension_type = dimension [ 'type' ] . lower ( ) if dimension_type == 'vertical' : raster_info [ 'vertical_count' ] = dimension [ 'size' ] elif dimension_type == 'column' : raster_info [ 'column_count' ] = dimension [ 'size' ] raster_info [ 'x_resolution' ] = u' ' . join ( dimension [ k ] for k in [ 'value' , 'units' ] ) . strip ( ) elif dimension_type == 'row' : raster_info [ 'row_count' ] = dimension [ 'size' ] raster_info [ 'y_resolution' ] = u' ' . join ( dimension [ k ] for k in [ 'value' , 'units' ] ) . strip ( ) return raster_info if any ( raster_info [ k ] for k in raster_info ) else { } | 221 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L472-L502 | [
"def",
"remove_stale_javascripts",
"(",
"portal",
")",
":",
"logger",
".",
"info",
"(",
"\"Removing stale javascripts ...\"",
")",
"for",
"js",
"in",
"JAVASCRIPTS_TO_REMOVE",
":",
"logger",
".",
"info",
"(",
"\"Unregistering JS %s\"",
"%",
"js",
")",
"portal",
".",
"portal_javascripts",
".",
"unregisterResource",
"(",
"js",
")"
] |
Derives multiple dimensions from a single raster_info complex struct | def _update_raster_info ( self , * * update_props ) : tree_to_update = update_props [ 'tree_to_update' ] prop = update_props [ 'prop' ] values = update_props . pop ( 'values' ) # Update number of dimensions at raster_info root (applies to all dimensions below) xroot , xpath = None , self . _data_map [ '_ri_num_dims' ] raster_info = [ update_property ( tree_to_update , xroot , xpath , prop , values . get ( 'dimensions' , u'' ) ) ] # Derive vertical, longitude, and latitude dimensions from raster_info xpath_root = self . _get_xroot_for ( prop ) xpath_map = self . _data_structures [ prop ] v_dimension = { } if values . get ( 'vertical_count' ) : v_dimension = v_dimension . fromkeys ( xpath_map , u'' ) v_dimension [ 'type' ] = 'vertical' v_dimension [ 'size' ] = values . get ( 'vertical_count' , u'' ) x_dimension = { } if values . get ( 'column_count' ) or values . get ( 'x_resolution' ) : x_dimension = x_dimension . fromkeys ( xpath_map , u'' ) x_dimension [ 'type' ] = 'column' x_dimension [ 'size' ] = values . get ( 'column_count' , u'' ) x_dimension [ 'value' ] = values . get ( 'x_resolution' , u'' ) y_dimension = { } if values . get ( 'row_count' ) or values . get ( 'y_resolution' ) : y_dimension = y_dimension . fromkeys ( xpath_map , u'' ) y_dimension [ 'type' ] = 'row' y_dimension [ 'size' ] = values . get ( 'row_count' , u'' ) y_dimension [ 'value' ] = values . get ( 'y_resolution' , u'' ) # Update derived dimensions as complex list, and append affected elements for return update_props [ 'prop' ] = RASTER_DIMS update_props [ 'values' ] = [ v_dimension , x_dimension , y_dimension ] raster_info += update_complex_list ( xpath_root = xpath_root , xpath_map = xpath_map , * * update_props ) return raster_info | 222 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L622-L666 | [
"def",
"remove_stale_javascripts",
"(",
"portal",
")",
":",
"logger",
".",
"info",
"(",
"\"Removing stale javascripts ...\"",
")",
"for",
"js",
"in",
"JAVASCRIPTS_TO_REMOVE",
":",
"logger",
".",
"info",
"(",
"\"Unregistering JS %s\"",
"%",
"js",
")",
"portal",
".",
"portal_javascripts",
".",
"unregisterResource",
"(",
"js",
")"
] |
Removes primitive type tags from an XPATH | def _trim_xpath ( self , xpath , prop ) : xroot = self . _get_xroot_for ( prop ) if xroot is None and isinstance ( xpath , string_types ) : xtags = xpath . split ( XPATH_DELIM ) if xtags [ - 1 ] in _iso_tag_primitives : xroot = XPATH_DELIM . join ( xtags [ : - 1 ] ) return xroot | 223 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L691-L702 | [
"def",
"cli",
"(",
"sock",
",",
"configs",
",",
"modules",
",",
"files",
",",
"log",
",",
"debug",
")",
":",
"setup_logging",
"(",
"log",
",",
"debug",
")",
"config",
"=",
"join_configs",
"(",
"configs",
")",
"# load python modules",
"load_modules",
"(",
"modules",
")",
"# load python files",
"load_files",
"(",
"files",
")",
"# summarize active events and callbacks",
"summarize_events",
"(",
")",
"gloop",
"=",
"gevent",
".",
"Greenlet",
".",
"spawn",
"(",
"loop",
",",
"sock",
"=",
"sock",
",",
"config",
"=",
"config",
")",
"gloop",
".",
"start",
"(",
")",
"gloop",
".",
"join",
"(",
")"
] |
Generates the app id for a given shortcut . Steam uses app ids as a unique identifier for games but since shortcuts dont have a canonical serverside representation they need to be generated on the fly . The important part about this function is that it will generate the same app id as Steam does for a given shortcut | def shortcut_app_id ( shortcut ) : algorithm = Crc ( width = 32 , poly = 0x04C11DB7 , reflect_in = True , xor_in = 0xffffffff , reflect_out = True , xor_out = 0xffffffff ) crc_input = '' . join ( [ shortcut . exe , shortcut . name ] ) high_32 = algorithm . bit_by_bit ( crc_input ) | 0x80000000 full_64 = ( high_32 << 32 ) | 0x02000000 return str ( full_64 ) | 224 | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/shortcuts.py#L9-L21 | [
"def",
"set_end_date",
"(",
"self",
",",
"lifetime",
")",
":",
"self",
".",
"end_date",
"=",
"(",
"datetime",
".",
"datetime",
".",
"now",
"(",
")",
"+",
"datetime",
".",
"timedelta",
"(",
"0",
",",
"lifetime",
")",
")"
] |
Execute git config . | def _config ( self ) : cfg_wr = self . repo . config_writer ( ) cfg_wr . add_section ( 'user' ) cfg_wr . set_value ( 'user' , 'name' , self . metadata . author ) cfg_wr . set_value ( 'user' , 'email' , self . metadata . email ) cfg_wr . release ( ) | 225 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/vcs.py#L35-L41 | [
"def",
"revoke_session",
"(",
"self",
",",
"sid",
"=",
"''",
",",
"token",
"=",
"''",
")",
":",
"if",
"not",
"sid",
":",
"if",
"token",
":",
"sid",
"=",
"self",
".",
"handler",
".",
"sid",
"(",
"token",
")",
"else",
":",
"raise",
"ValueError",
"(",
"'Need one of \"sid\" or \"token\"'",
")",
"for",
"typ",
"in",
"[",
"'access_token'",
",",
"'refresh_token'",
",",
"'code'",
"]",
":",
"try",
":",
"self",
".",
"revoke_token",
"(",
"self",
"[",
"sid",
"]",
"[",
"typ",
"]",
",",
"typ",
")",
"except",
"KeyError",
":",
"# If no such token has been issued",
"pass",
"self",
".",
"update",
"(",
"sid",
",",
"revoked",
"=",
"True",
")"
] |
Execute git remote add . | def _remote_add ( self ) : self . repo . create_remote ( 'origin' , 'git@github.com:{username}/{repo}.git' . format ( username = self . metadata . username , repo = self . metadata . name ) ) | 226 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/vcs.py#L47-L53 | [
"def",
"delete_everything",
"(",
"self",
")",
":",
"for",
"k",
"in",
"self",
".",
"_backup_list",
"(",
"prefix",
"=",
"self",
".",
"layout",
".",
"basebackups",
"(",
")",
")",
":",
"self",
".",
"_maybe_delete_key",
"(",
"k",
",",
"'part of a base backup'",
")",
"for",
"k",
"in",
"self",
".",
"_backup_list",
"(",
"prefix",
"=",
"self",
".",
"layout",
".",
"wal_directory",
"(",
")",
")",
":",
"self",
".",
"_maybe_delete_key",
"(",
"k",
",",
"'part of wal logs'",
")",
"if",
"self",
".",
"deleter",
":",
"self",
".",
"deleter",
".",
"close",
"(",
")"
] |
Starts execution of the script | def start ( self ) : # invoke the appropriate sub-command as requested from command-line try : self . args . func ( ) except SystemExit as e : if e . code != 0 : raise except KeyboardInterrupt : self . log . warning ( "exited via keyboard interrupt" ) except : self . log . exception ( "exited start function" ) # set exit code so we know it did not end successfully # TODO different exit codes based on signals ? finally : self . _flush_metrics_q . put ( None , block = True ) self . _flush_metrics_q . put ( None , block = True , timeout = 1 ) self . log . debug ( "exited_successfully" ) | 227 | https://github.com/deep-compute/basescript/blob/f7233963c5291530fcb2444a7f45b556e6407b90/basescript/basescript.py#L67-L87 | [
"def",
"get_listing",
"(",
"self",
")",
":",
"if",
"not",
"hasattr",
"(",
"self",
",",
"'listing'",
")",
":",
"allEvents",
"=",
"self",
".",
"get_allEvents",
"(",
")",
"openEvents",
"=",
"allEvents",
".",
"filter",
"(",
"registrationOpen",
"=",
"True",
")",
"closedEvents",
"=",
"allEvents",
".",
"filter",
"(",
"registrationOpen",
"=",
"False",
")",
"publicEvents",
"=",
"allEvents",
".",
"instance_of",
"(",
"PublicEvent",
")",
"allSeries",
"=",
"allEvents",
".",
"instance_of",
"(",
"Series",
")",
"self",
".",
"listing",
"=",
"{",
"'allEvents'",
":",
"allEvents",
",",
"'openEvents'",
":",
"openEvents",
",",
"'closedEvents'",
":",
"closedEvents",
",",
"'publicEvents'",
":",
"publicEvents",
",",
"'allSeries'",
":",
"allSeries",
",",
"'regOpenEvents'",
":",
"publicEvents",
".",
"filter",
"(",
"registrationOpen",
"=",
"True",
")",
".",
"filter",
"(",
"Q",
"(",
"publicevent__category__isnull",
"=",
"True",
")",
"|",
"Q",
"(",
"publicevent__category__separateOnRegistrationPage",
"=",
"False",
")",
")",
",",
"'regClosedEvents'",
":",
"publicEvents",
".",
"filter",
"(",
"registrationOpen",
"=",
"False",
")",
".",
"filter",
"(",
"Q",
"(",
"publicevent__category__isnull",
"=",
"True",
")",
"|",
"Q",
"(",
"publicevent__category__separateOnRegistrationPage",
"=",
"False",
")",
")",
",",
"'categorySeparateEvents'",
":",
"publicEvents",
".",
"filter",
"(",
"publicevent__category__separateOnRegistrationPage",
"=",
"True",
")",
".",
"order_by",
"(",
"'publicevent__category'",
")",
",",
"'regOpenSeries'",
":",
"allSeries",
".",
"filter",
"(",
"registrationOpen",
"=",
"True",
")",
".",
"filter",
"(",
"Q",
"(",
"series__category__isnull",
"=",
"True",
")",
"|",
"Q",
"(",
"series__category__separateOnRegistrationPage",
"=",
"False",
")",
")",
",",
"'regClosedSeries'",
":",
"allSeries",
".",
"filter",
"(",
"registrationOpen",
"=",
"False",
")",
".",
"filter",
"(",
"Q",
"(",
"series__category__isnull",
"=",
"True",
")",
"|",
"Q",
"(",
"series__category__separateOnRegistrationPage",
"=",
"False",
")",
")",
",",
"'categorySeparateSeries'",
":",
"allSeries",
".",
"filter",
"(",
"series__category__separateOnRegistrationPage",
"=",
"True",
")",
".",
"order_by",
"(",
"'series__category'",
")",
",",
"}",
"return",
"self",
".",
"listing"
] |
Define basic command - line arguments required by the script . | def define_baseargs ( self , parser ) : parser . add_argument ( '--name' , default = sys . argv [ 0 ] , help = 'Name to identify this instance' ) parser . add_argument ( '--log-level' , default = None , help = 'Logging level as picked from the logging module' ) parser . add_argument ( '--log-format' , default = None , # TODO add more formats choices = ( "json" , "pretty" , ) , help = ( "Force the format of the logs. By default, if the " "command is from a terminal, print colorful logs. " "Otherwise print json." ) , ) parser . add_argument ( '--log-file' , default = None , help = 'Writes logs to log file if specified, default: %(default)s' , ) parser . add_argument ( '--quiet' , default = False , action = "store_true" , help = 'if true, does not print logs to stderr, default: %(default)s' , ) parser . add_argument ( '--metric-grouping-interval' , default = None , type = int , help = 'To group metrics based on time interval ex:10 i.e;(10 sec)' , ) parser . add_argument ( '--debug' , default = False , action = "store_true" , help = 'To run the code in debug mode' , ) | 228 | https://github.com/deep-compute/basescript/blob/f7233963c5291530fcb2444a7f45b556e6407b90/basescript/basescript.py#L123-L151 | [
"def",
"cache_affected_objects_review_history",
"(",
"portal",
")",
":",
"logger",
".",
"info",
"(",
"\"Caching review_history ...\"",
")",
"query",
"=",
"dict",
"(",
"portal_type",
"=",
"NEW_SENAITE_WORKFLOW_BINDINGS",
")",
"brains",
"=",
"api",
".",
"search",
"(",
"query",
",",
"UID_CATALOG",
")",
"total",
"=",
"len",
"(",
"brains",
")",
"for",
"num",
",",
"brain",
"in",
"enumerate",
"(",
"brains",
")",
":",
"if",
"num",
"%",
"100",
"==",
"0",
":",
"logger",
".",
"info",
"(",
"\"Caching review_history: {}/{}\"",
".",
"format",
"(",
"num",
",",
"total",
")",
")",
"review_history",
"=",
"get_review_history_for",
"(",
"brain",
")",
"review_history_cache",
"[",
"api",
".",
"get_uid",
"(",
"brain",
")",
"]",
"=",
"review_history"
] |
Basically turns payload that looks like \\ n to . In the calling function if this function returns no object is added for that payload . | def cleanup_payload ( self , payload ) : p = payload . replace ( '\n' , '' ) p = p . rstrip ( ) p = p . lstrip ( ) return p | 229 | https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/parser/source_coder.py#L73-L82 | [
"def",
"MemoryExceeded",
"(",
"self",
")",
":",
"rss_size",
"=",
"self",
".",
"proc",
".",
"memory_info",
"(",
")",
".",
"rss",
"return",
"rss_size",
"//",
"1024",
"//",
"1024",
">",
"config",
".",
"CONFIG",
"[",
"\"Client.rss_max\"",
"]"
] |
Ensures complex property types have the correct default values | def get_default_for ( prop , value ) : prop = prop . strip ( '_' ) # Handle alternate props (leading underscores) val = reduce_value ( value ) # Filtering of value happens here if prop in _COMPLEX_LISTS : return wrap_value ( val ) elif prop in _COMPLEX_STRUCTS : return val or { } else : return u'' if val is None else val | 230 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L223-L234 | [
"def",
"write",
"(",
"self",
",",
"text",
")",
":",
"if",
"text",
":",
"if",
"text",
"[",
"0",
"]",
"in",
"'(w'",
":",
"# write thread and wsgi messages to debug only",
"self",
".",
"log",
".",
"debug",
"(",
"text",
"[",
":",
"-",
"1",
"]",
")",
"return",
"if",
"self",
".",
"access_log",
":",
"self",
".",
"access_log",
".",
"write",
"(",
"text",
")",
"self",
".",
"log",
".",
"info",
"(",
"text",
"[",
":",
"-",
"1",
"]",
")"
] |
Either update the tree the default way or call the custom updater | def update_property ( tree_to_update , xpath_root , xpaths , prop , values , supported = None ) : if supported and prop . startswith ( '_' ) and prop . strip ( '_' ) in supported : values = u'' # Remove alternate elements: write values only to primary location else : values = get_default_for ( prop , values ) # Enforce defaults as required per property if not xpaths : return [ ] elif not isinstance ( xpaths , ParserProperty ) : return _update_property ( tree_to_update , xpath_root , xpaths , values ) else : # Call ParserProperty.set_prop without xpath_root (managed internally) return xpaths . set_prop ( tree_to_update = tree_to_update , prop = prop , values = values ) | 231 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L392-L423 | [
"def",
"end_stream",
"(",
"self",
",",
"stream_id",
")",
":",
"with",
"(",
"yield",
"from",
"self",
".",
"_get_stream",
"(",
"stream_id",
")",
".",
"wlock",
")",
":",
"yield",
"from",
"self",
".",
"_resumed",
".",
"wait",
"(",
")",
"self",
".",
"_conn",
".",
"end_stream",
"(",
"stream_id",
")",
"self",
".",
"_flush",
"(",
")"
] |
Default update operation for a single parser property . If xpaths contains one xpath then one element per value will be inserted at that location in the tree_to_update ; otherwise the number of values must match the number of xpaths . | def _update_property ( tree_to_update , xpath_root , xpaths , values ) : # Inner function to update a specific XPATH with the values provided def update_element ( elem , idx , root , path , vals ) : """ Internal helper function to encapsulate single item update """ has_root = bool ( root and len ( path ) > len ( root ) and path . startswith ( root ) ) path , attr = get_xpath_tuple ( path ) # 'path/@attr' to ('path', 'attr') if attr : removed = [ get_element ( elem , path ) ] remove_element_attributes ( removed [ 0 ] , attr ) elif not has_root : removed = wrap_value ( remove_element ( elem , path ) ) else : path = get_xpath_branch ( root , path ) removed = [ ] if idx != 0 else [ remove_element ( e , path , True ) for e in get_elements ( elem , root ) ] if not vals : return removed items = [ ] for i , val in enumerate ( wrap_value ( vals ) ) : elem_to_update = elem if has_root : elem_to_update = insert_element ( elem , ( i + idx ) , root ) val = val . decode ( 'utf-8' ) if not isinstance ( val , string_types ) else val if not attr : items . append ( insert_element ( elem_to_update , i , path , val ) ) elif path : items . append ( insert_element ( elem_to_update , i , path , * * { attr : val } ) ) else : set_element_attributes ( elem_to_update , * * { attr : val } ) items . append ( elem_to_update ) return items # Code to update each of the XPATHs with each of the values xpaths = reduce_value ( xpaths ) values = filter_empty ( values ) if isinstance ( xpaths , string_types ) : return update_element ( tree_to_update , 0 , xpath_root , xpaths , values ) else : each = [ ] for index , xpath in enumerate ( xpaths ) : value = values [ index ] if values else None each . extend ( update_element ( tree_to_update , index , xpath_root , xpath , value ) ) return each | 232 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L426-L486 | [
"def",
"create",
"(",
"cls",
",",
"destination",
")",
":",
"mdb_gz_b64",
"=",
"\"\"\"\\\n H4sICIenn1gC/25ldzIwMDMubWRiAO2de2wcRx3Hf7O7Pt/d3u6eLyEtVaOaqg+EkjQvuVVDwa9a\n jWXHdZxQQlCJ7fOrfp3OTpqkhVxTItFWIhVQVFBRVNIKRaColVpAUKGKRwwFqUAhKiBIpUaoVWP+\n qKgIIHL8Znb39u72znWJiWP3+9l473fzm/nNY3cdf2fmbBJEPdO9E+nebLq+fWC6vrWZOImen9D7\n 9sR+vPPNE0PZxo/TE5879mj+yNc3/OzAD2bXv3DmV9/o/8PZnxxr+/fDL2w79ulzN7e+/sS/zvzz\n w3+N1z28p3PTfQ3nfn/m2YmeFS2no89uWnvqwO5HUvd/5Phr938tes3j/zm5+qT41J8/P/iZx87/\n +qHrjgyduubG1t/+7eWB2XztTNuT+1clZt9c2/e7HRGizevWEwAAAAAAAACAhUEIwvE+PoRIO8K7\n FzT6obPPwTMBAAAAAAAAAABcfpzPXwya+Ispo1xlEO2KEEX9eaGyWnrqyKQ60tQ0AcNZRcR1RYuy\n +XZCxoqRzmaMI6cKGRJuJVrIEZUOQ9UrHStUYpyzKkdNmSPFDkM6aguhXMdVHCMuHXE2Suu4IFQJ\n l6CErNWUDouDlbdKOZIcrKLD4S5WdNhqIEodqlVaofKgVTHpiBQ6uLG0uaKsuYbf3IS8BmV1qFAm\n j1Z5Hbp06GWDKC+DTS00SRN8DFA/TXNfW6mXX3upj7+mOHWllzLAObN8du0gdSdlKO3ZcWqjMbaH\n uOQqtidViRF+P0HbOH2c3xm0lfMb1EH7uHZ5vp32c+ks+5PqfSeXS9NejjTAvZQpd7J3kuuJFqLE\n qYvuVa3Ocqk7OVXWNMFxZPRVtJ1zSXuCBrlkh+rjEF1Zlt5Dw6qN0xx5Bx3gGgbowVo56EIjkc9T\n xX9Jdd+5PKDOD6q3VQvwv7qiZ8st419cdYHlo6iuriF8X4HA590AsodXhvrsj0yMDPnAuI+ZvOrq\n 1o7K51Hdy7a8cdXNm5AedbfG5W3j3lOybxFZKb6zAgAAAAAAsNzQxAlbvnYJV3VcUU3/S2luBIKF\n ha+IlWp+wxW4IiRXRSXxKeNU1eOxUuUbSOIINbEM7WT506ZE3LASgCOeYJWCMcnCsI/u8eSsFEYR\n lnlbWa6+u0jTYqSkvuQL9G5CLFwTRBMAAAAAAAAAgMtW/79lyVdLKxW7oqDF3bXOniib0UD/m/xq\n loWqvFwt3DX/mrLNALIu3V35NkpK1JDmL+2XOmr9pf1gKiFY4I672wc0mveaf6zaenyKmljPT6t5\n hT7a6y13y0XqjFpwneJjRC0oRwvL3eUL2fHCcuyGIntjhTkDuZCd5Vc5j+HNUMyx+myYcpHW5YG5\n ZijUdbg2VFu4ZzzcHFM3seQLAAAAAAAAAMtc//9S6cm1emX97ytK1v81rHelhtfVfAFnseZXRdV9\n Ad7+dhGS5kbl3eqe/K8pU/nnYwX5X2VeoLbCZwHi7txD6aTELabnoLJ5AfPFC8JmFd3Pun+MlfM4\n q/846/4s62i5+8Dmc7EvSVN0UG2tL00p1uPXqZTt/G5QqX+5lbufz+mSctVzFce6upBrTG3Fd+cn\n pmiYrUyw8+GNfL4hn8/k83qZrVlyGzgPeqbhjcOqx7KMEZRpU/MPQ+rsldEtuYm8vExkznoMS+6b\n KC5TZRt8wVf4xEkFX4V5D/X2vYz1/EcR8yMAAAAAAACAJY0Qf/d3vLPUlb//b4Nzzv6W3Wevtl+1\n vmxts2LWTxOHErcm3jGfMUfNG0yMGQAAAAAAeJ/8rLwAMXIYRgCARFv8IIaYtKpGqCdqlN/2kupD\n /ob67qXhsi0lDh2Vp6728faO9tHuUflfWJ1wE0e6724f35XuG71r16Dr0FwH573by6rKi0N7RveN\n tnd6aTVBWrpjd3fnuJtsBMnDk90ju7zckSA5XGGtdGrK2dWhUnRcMgAAAAAAAAD4v2CIV6vqf82I\n Jusbcwsy7wkWSf/n1JQNq/Oc+uQGq/ecmsphYZ6Tn6XwRLjwxb7mTxDoakLgURUFshwAAAAAAAAA\n ljpCrHZ8W/f2/2NUAAAAAAAAAAAAhXH5RLm4IIbotqot7hbW/0MGWCp46/+pgpHwjZS3IyAlfMPy\n tgakNN+wfcPxNgukdN9I+kadt30gZfhGjW+s8I2V3s6CVNTbWZCK+Eatb3zAN1Z5mw5SMd+I+wZ+\n +QQAAAAAAAAA/K8IcdT27Zqi3/+HkQEAAAAAAAAAsGgkMQQLjSHqbQPDAAAAAAAAAAAALGuw/g8A\n AAAAAAAA4DJUqwsQI7cQDWlcLiMq1/9rcGMBAAAAAAAAAADLGuh/AAAAAAAAAAAA+h8AAAAAAAAA\n AABLHyHusDTPjtLzTtoxnRftUftqe8YatDA+AAAAAAAAAPDeqJN/KVt+et0R9PYnzz7W8PrZRv+V\n HblO6qEDNEXbaYDGqJemaYQmaYJThtnK8Gvzb1opfDRTPZmUlxUY86qgm/ZyFVkOOqCC3kLhoyEI\n qs8raBO10O0q3EYKH+uDcNq8wnVRH93D7evnYZhHG5kkB3a0OYO2ctCWV9ZR+FhT0l2HCzl6xVBz\n XZyPUvi4taTjcwRuVUF7uYW9HMy9MJspfGwMAoo5A+5Qwca8UHN2WogeU/fu0ito1vmjM+M85zzp\n fNG5zxl2djrNzk3O9+0m+yWrx2q0fpH4buJ4Yk3ig4lvmkfxx9gBAAAAAAC4OAylQfJ5h5pfSVCc\n f853gqSmWPSZux6xjUznltH2HT/flNu7++0NZ7/07cg/vnPbVu30y6d/NLvlabPh+j81v/Xc5g9l\n 1h2f+epn9+VPdN90OHHvU50fm94y/ZXvWQ/tP/yJG/NH3llz8A79tlNPG72DHSePHdzz2s3XPzVj\n vzSUvSHjVys1Rv5CSUv8pEvcEqkbV/KX35JaQ+npikmRS9o4rtYIt8RYnJa4Ou6SV6stTm+l7rcX\n q9qSy+23pCVIcgV/SZKuJj5CSRc4Y/PpkiesLJcI53J37NvFuQzv4peGL0/SypP+C+45xVAAMAEA\n \"\"\"",
"pristine",
"=",
"StringIO",
"(",
")",
"pristine",
".",
"write",
"(",
"base64",
".",
"b64decode",
"(",
"mdb_gz_b64",
")",
")",
"pristine",
".",
"seek",
"(",
"0",
")",
"pristine",
"=",
"gzip",
".",
"GzipFile",
"(",
"fileobj",
"=",
"pristine",
",",
"mode",
"=",
"'rb'",
")",
"with",
"open",
"(",
"destination",
",",
"'wb'",
")",
"as",
"handle",
":",
"shutil",
".",
"copyfileobj",
"(",
"pristine",
",",
"handle",
")",
"return",
"cls",
"(",
"destination",
")"
] |
Default validation for single complex data structure | def validate_complex ( prop , value , xpath_map = None ) : if value is not None : validate_type ( prop , value , dict ) if prop in _complex_definitions : complex_keys = _complex_definitions [ prop ] else : complex_keys = { } if xpath_map is None else xpath_map for complex_prop , complex_val in iteritems ( value ) : complex_key = '.' . join ( ( prop , complex_prop ) ) if complex_prop not in complex_keys : _validation_error ( prop , None , value , ( 'keys: {0}' . format ( ',' . join ( complex_keys ) ) ) ) validate_type ( complex_key , complex_val , ( string_types , list ) ) | 233 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L572-L589 | [
"def",
"get_vocab",
"(",
"self",
",",
"vocab_name",
",",
"*",
"*",
"kwargs",
")",
":",
"vocab_dict",
"=",
"self",
".",
"__get_vocab_dict__",
"(",
"vocab_name",
",",
"*",
"*",
"kwargs",
")",
"filepaths",
"=",
"list",
"(",
"set",
"(",
"[",
"os",
".",
"path",
".",
"join",
"(",
"self",
".",
"cache_dir",
",",
"vocab_dict",
"[",
"'filename'",
"]",
")",
",",
"os",
".",
"path",
".",
"join",
"(",
"self",
".",
"vocab_dir",
",",
"vocab_dict",
"[",
"'filename'",
"]",
")",
"]",
")",
")",
"for",
"path",
"in",
"filepaths",
":",
"if",
"os",
".",
"path",
".",
"exists",
"(",
"path",
")",
":",
"with",
"open",
"(",
"path",
",",
"'rb'",
")",
"as",
"f_obj",
":",
"vocab_dict",
".",
"update",
"(",
"{",
"\"name\"",
":",
"vocab_name",
",",
"\"data\"",
":",
"f_obj",
".",
"read",
"(",
")",
",",
"\"modified\"",
":",
"os",
".",
"path",
".",
"getmtime",
"(",
"path",
")",
"}",
")",
"return",
"vocab_dict",
"download_locs",
"=",
"make_list",
"(",
"vocab_dict",
".",
"get",
"(",
"'download'",
",",
"[",
"]",
")",
")",
"for",
"loc",
"in",
"download_locs",
":",
"loc_web",
"=",
"urllib",
".",
"request",
".",
"urlopen",
"(",
"loc",
")",
"# loc_file_date = date_parse(loc_web.info()['Last-Modified'])",
"urllib",
".",
"request",
".",
"urlretrieve",
"(",
"loc",
",",
"filepaths",
"[",
"0",
"]",
")",
"with",
"open",
"(",
"filepaths",
"[",
"0",
"]",
",",
"'rb'",
")",
"as",
"f_obj",
":",
"vocab_dict",
".",
"update",
"(",
"{",
"\"name\"",
":",
"vocab_name",
",",
"\"data\"",
":",
"f_obj",
".",
"read",
"(",
")",
",",
"\"modified\"",
":",
"os",
".",
"path",
".",
"getmtime",
"(",
"filepaths",
"[",
"0",
"]",
")",
"}",
")",
"return",
"vocab_dict"
] |
Default validation for Attribute Details data structure | def validate_complex_list ( prop , value , xpath_map = None ) : if value is not None : validate_type ( prop , value , ( dict , list ) ) if prop in _complex_definitions : complex_keys = _complex_definitions [ prop ] else : complex_keys = { } if xpath_map is None else xpath_map for idx , complex_struct in enumerate ( wrap_value ( value ) ) : cs_idx = prop + '[' + str ( idx ) + ']' validate_type ( cs_idx , complex_struct , dict ) for cs_prop , cs_val in iteritems ( complex_struct ) : cs_key = '.' . join ( ( cs_idx , cs_prop ) ) if cs_prop not in complex_keys : _validation_error ( prop , None , value , ( 'keys: {0}' . format ( ',' . join ( complex_keys ) ) ) ) if not isinstance ( cs_val , list ) : validate_type ( cs_key , cs_val , ( string_types , list ) ) else : for list_idx , list_val in enumerate ( cs_val ) : list_prop = cs_key + '[' + str ( list_idx ) + ']' validate_type ( list_prop , list_val , string_types ) | 234 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L592-L618 | [
"def",
"compress_pdf",
"(",
"pdf_fpath",
",",
"output_fname",
"=",
"None",
")",
":",
"import",
"utool",
"as",
"ut",
"ut",
".",
"assertpath",
"(",
"pdf_fpath",
")",
"suffix",
"=",
"'_'",
"+",
"ut",
".",
"get_datestamp",
"(",
"False",
")",
"+",
"'_compressed'",
"print",
"(",
"'pdf_fpath = %r'",
"%",
"(",
"pdf_fpath",
",",
")",
")",
"output_pdf_fpath",
"=",
"ut",
".",
"augpath",
"(",
"pdf_fpath",
",",
"suffix",
",",
"newfname",
"=",
"output_fname",
")",
"print",
"(",
"'output_pdf_fpath = %r'",
"%",
"(",
"output_pdf_fpath",
",",
")",
")",
"gs_exe",
"=",
"find_ghostscript_exe",
"(",
")",
"cmd_list",
"=",
"(",
"gs_exe",
",",
"'-sDEVICE=pdfwrite'",
",",
"'-dCompatibilityLevel=1.4'",
",",
"'-dNOPAUSE'",
",",
"'-dQUIET'",
",",
"'-dBATCH'",
",",
"'-sOutputFile='",
"+",
"output_pdf_fpath",
",",
"pdf_fpath",
")",
"ut",
".",
"cmd",
"(",
"*",
"cmd_list",
")",
"return",
"output_pdf_fpath"
] |
Default validation for Date Types data structure | def validate_dates ( prop , value , xpath_map = None ) : if value is not None : validate_type ( prop , value , dict ) date_keys = set ( value ) if date_keys : if DATE_TYPE not in date_keys or DATE_VALUES not in date_keys : if prop in _complex_definitions : complex_keys = _complex_definitions [ prop ] else : complex_keys = _complex_definitions [ DATES ] if xpath_map is None else xpath_map _validation_error ( prop , None , value , ( 'keys: {0}' . format ( ',' . join ( complex_keys ) ) ) ) date_type = value [ DATE_TYPE ] if date_type not in DATE_TYPES : _validation_error ( 'dates.type' , None , date_type , DATE_TYPES ) date_vals = value [ DATE_VALUES ] validate_type ( 'dates.values' , date_vals , list ) dates_len = len ( date_vals ) if date_type == DATE_TYPE_MISSING and dates_len != 0 : _validation_error ( 'len(dates.values)' , None , dates_len , 0 ) if date_type == DATE_TYPE_SINGLE and dates_len != 1 : _validation_error ( 'len(dates.values)' , None , dates_len , 1 ) if date_type == DATE_TYPE_RANGE and dates_len != 2 : _validation_error ( 'len(dates.values)' , None , dates_len , 2 ) if date_type == DATE_TYPE_MULTIPLE and dates_len < 2 : _validation_error ( 'len(dates.values)' , None , dates_len , 'at least two' ) for idx , date in enumerate ( date_vals ) : date_key = 'dates.value[' + str ( idx ) + ']' validate_type ( date_key , date , string_types ) | 235 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L621-L663 | [
"def",
"_unregister_bundle_factories",
"(",
"self",
",",
"bundle",
")",
":",
"# type: (Bundle) -> None",
"with",
"self",
".",
"__factories_lock",
":",
"# Find out which factories must be removed",
"to_remove",
"=",
"[",
"factory_name",
"for",
"factory_name",
"in",
"self",
".",
"__factories",
"if",
"self",
".",
"get_factory_bundle",
"(",
"factory_name",
")",
"is",
"bundle",
"]",
"# Remove all of them",
"for",
"factory_name",
"in",
"to_remove",
":",
"try",
":",
"self",
".",
"unregister_factory",
"(",
"factory_name",
")",
"except",
"ValueError",
"as",
"ex",
":",
"_logger",
".",
"warning",
"(",
"\"Error unregistering factory '%s': %s\"",
",",
"factory_name",
",",
"ex",
")"
] |
Default validation for Process Steps data structure | def validate_process_steps ( prop , value ) : if value is not None : validate_type ( prop , value , ( dict , list ) ) procstep_keys = set ( _complex_definitions [ prop ] ) for idx , procstep in enumerate ( wrap_value ( value ) ) : ps_idx = prop + '[' + str ( idx ) + ']' validate_type ( ps_idx , procstep , dict ) for ps_prop , ps_val in iteritems ( procstep ) : ps_key = '.' . join ( ( ps_idx , ps_prop ) ) if ps_prop not in procstep_keys : _validation_error ( prop , None , value , ( 'keys: {0}' . format ( ',' . join ( procstep_keys ) ) ) ) if ps_prop != 'sources' : validate_type ( ps_key , ps_val , string_types ) else : validate_type ( ps_key , ps_val , ( string_types , list ) ) for src_idx , src_val in enumerate ( wrap_value ( ps_val ) ) : src_key = ps_key + '[' + str ( src_idx ) + ']' validate_type ( src_key , src_val , string_types ) | 236 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L666-L691 | [
"def",
"create_api_call",
"(",
"func",
",",
"settings",
")",
":",
"def",
"base_caller",
"(",
"api_call",
",",
"_",
",",
"*",
"args",
")",
":",
"\"\"\"Simply call api_call and ignore settings.\"\"\"",
"return",
"api_call",
"(",
"*",
"args",
")",
"def",
"inner",
"(",
"request",
",",
"options",
"=",
"None",
")",
":",
"\"\"\"Invoke with the actual settings.\"\"\"",
"this_options",
"=",
"_merge_options_metadata",
"(",
"options",
",",
"settings",
")",
"this_settings",
"=",
"settings",
".",
"merge",
"(",
"this_options",
")",
"if",
"this_settings",
".",
"retry",
"and",
"this_settings",
".",
"retry",
".",
"retry_codes",
":",
"api_call",
"=",
"gax",
".",
"retry",
".",
"retryable",
"(",
"func",
",",
"this_settings",
".",
"retry",
",",
"*",
"*",
"this_settings",
".",
"kwargs",
")",
"else",
":",
"api_call",
"=",
"gax",
".",
"retry",
".",
"add_timeout_arg",
"(",
"func",
",",
"this_settings",
".",
"timeout",
",",
"*",
"*",
"this_settings",
".",
"kwargs",
")",
"api_call",
"=",
"_catch_errors",
"(",
"api_call",
",",
"gax",
".",
"config",
".",
"API_ERRORS",
")",
"return",
"api_caller",
"(",
"api_call",
",",
"this_settings",
",",
"request",
")",
"if",
"settings",
".",
"page_descriptor",
":",
"if",
"settings",
".",
"bundler",
"and",
"settings",
".",
"bundle_descriptor",
":",
"raise",
"ValueError",
"(",
"'The API call has incompatible settings: '",
"'bundling and page streaming'",
")",
"api_caller",
"=",
"_page_streamable",
"(",
"settings",
".",
"page_descriptor",
")",
"elif",
"settings",
".",
"bundler",
"and",
"settings",
".",
"bundle_descriptor",
":",
"api_caller",
"=",
"_bundleable",
"(",
"settings",
".",
"bundle_descriptor",
")",
"else",
":",
"api_caller",
"=",
"base_caller",
"return",
"inner"
] |
Default validation for all types | def validate_type ( prop , value , expected ) : # Validate on expected type(s), but ignore None: defaults handled elsewhere if value is not None and not isinstance ( value , expected ) : _validation_error ( prop , type ( value ) . __name__ , None , expected ) | 237 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L710-L715 | [
"def",
"handlePortfolio",
"(",
"self",
",",
"msg",
")",
":",
"# log handler msg",
"self",
".",
"log_msg",
"(",
"\"portfolio\"",
",",
"msg",
")",
"# contract identifier",
"contract_tuple",
"=",
"self",
".",
"contract_to_tuple",
"(",
"msg",
".",
"contract",
")",
"contractString",
"=",
"self",
".",
"contractString",
"(",
"contract_tuple",
")",
"# try creating the contract",
"self",
".",
"registerContract",
"(",
"msg",
".",
"contract",
")",
"# new account?",
"if",
"msg",
".",
"accountName",
"not",
"in",
"self",
".",
"_portfolios",
".",
"keys",
"(",
")",
":",
"self",
".",
"_portfolios",
"[",
"msg",
".",
"accountName",
"]",
"=",
"{",
"}",
"self",
".",
"_portfolios",
"[",
"msg",
".",
"accountName",
"]",
"[",
"contractString",
"]",
"=",
"{",
"\"symbol\"",
":",
"contractString",
",",
"\"position\"",
":",
"int",
"(",
"msg",
".",
"position",
")",
",",
"\"marketPrice\"",
":",
"float",
"(",
"msg",
".",
"marketPrice",
")",
",",
"\"marketValue\"",
":",
"float",
"(",
"msg",
".",
"marketValue",
")",
",",
"\"averageCost\"",
":",
"float",
"(",
"msg",
".",
"averageCost",
")",
",",
"\"unrealizedPNL\"",
":",
"float",
"(",
"msg",
".",
"unrealizedPNL",
")",
",",
"\"realizedPNL\"",
":",
"float",
"(",
"msg",
".",
"realizedPNL",
")",
",",
"\"totalPNL\"",
":",
"float",
"(",
"msg",
".",
"realizedPNL",
")",
"+",
"float",
"(",
"msg",
".",
"unrealizedPNL",
")",
",",
"\"account\"",
":",
"msg",
".",
"accountName",
"}",
"# fire callback",
"self",
".",
"ibCallback",
"(",
"caller",
"=",
"\"handlePortfolio\"",
",",
"msg",
"=",
"msg",
")"
] |
Default validation for updated properties | def _validation_error ( prop , prop_type , prop_value , expected ) : if prop_type is None : attrib = 'value' assigned = prop_value else : attrib = 'type' assigned = prop_type raise ValidationError ( 'Invalid property {attrib} for {prop}:\n\t{attrib}: {assigned}\n\texpected: {expected}' , attrib = attrib , prop = prop , assigned = assigned , expected = expected , invalid = { prop : prop_value } if attrib == 'value' else { } ) | 238 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L718-L732 | [
"def",
"handle_exit_code",
"(",
"d",
",",
"code",
")",
":",
"# d is supposed to be a Dialog instance",
"if",
"code",
"in",
"(",
"d",
".",
"DIALOG_CANCEL",
",",
"d",
".",
"DIALOG_ESC",
")",
":",
"if",
"code",
"==",
"d",
".",
"DIALOG_CANCEL",
":",
"msg",
"=",
"\"You chose cancel in the last dialog box. Do you want to \"",
"\"exit this demo?\"",
"else",
":",
"msg",
"=",
"\"You pressed ESC in the last dialog box. Do you want to \"",
"\"exit this demo?\"",
"# \"No\" or \"ESC\" will bring the user back to the demo.",
"# DIALOG_ERROR is propagated as an exception and caught in main().",
"# So we only need to handle OK here.",
"if",
"d",
".",
"yesno",
"(",
"msg",
")",
"==",
"d",
".",
"DIALOG_OK",
":",
"sys",
".",
"exit",
"(",
"0",
")",
"return",
"0",
"else",
":",
"return",
"1"
] |
Calls the getter with no arguments and returns its value | def get_prop ( self , prop ) : if self . _parser is None : raise ConfigurationError ( 'Cannot call ParserProperty."get_prop" with no parser configured' ) return self . _parser ( prop ) if prop else self . _parser ( ) | 239 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L765-L771 | [
"def",
"_write_packet",
"(",
"self",
",",
"packet",
",",
"sec",
"=",
"None",
",",
"usec",
"=",
"None",
",",
"caplen",
"=",
"None",
",",
"wirelen",
"=",
"None",
")",
":",
"if",
"caplen",
"is",
"None",
":",
"caplen",
"=",
"len",
"(",
"packet",
")",
"if",
"wirelen",
"is",
"None",
":",
"wirelen",
"=",
"caplen",
"if",
"sec",
"is",
"None",
"or",
"usec",
"is",
"None",
":",
"t",
"=",
"time",
".",
"time",
"(",
")",
"it",
"=",
"int",
"(",
"t",
")",
"if",
"sec",
"is",
"None",
":",
"sec",
"=",
"it",
"if",
"usec",
"is",
"None",
":",
"usec",
"=",
"int",
"(",
"round",
"(",
"(",
"t",
"-",
"it",
")",
"*",
"1000000",
")",
")",
"self",
".",
"f",
".",
"write",
"(",
"struct",
".",
"pack",
"(",
"self",
".",
"endian",
"+",
"\"IIII\"",
",",
"sec",
",",
"usec",
",",
"caplen",
",",
"wirelen",
")",
")",
"self",
".",
"f",
".",
"write",
"(",
"packet",
")",
"if",
"self",
".",
"gz",
"and",
"self",
".",
"sync",
":",
"self",
".",
"f",
".",
"flush",
"(",
")"
] |
Returns a boolean representing whether these commands can be grouped together or not . | def can_group_commands ( command , next_command ) : multi_capable_commands = ( 'get' , 'set' , 'delete' ) if next_command is None : return False name = command . get_name ( ) # TODO: support multi commands if name not in multi_capable_commands : return False if name != next_command . get_name ( ) : return False # if the shared args (key, or key/value) do not match, we cannot group if grouped_args_for_command ( command ) != grouped_args_for_command ( next_command ) : return False # If the keyword arguments do not much (e.g. key_prefix, or timeout on set) # then we cannot group if command . get_kwargs ( ) != next_command . get_kwargs ( ) : return False return True | 240 | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/backends/memcache.py#L97-L135 | [
"def",
"get_stream_duration",
"(",
"stream",
")",
":",
"epoch",
"=",
"lal",
".",
"LIGOTimeGPS",
"(",
"stream",
".",
"epoch",
".",
"gpsSeconds",
",",
"stream",
".",
"epoch",
".",
"gpsNanoSeconds",
")",
"# loop over each file in the stream cache and query its duration",
"nfile",
"=",
"stream",
".",
"cache",
".",
"length",
"duration",
"=",
"0",
"for",
"dummy_i",
"in",
"range",
"(",
"nfile",
")",
":",
"for",
"dummy_j",
"in",
"range",
"(",
"lalframe",
".",
"FrFileQueryNFrame",
"(",
"stream",
".",
"file",
")",
")",
":",
"duration",
"+=",
"lalframe",
".",
"FrFileQueryDt",
"(",
"stream",
".",
"file",
",",
"0",
")",
"lalframe",
".",
"FrStreamNext",
"(",
"stream",
")",
"# rewind stream and return",
"lalframe",
".",
"FrStreamSeek",
"(",
"stream",
",",
"epoch",
")",
"return",
"duration"
] |
define ribosomal proteins and location of curated databases | def find_databases ( databases ) : # 16 ribosomal proteins in their expected order proteins = [ 'L15' , 'L18' , 'L6' , 'S8' , 'L5' , 'L24' , 'L14' , 'S17' , 'L16' , 'S3' , 'L22' , 'S19' , 'L2' , 'L4' , 'L3' , 'S10' ] # curated databases protein_databases = { 'L14' : 'rpL14_JGI_MDM.filtered.faa' , 'L15' : 'rpL15_JGI_MDM.filtered.faa' , 'L16' : 'rpL16_JGI_MDM.filtered.faa' , 'L18' : 'rpL18_JGI_MDM.filtered.faa' , 'L22' : 'rpL22_JGI_MDM.filtered.faa' , 'L24' : 'rpL24_JGI_MDM.filtered.faa' , 'L2' : 'rpL2_JGI_MDM.filtered.faa' , 'L3' : 'rpL3_JGI_MDM.filtered.faa' , 'L4' : 'rpL4_JGI_MDM.filtered.faa' , 'L5' : 'rpL5_JGI_MDM.filtered.faa' , 'L6' : 'rpL6_JGI_MDM.filtered.faa' , 'S10' : 'rpS10_JGI_MDM.filtered.faa' , 'S17' : 'rpS17_JGI_MDM.filtered.faa' , 'S19' : 'rpS19_JGI_MDM.filtered.faa' , 'S3' : 'rpS3_JGI_MDM.filtered.faa' , 'S8' : 'rpS8_JGI_MDM.filtered.faa' } protein_databases = { key : '%s/%s' % ( databases , database ) for key , database in list ( protein_databases . items ( ) ) } return proteins , protein_databases | 241 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rp16.py#L21-L48 | [
"def",
"_sendStatCmd",
"(",
"self",
",",
"cmd",
")",
":",
"try",
":",
"self",
".",
"_conn",
".",
"write",
"(",
"\"%s\\r\\n\"",
"%",
"cmd",
")",
"regex",
"=",
"re",
".",
"compile",
"(",
"'^(END|ERROR)\\r\\n'",
",",
"re",
".",
"MULTILINE",
")",
"(",
"idx",
",",
"mobj",
",",
"text",
")",
"=",
"self",
".",
"_conn",
".",
"expect",
"(",
"[",
"regex",
",",
"]",
",",
"self",
".",
"_timeout",
")",
"#@UnusedVariable",
"except",
":",
"raise",
"Exception",
"(",
"\"Communication with %s failed\"",
"%",
"self",
".",
"_instanceName",
")",
"if",
"mobj",
"is",
"not",
"None",
":",
"if",
"mobj",
".",
"group",
"(",
"1",
")",
"==",
"'END'",
":",
"return",
"text",
".",
"splitlines",
"(",
")",
"[",
":",
"-",
"1",
"]",
"elif",
"mobj",
".",
"group",
"(",
"1",
")",
"==",
"'ERROR'",
":",
"raise",
"Exception",
"(",
"\"Protocol error in communication with %s.\"",
"%",
"self",
".",
"_instanceName",
")",
"else",
":",
"raise",
"Exception",
"(",
"\"Connection with %s timed out.\"",
"%",
"self",
".",
"_instanceName",
")"
] |
which protein has the best hit the one to the right or to the left? | def find_next ( start , stop , i2hits ) : if start not in i2hits and stop in i2hits : index = stop elif stop not in i2hits and start in i2hits : index = start elif start not in i2hits and stop not in i2hits : index = choice ( [ start , stop ] ) i2hits [ index ] = [ [ False ] ] else : A , B = i2hits [ start ] [ 0 ] , i2hits [ stop ] [ 0 ] if B [ 10 ] <= A [ 10 ] : index = stop else : index = start if index == start : nstart = start - 1 nstop = stop else : nstop = stop + 1 nstart = start match = i2hits [ index ] [ 0 ] rp = match [ - 1 ] return index , nstart , nstop , rp , match | 242 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rp16.py#L77-L102 | [
"def",
"construct_error_message",
"(",
"driver_id",
",",
"error_type",
",",
"message",
",",
"timestamp",
")",
":",
"builder",
"=",
"flatbuffers",
".",
"Builder",
"(",
"0",
")",
"driver_offset",
"=",
"builder",
".",
"CreateString",
"(",
"driver_id",
".",
"binary",
"(",
")",
")",
"error_type_offset",
"=",
"builder",
".",
"CreateString",
"(",
"error_type",
")",
"message_offset",
"=",
"builder",
".",
"CreateString",
"(",
"message",
")",
"ray",
".",
"core",
".",
"generated",
".",
"ErrorTableData",
".",
"ErrorTableDataStart",
"(",
"builder",
")",
"ray",
".",
"core",
".",
"generated",
".",
"ErrorTableData",
".",
"ErrorTableDataAddDriverId",
"(",
"builder",
",",
"driver_offset",
")",
"ray",
".",
"core",
".",
"generated",
".",
"ErrorTableData",
".",
"ErrorTableDataAddType",
"(",
"builder",
",",
"error_type_offset",
")",
"ray",
".",
"core",
".",
"generated",
".",
"ErrorTableData",
".",
"ErrorTableDataAddErrorMessage",
"(",
"builder",
",",
"message_offset",
")",
"ray",
".",
"core",
".",
"generated",
".",
"ErrorTableData",
".",
"ErrorTableDataAddTimestamp",
"(",
"builder",
",",
"timestamp",
")",
"error_data_offset",
"=",
"ray",
".",
"core",
".",
"generated",
".",
"ErrorTableData",
".",
"ErrorTableDataEnd",
"(",
"builder",
")",
"builder",
".",
"Finish",
"(",
"error_data_offset",
")",
"return",
"bytes",
"(",
"builder",
".",
"Output",
"(",
")",
")"
] |
determine which hits represent real ribosomal proteins identify each in syntenic block max_hits_rp = maximum number of hits to consider per ribosomal protein per scaffold | def find_ribosomal ( rps , scaffolds , s2rp , min_hits , max_hits_rp , max_errors ) : for scaffold , proteins in list ( s2rp . items ( ) ) : # for each scaffold, get best hits for each rp hits = { p : [ i for i in sorted ( hits , key = itemgetter ( 10 ) ) ] [ 0 : max_hits_rp ] for p , hits in list ( proteins . items ( ) ) if len ( hits ) > 0 } # skip if fewer than min_hits RPs are identified if len ( hits ) < min_hits : continue best = sorted ( [ hit [ 0 ] + [ p ] for p , hit in list ( hits . items ( ) ) ] , key = itemgetter ( 10 ) ) [ 0 ] block = find_block ( rps , scaffolds [ scaffold ] , hits , best , max_errors ) if ( len ( block ) - 1 ) >= min_hits : yield scaffold , block | 243 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rp16.py#L134-L150 | [
"def",
"row_value",
"(",
"self",
",",
"row",
")",
":",
"irow",
"=",
"int",
"(",
"row",
")",
"i",
"=",
"self",
".",
"_get_key_index",
"(",
"irow",
")",
"if",
"i",
"==",
"-",
"1",
":",
"return",
"0.0",
"# Are we dealing with the last key?",
"if",
"i",
"==",
"len",
"(",
"self",
".",
"keys",
")",
"-",
"1",
":",
"return",
"self",
".",
"keys",
"[",
"-",
"1",
"]",
".",
"value",
"return",
"TrackKey",
".",
"interpolate",
"(",
"self",
".",
"keys",
"[",
"i",
"]",
",",
"self",
".",
"keys",
"[",
"i",
"+",
"1",
"]",
",",
"row",
")"
] |
Parse the rep set file and remove all sequences not associated with unique OTUs . | def filter_rep_set ( inF , otuSet ) : seqs = [ ] for record in SeqIO . parse ( inF , "fasta" ) : if record . id in otuSet : seqs . append ( record ) return seqs | 244 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/filter_rep_set.py#L32-L47 | [
"def",
"set_energy_range",
"(",
"self",
",",
"logemin",
",",
"logemax",
")",
":",
"if",
"logemin",
"is",
"None",
":",
"logemin",
"=",
"self",
".",
"log_energies",
"[",
"0",
"]",
"if",
"logemax",
"is",
"None",
":",
"logemax",
"=",
"self",
".",
"log_energies",
"[",
"-",
"1",
"]",
"imin",
"=",
"int",
"(",
"utils",
".",
"val_to_edge",
"(",
"self",
".",
"log_energies",
",",
"logemin",
")",
"[",
"0",
"]",
")",
"imax",
"=",
"int",
"(",
"utils",
".",
"val_to_edge",
"(",
"self",
".",
"log_energies",
",",
"logemax",
")",
"[",
"0",
"]",
")",
"if",
"imin",
"-",
"imax",
"==",
"0",
":",
"imin",
"=",
"int",
"(",
"len",
"(",
"self",
".",
"log_energies",
")",
"-",
"1",
")",
"imax",
"=",
"int",
"(",
"len",
"(",
"self",
".",
"log_energies",
")",
"-",
"1",
")",
"klims",
"=",
"self",
".",
"like",
".",
"logLike",
".",
"klims",
"(",
")",
"if",
"imin",
"!=",
"klims",
"[",
"0",
"]",
"or",
"imax",
"!=",
"klims",
"[",
"1",
"]",
":",
"self",
".",
"like",
".",
"selectEbounds",
"(",
"imin",
",",
"imax",
")",
"return",
"np",
".",
"array",
"(",
"[",
"self",
".",
"log_energies",
"[",
"imin",
"]",
",",
"self",
".",
"log_energies",
"[",
"imax",
"]",
"]",
")"
] |
Update the text for each element at the configured path if attribute matches | def _update_report_item ( self , * * update_props ) : tree_to_update = update_props [ 'tree_to_update' ] prop = update_props [ 'prop' ] values = wrap_value ( update_props [ 'values' ] ) xroot = self . _get_xroot_for ( prop ) attr_key = 'type' attr_val = u'' if prop == 'attribute_accuracy' : attr_val = 'DQQuanAttAcc' elif prop == 'dataset_completeness' : attr_val = 'DQCompOm' # Clear (make empty) all elements of the appropriate type for elem in get_elements ( tree_to_update , xroot ) : if get_element_attributes ( elem ) . get ( attr_key ) == attr_val : clear_element ( elem ) # Remove all empty elements, including those previously cleared remove_empty_element ( tree_to_update , xroot ) # Insert elements with correct attributes for each new value attrs = { attr_key : attr_val } updated = [ ] for idx , value in enumerate ( values ) : elem = insert_element ( tree_to_update , idx , xroot , * * attrs ) updated . append ( insert_element ( elem , idx , 'measDesc' , value ) ) return updated | 245 | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/arcgis_metadata_parser.py#L407-L440 | [
"def",
"remove_headers",
"(",
"self",
",",
"header_name",
")",
":",
"if",
"self",
".",
"__ro_flag",
":",
"raise",
"RuntimeError",
"(",
"'ro'",
")",
"header_name",
"=",
"self",
".",
"normalize_name",
"(",
"header_name",
")",
"if",
"header_name",
"in",
"self",
".",
"__headers",
".",
"keys",
"(",
")",
":",
"self",
".",
"__headers",
".",
"pop",
"(",
"header_name",
")"
] |
Clear the specified interrupt bit in the interrupt status register . | def _clear_interrupt ( self , intbit ) : int_status = self . _device . readU8 ( VCNL4010_INTSTAT ) int_status &= ~ intbit self . _device . write8 ( VCNL4010_INTSTAT , int_status ) | 246 | https://github.com/adafruit/Adafruit_Python_VCNL40xx/blob/f88ec755fd23017028b6dec1be0607ff4a018e10/Adafruit_VCNL40xx/VCNL40xx.py#L123-L128 | [
"def",
"create_dirs",
"(",
"self",
")",
":",
"if",
"not",
"os",
".",
"path",
".",
"isdir",
"(",
"self",
".",
"_path",
")",
":",
"os",
".",
"makedirs",
"(",
"self",
".",
"_path",
")",
"for",
"dir_name",
"in",
"[",
"self",
".",
"OBJ_DIR",
",",
"self",
".",
"TMP_OBJ_DIR",
",",
"self",
".",
"PKG_DIR",
",",
"self",
".",
"CACHE_DIR",
"]",
":",
"path",
"=",
"os",
".",
"path",
".",
"join",
"(",
"self",
".",
"_path",
",",
"dir_name",
")",
"if",
"not",
"os",
".",
"path",
".",
"isdir",
"(",
"path",
")",
":",
"os",
".",
"mkdir",
"(",
"path",
")",
"if",
"not",
"os",
".",
"path",
".",
"exists",
"(",
"self",
".",
"_version_path",
"(",
")",
")",
":",
"self",
".",
"_write_format_version",
"(",
")"
] |
Swaps two nodes | def move ( self ) : a = random . randint ( 0 , len ( self . state ) - 1 ) b = random . randint ( 0 , len ( self . state ) - 1 ) self . state [ [ a , b ] ] = self . state [ [ b , a ] ] | 247 | https://github.com/skojaku/core-periphery-detection/blob/d724e6441066622506ddb54d81ee9a1cfd15f766/cpalgorithm/Rombach.py#L19-L23 | [
"def",
"signalize_extensions",
"(",
")",
":",
"warnings",
".",
"warn",
"(",
"\"DB-API extension cursor.rownumber used\"",
",",
"SalesforceWarning",
")",
"warnings",
".",
"warn",
"(",
"\"DB-API extension connection.<exception> used\"",
",",
"SalesforceWarning",
")",
"# TODO",
"warnings",
".",
"warn",
"(",
"\"DB-API extension cursor.connection used\"",
",",
"SalesforceWarning",
")",
"# not implemented DB-API extension cursor.scroll(, SalesforceWarning)",
"warnings",
".",
"warn",
"(",
"\"DB-API extension cursor.messages used\"",
",",
"SalesforceWarning",
")",
"warnings",
".",
"warn",
"(",
"\"DB-API extension connection.messages used\"",
",",
"SalesforceWarning",
")",
"warnings",
".",
"warn",
"(",
"\"DB-API extension cursor.next(, SalesforceWarning) used\"",
")",
"warnings",
".",
"warn",
"(",
"\"DB-API extension cursor.__iter__(, SalesforceWarning) used\"",
")",
"warnings",
".",
"warn",
"(",
"\"DB-API extension cursor.lastrowid used\"",
",",
"SalesforceWarning",
")",
"warnings",
".",
"warn",
"(",
"\"DB-API extension .errorhandler used\"",
",",
"SalesforceWarning",
")"
] |
A bool - if the certificate should be self - signed . | def self_signed ( self , value ) : self . _self_signed = bool ( value ) if self . _self_signed : self . _issuer = None | 248 | https://github.com/wbond/certbuilder/blob/969dae884fa7f73988bbf1dcbec4fb51e234a3c5/certbuilder/__init__.py#L122-L130 | [
"def",
"get_context_data",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"context",
"=",
"super",
"(",
"TabView",
",",
"self",
")",
".",
"get_context_data",
"(",
"*",
"*",
"kwargs",
")",
"try",
":",
"tab_group",
"=",
"self",
".",
"get_tabs",
"(",
"self",
".",
"request",
",",
"*",
"*",
"kwargs",
")",
"context",
"[",
"\"tab_group\"",
"]",
"=",
"tab_group",
"# Make sure our data is pre-loaded to capture errors.",
"context",
"[",
"\"tab_group\"",
"]",
".",
"load_tab_data",
"(",
")",
"except",
"Exception",
":",
"exceptions",
".",
"handle",
"(",
"self",
".",
"request",
")",
"return",
"context"
] |
Grabs the first URL out of a asn1crypto . x509 . CRLDistributionPoints object | def _get_crl_url ( self , distribution_points ) : if distribution_points is None : return None for distribution_point in distribution_points : name = distribution_point [ 'distribution_point' ] if name . name == 'full_name' and name . chosen [ 0 ] . name == 'uniform_resource_identifier' : return name . chosen [ 0 ] . chosen . native return None | 249 | https://github.com/wbond/certbuilder/blob/969dae884fa7f73988bbf1dcbec4fb51e234a3c5/certbuilder/__init__.py#L544-L564 | [
"def",
"set_sync_limit",
"(",
"self",
",",
"limit",
":",
"int",
")",
"->",
"Optional",
"[",
"int",
"]",
":",
"try",
":",
"prev_limit",
"=",
"json",
".",
"loads",
"(",
"self",
".",
"sync_filter",
")",
"[",
"'room'",
"]",
"[",
"'timeline'",
"]",
"[",
"'limit'",
"]",
"except",
"(",
"json",
".",
"JSONDecodeError",
",",
"KeyError",
")",
":",
"prev_limit",
"=",
"None",
"self",
".",
"sync_filter",
"=",
"json",
".",
"dumps",
"(",
"{",
"'room'",
":",
"{",
"'timeline'",
":",
"{",
"'limit'",
":",
"limit",
"}",
"}",
"}",
")",
"return",
"prev_limit"
] |
A bool - if the certificate should have the OCSP no check extension . Only applicable to certificates created for signing OCSP responses . Such certificates should normally be issued for a very short period of time since they are effectively whitelisted by clients . | def ocsp_no_check ( self , value ) : if value is None : self . _ocsp_no_check = None else : self . _ocsp_no_check = bool ( value ) | 250 | https://github.com/wbond/certbuilder/blob/969dae884fa7f73988bbf1dcbec4fb51e234a3c5/certbuilder/__init__.py#L688-L699 | [
"def",
"add_to_virtualbox",
"(",
"self",
")",
":",
"# VirtualBox Image",
"if",
"'vmname'",
"not",
"in",
"self",
".",
"node",
"[",
"'properties'",
"]",
":",
"self",
".",
"node",
"[",
"'properties'",
"]",
"[",
"'vmname'",
"]",
"=",
"self",
".",
"hypervisor",
"[",
"'VBoxDevice'",
"]",
"[",
"'image'",
"]",
"# Number of adapters",
"if",
"'adapters'",
"not",
"in",
"self",
".",
"node",
"[",
"'properties'",
"]",
":",
"self",
".",
"node",
"[",
"'properties'",
"]",
"[",
"'adapters'",
"]",
"=",
"self",
".",
"hypervisor",
"[",
"'VBoxDevice'",
"]",
"[",
"'nics'",
"]",
"# Console Port",
"if",
"'console'",
"not",
"in",
"self",
".",
"node",
"[",
"'properties'",
"]",
":",
"self",
".",
"node",
"[",
"'properties'",
"]",
"[",
"'console'",
"]",
"=",
"self",
".",
"base_ports",
"[",
"'vbox_console'",
"]",
"+",
"self",
".",
"node",
"[",
"'vbox_id'",
"]",
"-",
"1"
] |
Removes empty line . | def emptylineless ( parser , token ) : nodelist = parser . parse ( ( 'endemptylineless' , ) ) parser . delete_first_token ( ) return EmptylinelessNode ( nodelist ) | 251 | https://github.com/tell-k/django-modelsdoc/blob/c9d336e76251feb142347b3a41365430d3365436/modelsdoc/templatetags/modelsdoc_tags.py#L31-L54 | [
"def",
"_GetPrimitiveEncoder",
"(",
"self",
")",
":",
"# Decide what should the primitive type be for packing the target rdfvalue",
"# into the protobuf and create a delegate descriptor to control that.",
"primitive_cls",
"=",
"self",
".",
"_PROTO_DATA_STORE_LOOKUP",
"[",
"self",
".",
"type",
".",
"data_store_type",
"]",
"self",
".",
"primitive_desc",
"=",
"primitive_cls",
"(",
"*",
"*",
"self",
".",
"_kwargs",
")",
"# Our wiretype is the same as the delegate's.",
"self",
".",
"wire_type",
"=",
"self",
".",
"primitive_desc",
".",
"wire_type",
"self",
".",
"proto_type_name",
"=",
"self",
".",
"primitive_desc",
".",
"proto_type_name",
"# Recalculate our tags.",
"self",
".",
"CalculateTags",
"(",
")"
] |
Do an HTTP PURGE of the given asset . The URL is run through urlparse and must point to the varnish instance not the varnishadm | def http_purge_url ( url ) : url = urlparse ( url ) connection = HTTPConnection ( url . hostname , url . port or 80 ) path = url . path or '/' connection . request ( 'PURGE' , '%s?%s' % ( path , url . query ) if url . query else path , '' , { 'Host' : '%s:%s' % ( url . hostname , url . port ) if url . port else url . hostname } ) response = connection . getresponse ( ) if response . status != 200 : logging . error ( 'Purge failed with status: %s' % response . status ) return response | 252 | https://github.com/justquick/python-varnish/blob/8f114c74898e6c5ade2ce49c8b595040bd150465/varnish.py#L47-L60 | [
"def",
"row_completed",
"(",
"self",
",",
"index",
")",
":",
"self",
".",
"_completed_rows",
".",
"append",
"(",
"index",
")",
"for",
"row_completed",
"in",
"self",
".",
"_on_row_completed",
":",
"row_completed",
"(",
"index",
")"
] |
Non - threaded batch command runner returning output results | def run ( addr , * commands , * * kwargs ) : results = [ ] handler = VarnishHandler ( addr , * * kwargs ) for cmd in commands : if isinstance ( cmd , tuple ) and len ( cmd ) > 1 : results . extend ( [ getattr ( handler , c [ 0 ] . replace ( '.' , '_' ) ) ( * c [ 1 : ] ) for c in cmd ] ) else : results . append ( getattr ( handler , cmd . replace ( '.' , '_' ) ) ( * commands [ 1 : ] ) ) break handler . close ( ) return results | 253 | https://github.com/justquick/python-varnish/blob/8f114c74898e6c5ade2ce49c8b595040bd150465/varnish.py#L289-L302 | [
"def",
"isomorphic_to",
"(",
"self",
",",
"other",
")",
":",
"if",
"self",
".",
"molecule",
".",
"composition",
"!=",
"other",
".",
"molecule",
".",
"composition",
":",
"return",
"False",
"else",
":",
"self_undir",
"=",
"self",
".",
"graph",
".",
"to_undirected",
"(",
")",
"other_undir",
"=",
"other",
".",
"graph",
".",
"to_undirected",
"(",
")",
"nm",
"=",
"iso",
".",
"categorical_node_match",
"(",
"\"specie\"",
",",
"\"ERROR\"",
")",
"isomorphic",
"=",
"nx",
".",
"is_isomorphic",
"(",
"self_undir",
",",
"other_undir",
",",
"node_match",
"=",
"nm",
")",
"return",
"isomorphic"
] |
add stylesheet files in HTML head | def add_stylesheets ( self , * css_files ) : for css_file in css_files : self . main_soup . style . append ( self . _text_file ( css_file ) ) | 254 | https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L43-L46 | [
"def",
"get_command",
"(",
"self",
",",
"version",
"=",
"2",
")",
":",
"try",
":",
"options",
"=",
"_C",
"[",
"'options'",
"]",
"options_str",
"=",
"\" -o \"",
".",
"join",
"(",
"options",
")",
"if",
"options_str",
":",
"options_str",
"=",
"\"-o \"",
"+",
"options_str",
"+",
"\" \"",
"except",
"KeyError",
":",
"options_str",
"=",
"\"\"",
"if",
"self",
".",
"username",
":",
"# Not supported on SunOS",
"# \"-o ConnectTimeout={}",
"command",
"=",
"\"ssh {}\"",
"\"-{} \"",
"\"-p {} {}@{}\"",
".",
"format",
"(",
"options_str",
",",
"version",
",",
"self",
".",
"port",
",",
"self",
".",
"username",
",",
"self",
".",
"hostname",
")",
"else",
":",
"command",
"=",
"\"ssh {} \"",
"\"-{} \"",
"\"-p {} {}\"",
".",
"format",
"(",
"options_str",
",",
"version",
",",
"self",
".",
"port",
",",
"self",
".",
"hostname",
")",
"return",
"command"
] |
add javascripts files in HTML body | def add_javascripts ( self , * js_files ) : # create the script tag if don't exists if self . main_soup . script is None : script_tag = self . main_soup . new_tag ( 'script' ) self . main_soup . body . append ( script_tag ) for js_file in js_files : self . main_soup . script . append ( self . _text_file ( js_file ) ) | 255 | https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L48-L56 | [
"def",
"plugin_counts",
"(",
"self",
")",
":",
"ret",
"=",
"{",
"'total'",
":",
"0",
",",
"}",
"# As ususal, we need data before we can actually do anything ;)",
"data",
"=",
"self",
".",
"raw_query",
"(",
"'plugin'",
",",
"'init'",
")",
"# For backwards compatability purposes, we will be handling this a bit",
"# differently than I would like. We are going to check to see if each",
"# value exists and override the default value of 0. The only value that",
"# I know existed in bost 4.2 and 4.4 is pluginCount, the rest aren't",
"# listed in the API docs, however return back from my experimentation.",
"ret",
"[",
"'total'",
"]",
"=",
"data",
"[",
"'pluginCount'",
"]",
"if",
"'lastUpdates'",
"in",
"data",
":",
"for",
"item",
"in",
"[",
"'active'",
",",
"'passive'",
",",
"'compliance'",
",",
"'custom'",
",",
"'event'",
"]",
":",
"itemdata",
"=",
"{",
"}",
"if",
"item",
"in",
"data",
"[",
"'lastUpdates'",
"]",
":",
"itemdata",
"=",
"data",
"[",
"'lastUpdates'",
"]",
"[",
"item",
"]",
"if",
"item",
"in",
"data",
":",
"itemdata",
"[",
"'count'",
"]",
"=",
"data",
"[",
"item",
"]",
"else",
":",
"itemdata",
"[",
"'count'",
"]",
"=",
"0",
"ret",
"[",
"item",
"]",
"=",
"itemdata",
"return",
"ret"
] |
return the object in a file | def export ( self ) : with open ( self . export_url , 'w' , encoding = 'utf-8' ) as file : file . write ( self . build ( ) ) if self . open_browser : webbrowser . open_new_tab ( self . export_url ) | 256 | https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L58-L64 | [
"def",
"delete",
"(",
"name",
",",
"timeout",
"=",
"90",
")",
":",
"handle_scm",
"=",
"win32service",
".",
"OpenSCManager",
"(",
"None",
",",
"None",
",",
"win32service",
".",
"SC_MANAGER_CONNECT",
")",
"try",
":",
"handle_svc",
"=",
"win32service",
".",
"OpenService",
"(",
"handle_scm",
",",
"name",
",",
"win32service",
".",
"SERVICE_ALL_ACCESS",
")",
"except",
"pywintypes",
".",
"error",
"as",
"exc",
":",
"win32service",
".",
"CloseServiceHandle",
"(",
"handle_scm",
")",
"if",
"exc",
".",
"winerror",
"!=",
"1060",
":",
"raise",
"CommandExecutionError",
"(",
"'Failed to open {0}. {1}'",
".",
"format",
"(",
"name",
",",
"exc",
".",
"strerror",
")",
")",
"log",
".",
"debug",
"(",
"'Service \"%s\" is not present'",
",",
"name",
")",
"return",
"True",
"try",
":",
"win32service",
".",
"DeleteService",
"(",
"handle_svc",
")",
"except",
"pywintypes",
".",
"error",
"as",
"exc",
":",
"raise",
"CommandExecutionError",
"(",
"'Failed to delete {0}. {1}'",
".",
"format",
"(",
"name",
",",
"exc",
".",
"strerror",
")",
")",
"finally",
":",
"log",
".",
"debug",
"(",
"'Cleaning up'",
")",
"win32service",
".",
"CloseServiceHandle",
"(",
"handle_scm",
")",
"win32service",
".",
"CloseServiceHandle",
"(",
"handle_svc",
")",
"end_time",
"=",
"time",
".",
"time",
"(",
")",
"+",
"int",
"(",
"timeout",
")",
"while",
"name",
"in",
"get_all",
"(",
")",
"and",
"time",
".",
"time",
"(",
")",
"<",
"end_time",
":",
"time",
".",
"sleep",
"(",
"1",
")",
"return",
"name",
"not",
"in",
"get_all",
"(",
")"
] |
convert Markdown text as html . return the html file as string | def build ( self ) : markdown_html = markdown . markdown ( self . markdown_text , extensions = [ TocExtension ( ) , 'fenced_code' , 'markdown_checklist.extension' , 'markdown.extensions.tables' ] ) markdown_soup = BeautifulSoup ( markdown_html , 'html.parser' ) # include jquery & mermaid.js only if there are Mermaid graph if markdown_soup . find ( 'code' , attrs = { 'class' : 'mermaid' } ) : self . _add_mermaid_js ( ) # search in markdown html if there are Dot Graph & replace it with .svg result for dot_tag in markdown_soup . find_all ( 'code' , attrs = { 'class' : 'dotgraph' } ) : grap_svg = self . _text_to_graphiz ( dot_tag . string ) graph_soup = BeautifulSoup ( grap_svg , 'html.parser' ) dot_tag . parent . replaceWith ( graph_soup ) self . main_soup . body . append ( markdown_soup ) return self . main_soup . prettify ( ) | 257 | https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L66-L84 | [
"def",
"__normalize",
"(",
"self",
")",
":",
"# Don't normalize if we're already normalizing or intializing",
"if",
"self",
".",
"__normalizing",
"is",
"True",
"or",
"self",
".",
"__initialized",
"is",
"False",
":",
"return",
"self",
".",
"__normalizing",
"=",
"True",
"self",
".",
"__normalize_grades",
"(",
")",
"self",
".",
"__normalize_progress",
"(",
")",
"self",
".",
"__normalizing",
"=",
"False"
] |
return the content of a file | def _text_file ( self , url ) : try : with open ( url , 'r' , encoding = 'utf-8' ) as file : return file . read ( ) except FileNotFoundError : print ( 'File `{}` not found' . format ( url ) ) sys . exit ( 0 ) | 258 | https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L86-L93 | [
"def",
"catalogFactory",
"(",
"name",
",",
"*",
"*",
"kwargs",
")",
":",
"fn",
"=",
"lambda",
"member",
":",
"inspect",
".",
"isclass",
"(",
"member",
")",
"and",
"member",
".",
"__module__",
"==",
"__name__",
"catalogs",
"=",
"odict",
"(",
"inspect",
".",
"getmembers",
"(",
"sys",
".",
"modules",
"[",
"__name__",
"]",
",",
"fn",
")",
")",
"if",
"name",
"not",
"in",
"list",
"(",
"catalogs",
".",
"keys",
"(",
")",
")",
":",
"msg",
"=",
"\"%s not found in catalogs:\\n %s\"",
"%",
"(",
"name",
",",
"list",
"(",
"kernels",
".",
"keys",
"(",
")",
")",
")",
"logger",
".",
"error",
"(",
"msg",
")",
"msg",
"=",
"\"Unrecognized catalog: %s\"",
"%",
"name",
"raise",
"Exception",
"(",
"msg",
")",
"return",
"catalogs",
"[",
"name",
"]",
"(",
"*",
"*",
"kwargs",
")"
] |
create a graphviz graph from text | def _text_to_graphiz ( self , text ) : dot = Source ( text , format = 'svg' ) return dot . pipe ( ) . decode ( 'utf-8' ) | 259 | https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L95-L98 | [
"def",
"__get_vibration_code",
"(",
"self",
",",
"left_motor",
",",
"right_motor",
",",
"duration",
")",
":",
"inner_event",
"=",
"struct",
".",
"pack",
"(",
"'2h6x2h2x2H28x'",
",",
"0x50",
",",
"-",
"1",
",",
"duration",
",",
"0",
",",
"int",
"(",
"left_motor",
"*",
"65535",
")",
",",
"int",
"(",
"right_motor",
"*",
"65535",
")",
")",
"buf_conts",
"=",
"ioctl",
"(",
"self",
".",
"_write_device",
",",
"1076905344",
",",
"inner_event",
")",
"return",
"int",
"(",
"codecs",
".",
"encode",
"(",
"buf_conts",
"[",
"1",
":",
"3",
"]",
",",
"'hex'",
")",
",",
"16",
")"
] |
add js libraries and css files of mermaid js_file | def _add_mermaid_js ( self ) : self . add_javascripts ( '{}/js/jquery-1.11.3.min.js' . format ( self . resources_path ) ) self . add_javascripts ( '{}/js/mermaid.min.js' . format ( self . resources_path ) ) self . add_stylesheets ( '{}/css/mermaid.css' . format ( self . resources_path ) ) self . main_soup . script . append ( 'mermaid.initialize({startOnLoad:true });' ) | 260 | https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L100-L105 | [
"def",
"shape",
"(",
"self",
")",
":",
"if",
"len",
"(",
"self",
")",
"==",
"0",
":",
"return",
"(",
")",
"elif",
"self",
".",
"is_power_space",
":",
"try",
":",
"sub_shape",
"=",
"self",
"[",
"0",
"]",
".",
"shape",
"except",
"AttributeError",
":",
"sub_shape",
"=",
"(",
")",
"else",
":",
"sub_shape",
"=",
"(",
")",
"return",
"(",
"len",
"(",
"self",
")",
",",
")",
"+",
"sub_shape"
] |
Get a character set with individual members or ranges . | def getCharacterSet ( self ) : chars = u'' c = None cnt = 1 start = 0 while True : escaped_slash = False c = self . next ( ) # print "pattern : ", self.pattern # print "C : ", c # print "Slash : ", c == u'\\' # print 'chars : ', chars # print 'index : ', self.index # print 'last : ', self.last() # print 'lookahead : ', self.lookahead() if self . lookahead ( ) == u'-' and not c == u'\\' : f = c self . next ( ) # skip hyphen c = self . next ( ) # get far range if not c or ( c in self . meta_chars ) : raise StringGenerator . SyntaxError ( u"unexpected end of class range" ) chars += self . getCharacterRange ( f , c ) elif c == u'\\' : if self . lookahead ( ) in self . meta_chars : c = self . next ( ) chars += c continue elif self . lookahead ( ) in self . string_code : c = self . next ( ) chars += self . string_code [ c ] elif c and c not in self . meta_chars : chars += c if c == u']' : if self . lookahead ( ) == u'{' : [ start , cnt ] = self . getQuantifier ( ) else : start = - 1 cnt = 1 break if c and c in self . meta_chars and not self . last ( ) == u"\\" : raise StringGenerator . SyntaxError ( u"Un-escaped character in class definition: %s" % c ) if not c : break return StringGenerator . CharacterSet ( chars , start , cnt ) | 261 | https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L368-L419 | [
"def",
"WaitForVirtualMachineShutdown",
"(",
"self",
",",
"vm_to_poll",
",",
"timeout_seconds",
",",
"sleep_period",
"=",
"5",
")",
":",
"seconds_waited",
"=",
"0",
"# wait counter",
"while",
"seconds_waited",
"<",
"timeout_seconds",
":",
"# sleep first, since nothing shuts down instantly",
"seconds_waited",
"+=",
"sleep_period",
"time",
".",
"sleep",
"(",
"sleep_period",
")",
"vm",
"=",
"self",
".",
"get_vm",
"(",
"vm_to_poll",
".",
"name",
")",
"if",
"vm",
".",
"runtime",
".",
"powerState",
"==",
"vim",
".",
"VirtualMachinePowerState",
".",
"poweredOff",
":",
"return",
"True",
"return",
"False"
] |
Get a sequence of non - special characters . | def getLiteral ( self ) : # we are on the first non-special character chars = u'' c = self . current ( ) while True : if c and c == u"\\" : c = self . next ( ) if c : chars += c continue elif not c or ( c in self . meta_chars ) : break else : chars += c if self . lookahead ( ) and self . lookahead ( ) in self . meta_chars : break c = self . next ( ) return StringGenerator . Literal ( chars ) | 262 | https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L421-L439 | [
"def",
"initialize_communities_bucket",
"(",
")",
":",
"bucket_id",
"=",
"UUID",
"(",
"current_app",
".",
"config",
"[",
"'COMMUNITIES_BUCKET_UUID'",
"]",
")",
"if",
"Bucket",
".",
"query",
".",
"get",
"(",
"bucket_id",
")",
":",
"raise",
"FilesException",
"(",
"\"Bucket with UUID {} already exists.\"",
".",
"format",
"(",
"bucket_id",
")",
")",
"else",
":",
"storage_class",
"=",
"current_app",
".",
"config",
"[",
"'FILES_REST_DEFAULT_STORAGE_CLASS'",
"]",
"location",
"=",
"Location",
".",
"get_default",
"(",
")",
"bucket",
"=",
"Bucket",
"(",
"id",
"=",
"bucket_id",
",",
"location",
"=",
"location",
",",
"default_storage_class",
"=",
"storage_class",
")",
"db",
".",
"session",
".",
"add",
"(",
"bucket",
")",
"db",
".",
"session",
".",
"commit",
"(",
")"
] |
Get a sequence of nodes . | def getSequence ( self , level = 0 ) : seq = [ ] op = '' left_operand = None right_operand = None sequence_closed = False while True : c = self . next ( ) if not c : break if c and c not in self . meta_chars : seq . append ( self . getLiteral ( ) ) elif c and c == u'$' and self . lookahead ( ) == u'{' : seq . append ( self . getSource ( ) ) elif c == u'[' and not self . last ( ) == u'\\' : seq . append ( self . getCharacterSet ( ) ) elif c == u'(' and not self . last ( ) == u'\\' : seq . append ( self . getSequence ( level + 1 ) ) elif c == u')' and not self . last ( ) == u'\\' : # end of this sequence if level == 0 : # there should be no parens here raise StringGenerator . SyntaxError ( u"Extra closing parenthesis" ) sequence_closed = True break elif c == u'|' and not self . last ( ) == u'\\' : op = c elif c == u'&' and not self . last ( ) == u'\\' : op = c else : if c in self . meta_chars and not self . last ( ) == u"\\" : raise StringGenerator . SyntaxError ( u"Un-escaped special character: %s" % c ) #print( op,len(seq) ) if op and not left_operand : if not seq or len ( seq ) < 1 : raise StringGenerator . SyntaxError ( u"Operator: %s with no left operand" % op ) left_operand = seq . pop ( ) elif op and len ( seq ) >= 1 and left_operand : right_operand = seq . pop ( ) #print( "popped: [%s] %s:%s"%( op, left_operand, right_operand) ) if op == u'|' : seq . append ( StringGenerator . SequenceOR ( [ left_operand , right_operand ] ) ) elif op == u'&' : seq . append ( StringGenerator . SequenceAND ( [ left_operand , right_operand ] ) ) op = u'' left_operand = None right_operand = None # check for syntax errors if op : raise StringGenerator . SyntaxError ( u"Operator: %s with no right operand" % op ) if level > 0 and not sequence_closed : # it means we are finishing a non-first-level sequence without closing parens raise StringGenerator . SyntaxError ( u"Missing closing parenthesis" ) return StringGenerator . Sequence ( seq ) | 263 | https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L441-L501 | [
"def",
"crtPwBoxCarFn",
"(",
"varNumVol",
",",
"aryPngData",
",",
"aryPresOrd",
",",
"vecMtDrctn",
")",
":",
"print",
"(",
"'------Create pixel-wise boxcar functions'",
")",
"aryBoxCar",
"=",
"np",
".",
"empty",
"(",
"aryPngData",
".",
"shape",
"[",
"0",
":",
"2",
"]",
"+",
"(",
"len",
"(",
"vecMtDrctn",
")",
",",
")",
"+",
"(",
"varNumVol",
",",
")",
",",
"dtype",
"=",
"'int64'",
")",
"for",
"ind",
",",
"num",
"in",
"enumerate",
"(",
"vecMtDrctn",
")",
":",
"aryCondTemp",
"=",
"np",
".",
"zeros",
"(",
"(",
"aryPngData",
".",
"shape",
")",
",",
"dtype",
"=",
"'int64'",
")",
"lgcTempMtDrctn",
"=",
"[",
"aryPresOrd",
"==",
"num",
"]",
"[",
"0",
"]",
"aryCondTemp",
"[",
":",
",",
":",
",",
"lgcTempMtDrctn",
"]",
"=",
"np",
".",
"copy",
"(",
"aryPngData",
"[",
":",
",",
":",
",",
"lgcTempMtDrctn",
"]",
")",
"aryBoxCar",
"[",
":",
",",
":",
",",
"ind",
",",
":",
"]",
"=",
"aryCondTemp",
"return",
"aryBoxCar"
] |
Print the parse tree and then call render for an example . | def dump ( self , * * kwargs ) : import sys if not self . seq : self . seq = self . getSequence ( ) print ( "StringGenerator version: %s" % ( __version__ ) ) print ( "Python version: %s" % sys . version ) # this doesn't work anymore in p3 # print("Random method provider class: %s" % randint.im_class.__name__) self . seq . dump ( ) return self . render ( * * kwargs ) | 264 | https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L521-L531 | [
"def",
"wait_for_keypresses",
"(",
"self",
",",
"refresh_rate",
"=",
"1",
")",
":",
"if",
"not",
"self",
".",
"_enable_keyboard",
":",
"return",
"with",
"self",
".",
"_blessed_term",
".",
"cbreak",
"(",
")",
":",
"while",
"True",
":",
"yield",
"self",
".",
"_blessed_term",
".",
"inkey",
"(",
"timeout",
"=",
"refresh_rate",
")"
] |
Return a list of generated strings . | def render_list ( self , cnt , unique = False , progress_callback = None , * * kwargs ) : rendered_list = [ ] i = 0 total_attempts = 0 while True : if i >= cnt : break if total_attempts > cnt * self . unique_attempts_factor : raise StringGenerator . UniquenessError ( u"couldn't satisfy uniqueness" ) s = self . render ( * * kwargs ) if unique : if not s in rendered_list : rendered_list . append ( s ) i += 1 else : rendered_list . append ( s ) i += 1 total_attempts += 1 # Optionally trigger the progress indicator to inform others about our progress if progress_callback and callable ( progress_callback ) : progress_callback ( i , cnt ) return rendered_list | 265 | https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L533-L570 | [
"def",
"_is_binary_stl",
"(",
"data",
")",
":",
"is_bin",
"=",
"False",
"start_byte",
"=",
"0",
"end_byte",
"=",
"80",
"_",
"=",
"data",
"[",
"start_byte",
":",
"end_byte",
"]",
"# header data",
"start_byte",
"=",
"end_byte",
"end_byte",
"+=",
"4",
"facet_count",
"=",
"struct",
".",
"unpack",
"(",
"'I'",
",",
"data",
"[",
"start_byte",
":",
"end_byte",
"]",
")",
"[",
"0",
"]",
"if",
"facet_count",
">",
"0",
":",
"is_bin",
"=",
"True",
"return",
"is_bin"
] |
Establish the connection . This is done automatically for you . | def connect ( self ) : self . conn = boto . connect_s3 ( self . AWS_ACCESS_KEY_ID , self . AWS_SECRET_ACCESS_KEY , debug = self . S3UTILS_DEBUG_LEVEL ) self . bucket = self . conn . get_bucket ( self . AWS_STORAGE_BUCKET_NAME ) self . k = Key ( self . bucket ) | 266 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L145-L155 | [
"def",
"setOverlayTexelAspect",
"(",
"self",
",",
"ulOverlayHandle",
",",
"fTexelAspect",
")",
":",
"fn",
"=",
"self",
".",
"function_table",
".",
"setOverlayTexelAspect",
"result",
"=",
"fn",
"(",
"ulOverlayHandle",
",",
"fTexelAspect",
")",
"return",
"result"
] |
Connect to Cloud Front . This is done automatically for you when needed . | def connect_cloudfront ( self ) : self . conn_cloudfront = connect_cloudfront ( self . AWS_ACCESS_KEY_ID , self . AWS_SECRET_ACCESS_KEY , debug = self . S3UTILS_DEBUG_LEVEL ) | 267 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L166-L168 | [
"def",
"remove_organization",
"(",
"self",
",",
"service_desk_id",
",",
"organization_id",
")",
":",
"log",
".",
"warning",
"(",
"'Removing organization...'",
")",
"url",
"=",
"'rest/servicedeskapi/servicedesk/{}/organization'",
".",
"format",
"(",
"service_desk_id",
")",
"data",
"=",
"{",
"'organizationId'",
":",
"organization_id",
"}",
"return",
"self",
".",
"delete",
"(",
"url",
",",
"headers",
"=",
"self",
".",
"experimental_headers",
",",
"data",
"=",
"data",
")"
] |
Create a folder on S3 . | def mkdir ( self , target_folder ) : self . printv ( "Making directory: %s" % target_folder ) self . k . key = re . sub ( r"^/|/$" , "" , target_folder ) + "/" self . k . set_contents_from_string ( '' ) self . k . close ( ) | 268 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L171-L183 | [
"def",
"get_changed_devices",
"(",
"self",
",",
"timestamp",
")",
":",
"if",
"timestamp",
"is",
"None",
":",
"payload",
"=",
"{",
"}",
"else",
":",
"payload",
"=",
"{",
"'timeout'",
":",
"SUBSCRIPTION_WAIT",
",",
"'minimumdelay'",
":",
"SUBSCRIPTION_MIN_WAIT",
"}",
"payload",
".",
"update",
"(",
"timestamp",
")",
"# double the timeout here so requests doesn't timeout before vera",
"payload",
".",
"update",
"(",
"{",
"'id'",
":",
"'lu_sdata'",
",",
"}",
")",
"logger",
".",
"debug",
"(",
"\"get_changed_devices() requesting payload %s\"",
",",
"str",
"(",
"payload",
")",
")",
"r",
"=",
"self",
".",
"data_request",
"(",
"payload",
",",
"TIMEOUT",
"*",
"2",
")",
"r",
".",
"raise_for_status",
"(",
")",
"# If the Vera disconnects before writing a full response (as lu_sdata",
"# will do when interrupted by a Luup reload), the requests module will",
"# happily return 200 with an empty string. So, test for empty response,",
"# so we don't rely on the JSON parser to throw an exception.",
"if",
"r",
".",
"text",
"==",
"\"\"",
":",
"raise",
"PyveraError",
"(",
"\"Empty response from Vera\"",
")",
"# Catch a wide swath of what the JSON parser might throw, within",
"# reason. Unfortunately, some parsers don't specifically return",
"# json.decode.JSONDecodeError, but so far most seem to derive what",
"# they do throw from ValueError, so that's helpful.",
"try",
":",
"result",
"=",
"r",
".",
"json",
"(",
")",
"except",
"ValueError",
"as",
"ex",
":",
"raise",
"PyveraError",
"(",
"\"JSON decode error: \"",
"+",
"str",
"(",
"ex",
")",
")",
"if",
"not",
"(",
"type",
"(",
"result",
")",
"is",
"dict",
"and",
"'loadtime'",
"in",
"result",
"and",
"'dataversion'",
"in",
"result",
")",
":",
"raise",
"PyveraError",
"(",
"\"Unexpected/garbled response from Vera\"",
")",
"# At this point, all good. Update timestamp and return change data.",
"device_data",
"=",
"result",
".",
"get",
"(",
"'devices'",
")",
"timestamp",
"=",
"{",
"'loadtime'",
":",
"result",
".",
"get",
"(",
"'loadtime'",
")",
",",
"'dataversion'",
":",
"result",
".",
"get",
"(",
"'dataversion'",
")",
"}",
"return",
"[",
"device_data",
",",
"timestamp",
"]"
] |
Delete the path and anything under the path . | def rm ( self , path ) : list_of_files = list ( self . ls ( path ) ) if list_of_files : if len ( list_of_files ) == 1 : self . bucket . delete_key ( list_of_files [ 0 ] ) else : self . bucket . delete_keys ( list_of_files ) self . printv ( "Deleted: %s" % list_of_files ) else : logger . error ( "There was nothing to remove under %s" , path ) | 269 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L186-L204 | [
"def",
"map_system_entities",
"(",
"engine",
",",
"metadata",
",",
"reset",
")",
":",
"# Map the user message system entity.",
"msg_tbl",
"=",
"Table",
"(",
"'_user_messages'",
",",
"metadata",
",",
"Column",
"(",
"'guid'",
",",
"String",
",",
"nullable",
"=",
"False",
",",
"primary_key",
"=",
"True",
")",
",",
"Column",
"(",
"'text'",
",",
"String",
",",
"nullable",
"=",
"False",
")",
",",
"Column",
"(",
"'time_stamp'",
",",
"DateTime",
"(",
"timezone",
"=",
"True",
")",
",",
"nullable",
"=",
"False",
",",
"default",
"=",
"sa_func",
".",
"now",
"(",
")",
")",
",",
")",
"mapper",
"(",
"UserMessage",
",",
"msg_tbl",
",",
"id_attribute",
"=",
"'guid'",
")",
"if",
"reset",
":",
"metadata",
".",
"drop_all",
"(",
"bind",
"=",
"engine",
",",
"tables",
"=",
"[",
"msg_tbl",
"]",
")",
"metadata",
".",
"create_all",
"(",
"bind",
"=",
"engine",
",",
"tables",
"=",
"[",
"msg_tbl",
"]",
")"
] |
Copy a file to s3 . | def __put_key ( self , local_file , target_file , acl = 'public-read' , del_after_upload = False , overwrite = True , source = "filename" ) : action_word = "moving" if del_after_upload else "copying" try : self . k . key = target_file # setting the path (key) of file in the container if source == "filename" : # grabs the contents from local_file address. Note that it loads the whole file into memory self . k . set_contents_from_filename ( local_file , self . AWS_HEADERS ) elif source == "fileobj" : self . k . set_contents_from_file ( local_file , self . AWS_HEADERS ) elif source == "string" : self . k . set_contents_from_string ( local_file , self . AWS_HEADERS ) else : raise Exception ( "%s is not implemented as a source." % source ) self . k . set_acl ( acl ) # setting the file permissions self . k . close ( ) # not sure if it is needed. Somewhere I read it is recommended. self . printv ( "%s %s to %s" % ( action_word , local_file , target_file ) ) # if it is supposed to delete the local file after uploading if del_after_upload and source == "filename" : try : os . remove ( local_file ) except : logger . error ( "Unable to delete the file: " , local_file , exc_info = True ) return True except : logger . error ( "Error in writing to %s" , target_file , exc_info = True ) return False | 270 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L207-L238 | [
"def",
"parse_recommendations",
"(",
"self",
",",
"recommendations_page",
")",
":",
"user_info",
"=",
"self",
".",
"parse_sidebar",
"(",
"recommendations_page",
")",
"second_col",
"=",
"recommendations_page",
".",
"find",
"(",
"u'div'",
",",
"{",
"u'id'",
":",
"u'content'",
"}",
")",
".",
"find",
"(",
"u'table'",
")",
".",
"find",
"(",
"u'tr'",
")",
".",
"find_all",
"(",
"u'td'",
",",
"recursive",
"=",
"False",
")",
"[",
"1",
"]",
"try",
":",
"recommendations",
"=",
"second_col",
".",
"find_all",
"(",
"u\"div\"",
",",
"{",
"u\"class\"",
":",
"u\"spaceit borderClass\"",
"}",
")",
"if",
"recommendations",
":",
"user_info",
"[",
"u'recommendations'",
"]",
"=",
"{",
"}",
"for",
"row",
"in",
"recommendations",
"[",
"1",
":",
"]",
":",
"anime_table",
"=",
"row",
".",
"find",
"(",
"u'table'",
")",
"animes",
"=",
"anime_table",
".",
"find_all",
"(",
"u'td'",
")",
"liked_media_link",
"=",
"animes",
"[",
"0",
"]",
".",
"find",
"(",
"u'a'",
",",
"recursive",
"=",
"False",
")",
"link_parts",
"=",
"liked_media_link",
".",
"get",
"(",
"u'href'",
")",
".",
"split",
"(",
"u'/'",
")",
"# of the form /anime|manga/64/Rozen_Maiden",
"liked_media",
"=",
"getattr",
"(",
"self",
".",
"session",
",",
"link_parts",
"[",
"1",
"]",
")",
"(",
"int",
"(",
"link_parts",
"[",
"2",
"]",
")",
")",
".",
"set",
"(",
"{",
"u'title'",
":",
"liked_media_link",
".",
"text",
"}",
")",
"recommended_media_link",
"=",
"animes",
"[",
"1",
"]",
".",
"find",
"(",
"u'a'",
",",
"recursive",
"=",
"False",
")",
"link_parts",
"=",
"recommended_media_link",
".",
"get",
"(",
"u'href'",
")",
".",
"split",
"(",
"u'/'",
")",
"# of the form /anime|manga/64/Rozen_Maiden",
"recommended_media",
"=",
"getattr",
"(",
"self",
".",
"session",
",",
"link_parts",
"[",
"1",
"]",
")",
"(",
"int",
"(",
"link_parts",
"[",
"2",
"]",
")",
")",
".",
"set",
"(",
"{",
"u'title'",
":",
"recommended_media_link",
".",
"text",
"}",
")",
"recommendation_text",
"=",
"row",
".",
"find",
"(",
"u'p'",
")",
".",
"text",
"recommendation_menu",
"=",
"row",
".",
"find",
"(",
"u'div'",
",",
"recursive",
"=",
"False",
")",
"utilities",
".",
"extract_tags",
"(",
"recommendation_menu",
")",
"recommendation_date",
"=",
"utilities",
".",
"parse_profile_date",
"(",
"recommendation_menu",
".",
"text",
".",
"split",
"(",
"u' - '",
")",
"[",
"1",
"]",
")",
"user_info",
"[",
"u'recommendations'",
"]",
"[",
"liked_media",
"]",
"=",
"{",
"link_parts",
"[",
"1",
"]",
":",
"recommended_media",
",",
"'text'",
":",
"recommendation_text",
",",
"'date'",
":",
"recommendation_date",
"}",
"except",
":",
"if",
"not",
"self",
".",
"session",
".",
"suppress_parse_exceptions",
":",
"raise",
"return",
"user_info"
] |
Copy a file or folder from local to s3 . | def cp ( self , local_path , target_path , acl = 'public-read' , del_after_upload = False , overwrite = True , invalidate = False ) : result = None if overwrite : list_of_files = [ ] else : list_of_files = self . ls ( folder = target_path , begin_from_file = "" , num = - 1 , get_grants = False , all_grant_data = False ) # copying the contents of the folder and not folder itself if local_path . endswith ( "/*" ) : local_path = local_path [ : - 2 ] target_path = re . sub ( r"^/|/$" , "" , target_path ) # Amazon S3 doesn't let the name to begin with / # copying folder too else : local_base_name = os . path . basename ( local_path ) local_path = re . sub ( r"/$" , "" , local_path ) target_path = re . sub ( r"^/" , "" , target_path ) if not target_path . endswith ( local_base_name ) : target_path = os . path . join ( target_path , local_base_name ) if os . path . exists ( local_path ) : result = self . __find_files_and_copy ( local_path , target_path , acl , del_after_upload , overwrite , invalidate , list_of_files ) else : result = { 'file_does_not_exist' : local_path } logger . error ( "trying to upload to s3 but file doesn't exist: %s" % local_path ) return result | 271 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L240-L336 | [
"def",
"stop_experiment",
"(",
"args",
")",
":",
"experiment_id_list",
"=",
"parse_ids",
"(",
"args",
")",
"if",
"experiment_id_list",
":",
"experiment_config",
"=",
"Experiments",
"(",
")",
"experiment_dict",
"=",
"experiment_config",
".",
"get_all_experiments",
"(",
")",
"for",
"experiment_id",
"in",
"experiment_id_list",
":",
"print_normal",
"(",
"'Stoping experiment %s'",
"%",
"experiment_id",
")",
"nni_config",
"=",
"Config",
"(",
"experiment_dict",
"[",
"experiment_id",
"]",
"[",
"'fileName'",
"]",
")",
"rest_port",
"=",
"nni_config",
".",
"get_config",
"(",
"'restServerPort'",
")",
"rest_pid",
"=",
"nni_config",
".",
"get_config",
"(",
"'restServerPid'",
")",
"if",
"rest_pid",
":",
"kill_command",
"(",
"rest_pid",
")",
"tensorboard_pid_list",
"=",
"nni_config",
".",
"get_config",
"(",
"'tensorboardPidList'",
")",
"if",
"tensorboard_pid_list",
":",
"for",
"tensorboard_pid",
"in",
"tensorboard_pid_list",
":",
"try",
":",
"kill_command",
"(",
"tensorboard_pid",
")",
"except",
"Exception",
"as",
"exception",
":",
"print_error",
"(",
"exception",
")",
"nni_config",
".",
"set_config",
"(",
"'tensorboardPidList'",
",",
"[",
"]",
")",
"print_normal",
"(",
"'Stop experiment success!'",
")",
"experiment_config",
".",
"update_experiment",
"(",
"experiment_id",
",",
"'status'",
",",
"'STOPPED'",
")",
"time_now",
"=",
"time",
".",
"strftime",
"(",
"'%Y-%m-%d %H:%M:%S'",
",",
"time",
".",
"localtime",
"(",
"time",
".",
"time",
"(",
")",
")",
")",
"experiment_config",
".",
"update_experiment",
"(",
"experiment_id",
",",
"'endTime'",
",",
"str",
"(",
"time_now",
")",
")"
] |
Similar to Linux mv command . | def mv ( self , local_file , target_file , acl = 'public-read' , overwrite = True , invalidate = False ) : self . cp ( local_file , target_file , acl = acl , del_after_upload = True , overwrite = overwrite , invalidate = invalidate ) | 272 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L483-L507 | [
"def",
"__json_strnum_to_bignum",
"(",
"json_object",
")",
":",
"for",
"key",
"in",
"(",
"'id'",
",",
"'week'",
",",
"'in_reply_to_id'",
",",
"'in_reply_to_account_id'",
",",
"'logins'",
",",
"'registrations'",
",",
"'statuses'",
")",
":",
"if",
"(",
"key",
"in",
"json_object",
"and",
"isinstance",
"(",
"json_object",
"[",
"key",
"]",
",",
"six",
".",
"text_type",
")",
")",
":",
"try",
":",
"json_object",
"[",
"key",
"]",
"=",
"int",
"(",
"json_object",
"[",
"key",
"]",
")",
"except",
"ValueError",
":",
"pass",
"return",
"json_object"
] |
Deal with saving cropduster images to S3 . Cropduster is a Django library for resizing editorial images . S3utils was originally written to put cropduster images on S3 bucket . | def cp_cropduster_image ( self , the_image_path , del_after_upload = False , overwrite = False , invalidate = False ) : local_file = os . path . join ( settings . MEDIA_ROOT , the_image_path ) # only try to upload things if the origin cropduster file exists (so it is not already uploaded to the CDN) if os . path . exists ( local_file ) : the_image_crops_path = os . path . splitext ( the_image_path ) [ 0 ] the_image_crops_path_full_path = os . path . join ( settings . MEDIA_ROOT , the_image_crops_path ) self . cp ( local_path = local_file , target_path = os . path . join ( settings . S3_ROOT_BASE , the_image_path ) , del_after_upload = del_after_upload , overwrite = overwrite , invalidate = invalidate , ) self . cp ( local_path = the_image_crops_path_full_path + "/*" , target_path = os . path . join ( settings . S3_ROOT_BASE , the_image_crops_path ) , del_after_upload = del_after_upload , overwrite = overwrite , invalidate = invalidate , ) | 273 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L510-L551 | [
"def",
"revert_timefactor",
"(",
"cls",
",",
"values",
")",
":",
"if",
"cls",
".",
"TIME",
"is",
"True",
":",
"return",
"values",
"/",
"cls",
".",
"get_timefactor",
"(",
")",
"if",
"cls",
".",
"TIME",
"is",
"False",
":",
"return",
"values",
"*",
"cls",
".",
"get_timefactor",
"(",
")",
"return",
"values"
] |
sets permissions for a file on S3 | def chmod ( self , target_file , acl = 'public-read' ) : self . k . key = target_file # setting the path (key) of file in the container self . k . set_acl ( acl ) # setting the file permissions self . k . close ( ) | 274 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L582-L610 | [
"def",
"group_experiments_greedy",
"(",
"tomo_expt",
":",
"TomographyExperiment",
")",
":",
"diag_sets",
"=",
"_max_tpb_overlap",
"(",
"tomo_expt",
")",
"grouped_expt_settings_list",
"=",
"list",
"(",
"diag_sets",
".",
"values",
"(",
")",
")",
"grouped_tomo_expt",
"=",
"TomographyExperiment",
"(",
"grouped_expt_settings_list",
",",
"program",
"=",
"tomo_expt",
".",
"program",
")",
"return",
"grouped_tomo_expt"
] |
Get the list of files and permissions from S3 . | def ll ( self , folder = "" , begin_from_file = "" , num = - 1 , all_grant_data = False ) : return self . ls ( folder = folder , begin_from_file = begin_from_file , num = num , get_grants = True , all_grant_data = all_grant_data ) | 275 | https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L669-L764 | [
"def",
"from_indexed_arrays",
"(",
"cls",
",",
"name",
",",
"verts",
",",
"normals",
")",
":",
"# Put header in string",
"wavefront_str",
"=",
"\"o {name}\\n\"",
".",
"format",
"(",
"name",
"=",
"name",
")",
"new_verts",
",",
"face_indices",
"=",
"face_index",
"(",
"verts",
")",
"assert",
"new_verts",
".",
"shape",
"[",
"1",
"]",
"==",
"3",
",",
"\"verts should be Nx3 array\"",
"assert",
"face_indices",
".",
"ndim",
"==",
"2",
"face_indices",
"=",
"fan_triangulate",
"(",
"face_indices",
")",
"# Write Vertex data from vert_dict",
"for",
"vert",
"in",
"new_verts",
":",
"wavefront_str",
"+=",
"\"v {0} {1} {2}\\n\"",
".",
"format",
"(",
"*",
"vert",
")",
"# Write (false) UV Texture data",
"wavefront_str",
"+=",
"\"vt 1.0 1.0\\n\"",
"for",
"norm",
"in",
"normals",
":",
"wavefront_str",
"+=",
"\"vn {0} {1} {2}\\n\"",
".",
"format",
"(",
"*",
"norm",
")",
"assert",
"len",
"(",
"face_indices",
")",
"==",
"len",
"(",
"normals",
")",
"*",
"2",
"for",
"norm_idx",
",",
"vert_idx",
",",
"in",
"enumerate",
"(",
"face_indices",
")",
":",
"wavefront_str",
"+=",
"\"f\"",
"for",
"vv",
"in",
"vert_idx",
":",
"wavefront_str",
"+=",
"\" {}/{}/{}\"",
".",
"format",
"(",
"vv",
"+",
"1",
",",
"1",
",",
"(",
"norm_idx",
"//",
"2",
")",
"+",
"1",
")",
"wavefront_str",
"+=",
"\"\\n\"",
"return",
"cls",
"(",
"string",
"=",
"wavefront_str",
")"
] |
Get the path from a given url including the querystring . | def get_path ( url ) : url = urlsplit ( url ) path = url . path if url . query : path += "?{}" . format ( url . query ) return path | 276 | https://github.com/uktrade/directory-signature-auth/blob/1a1b1e887b25a938133d7bcc146d3fecf1079313/sigauth/helpers.py#L79-L94 | [
"def",
"hasReaders",
"(",
"self",
",",
"ulBuffer",
")",
":",
"fn",
"=",
"self",
".",
"function_table",
".",
"hasReaders",
"result",
"=",
"fn",
"(",
"ulBuffer",
")",
"return",
"result"
] |
Reads data from disk and generates CSV files . | def run ( self ) : # Try to create the directory if not os . path . exists ( self . output ) : try : os . mkdir ( self . output ) except : print 'failed to create output directory %s' % self . output # Be sure it is a directory if not os . path . isdir ( self . output ) : print 'invalid output directory %s' % self . output sys . exit ( 1 ) # Create the CSV handlers visitors = [ _CompaniesCSV ( self . output ) , _ActivitiesCSV ( self . output ) , _ActivitiesSeenCSV ( self . output ) , _QSACSV ( self . output ) , ] # Run by each company populating the CSV files for path in glob . glob ( os . path . join ( self . input , '*.json' ) ) : with open ( path , 'r' ) as f : try : data = json . load ( f , encoding = 'utf-8' ) except ValueError : continue for visitor in visitors : visitor . visit ( data ) | 277 | https://github.com/vkruoso/receita-tools/blob/fd62a252c76541c9feac6470b9048b31348ffe86/receita/tools/build.py#L144-L175 | [
"def",
"get_queryset",
"(",
"self",
")",
":",
"return",
"Event",
".",
"objects",
".",
"filter",
"(",
"Q",
"(",
"startTime__gte",
"=",
"timezone",
".",
"now",
"(",
")",
"-",
"timedelta",
"(",
"days",
"=",
"90",
")",
")",
"&",
"(",
"Q",
"(",
"series__isnull",
"=",
"False",
")",
"|",
"Q",
"(",
"publicevent__isnull",
"=",
"False",
")",
")",
")",
".",
"annotate",
"(",
"count",
"=",
"Count",
"(",
"'eventregistration'",
")",
")",
".",
"annotate",
"(",
"*",
"*",
"self",
".",
"get_annotations",
"(",
")",
")",
".",
"exclude",
"(",
"Q",
"(",
"count",
"=",
"0",
")",
"&",
"Q",
"(",
"status__in",
"=",
"[",
"Event",
".",
"RegStatus",
".",
"hidden",
",",
"Event",
".",
"RegStatus",
".",
"regHidden",
",",
"Event",
".",
"RegStatus",
".",
"disabled",
"]",
")",
")"
] |
Process a list of simple string field definitions and assign their order based on prefix . | def process_fields ( self , fields ) : result = [ ] strip = '' . join ( self . PREFIX_MAP ) for field in fields : direction = self . PREFIX_MAP [ '' ] if field [ 0 ] in self . PREFIX_MAP : direction = self . PREFIX_MAP [ field [ 0 ] ] field = field . lstrip ( strip ) result . append ( ( field , direction ) ) return result | 278 | https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/index.py#L60-L75 | [
"def",
"start",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"not",
"self",
".",
"is_running",
"(",
")",
":",
"self",
".",
"websock_url",
"=",
"self",
".",
"chrome",
".",
"start",
"(",
"*",
"*",
"kwargs",
")",
"self",
".",
"websock",
"=",
"websocket",
".",
"WebSocketApp",
"(",
"self",
".",
"websock_url",
")",
"self",
".",
"websock_thread",
"=",
"WebsockReceiverThread",
"(",
"self",
".",
"websock",
",",
"name",
"=",
"'WebsockThread:%s'",
"%",
"self",
".",
"chrome",
".",
"port",
")",
"self",
".",
"websock_thread",
".",
"start",
"(",
")",
"self",
".",
"_wait_for",
"(",
"lambda",
":",
"self",
".",
"websock_thread",
".",
"is_open",
",",
"timeout",
"=",
"30",
")",
"# tell browser to send us messages we're interested in",
"self",
".",
"send_to_chrome",
"(",
"method",
"=",
"'Network.enable'",
")",
"self",
".",
"send_to_chrome",
"(",
"method",
"=",
"'Page.enable'",
")",
"self",
".",
"send_to_chrome",
"(",
"method",
"=",
"'Console.enable'",
")",
"self",
".",
"send_to_chrome",
"(",
"method",
"=",
"'Runtime.enable'",
")",
"self",
".",
"send_to_chrome",
"(",
"method",
"=",
"'ServiceWorker.enable'",
")",
"self",
".",
"send_to_chrome",
"(",
"method",
"=",
"'ServiceWorker.setForceUpdateOnPageLoad'",
")",
"# disable google analytics",
"self",
".",
"send_to_chrome",
"(",
"method",
"=",
"'Network.setBlockedURLs'",
",",
"params",
"=",
"{",
"'urls'",
":",
"[",
"'*google-analytics.com/analytics.js'",
",",
"'*google-analytics.com/ga.js'",
"]",
"}",
")"
] |
Firms search in rubric | def search_in_rubric ( self , * * kwargs ) : point = kwargs . pop ( 'point' , False ) if point : kwargs [ 'point' ] = '%s,%s' % point bound = kwargs . pop ( 'bound' , False ) if bound : kwargs [ 'bound[point1]' ] = bound [ 0 ] kwargs [ 'bound[point2]' ] = bound [ 1 ] filters = kwargs . pop ( 'filters' , False ) if filters : for k , v in filters . items ( ) : kwargs [ 'filters[%s]' % k ] = v return self . _search_in_rubric ( * * kwargs ) | 279 | https://github.com/svartalf/python-2gis/blob/6eccd6073c99494b7abf20b38a5455cbd55d6420/dgis/__init__.py#L89-L109 | [
"def",
"__write_to_character_device",
"(",
"self",
",",
"event_list",
",",
"timeval",
"=",
"None",
")",
":",
"# Remember the position of the stream",
"pos",
"=",
"self",
".",
"_character_device",
".",
"tell",
"(",
")",
"# Go to the end of the stream",
"self",
".",
"_character_device",
".",
"seek",
"(",
"0",
",",
"2",
")",
"# Write the new data to the end",
"for",
"event",
"in",
"event_list",
":",
"self",
".",
"_character_device",
".",
"write",
"(",
"event",
")",
"# Add a sync marker",
"sync",
"=",
"self",
".",
"create_event_object",
"(",
"\"Sync\"",
",",
"0",
",",
"0",
",",
"timeval",
")",
"self",
".",
"_character_device",
".",
"write",
"(",
"sync",
")",
"# Put the stream back to its original position",
"self",
".",
"_character_device",
".",
"seek",
"(",
"pos",
")"
] |
Refresh the list and the screen | def refresh ( self ) : self . _screen . force_update ( ) self . _screen . refresh ( ) self . _update ( 1 ) | 280 | https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L54-L60 | [
"def",
"import_file",
"(",
"filename",
")",
":",
"#file_path = os.path.relpath(filename)",
"file_path",
"=",
"os",
".",
"path",
".",
"abspath",
"(",
"filename",
")",
"log",
"(",
"DEBUG",
",",
"\"Loading prices from %s\"",
",",
"file_path",
")",
"prices",
"=",
"__read_prices_from_file",
"(",
"file_path",
")",
"with",
"BookAggregate",
"(",
"for_writing",
"=",
"True",
")",
"as",
"svc",
":",
"svc",
".",
"prices",
".",
"import_prices",
"(",
"prices",
")",
"print",
"(",
"\"Saving book...\"",
")",
"svc",
".",
"book",
".",
"save",
"(",
")"
] |
Mark an action as started | def start ( self , activity , action ) : try : self . _start_action ( activity , action ) except ValueError : retox_log . debug ( "Could not find action %s in env %s" % ( activity , self . name ) ) self . refresh ( ) | 281 | https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L233-L247 | [
"def",
"_read",
"(",
"self",
",",
"size",
")",
":",
"if",
"self",
".",
"comptype",
"==",
"\"tar\"",
":",
"return",
"self",
".",
"__read",
"(",
"size",
")",
"c",
"=",
"len",
"(",
"self",
".",
"dbuf",
")",
"while",
"c",
"<",
"size",
":",
"buf",
"=",
"self",
".",
"__read",
"(",
"self",
".",
"bufsize",
")",
"if",
"not",
"buf",
":",
"break",
"try",
":",
"buf",
"=",
"self",
".",
"cmp",
".",
"decompress",
"(",
"buf",
")",
"except",
"IOError",
":",
"raise",
"ReadError",
"(",
"\"invalid compressed data\"",
")",
"self",
".",
"dbuf",
"+=",
"buf",
"c",
"+=",
"len",
"(",
"buf",
")",
"buf",
"=",
"self",
".",
"dbuf",
"[",
":",
"size",
"]",
"self",
".",
"dbuf",
"=",
"self",
".",
"dbuf",
"[",
"size",
":",
"]",
"return",
"buf"
] |
Mark a task as completed | def stop ( self , activity , action ) : try : self . _remove_running_action ( activity , action ) except ValueError : retox_log . debug ( "Could not find action %s in env %s" % ( activity , self . name ) ) self . _mark_action_completed ( activity , action ) self . refresh ( ) | 282 | https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L249-L264 | [
"def",
"rate_limit",
"(",
"f",
")",
":",
"def",
"new_f",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"errors",
"=",
"0",
"while",
"True",
":",
"resp",
"=",
"f",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
"if",
"resp",
".",
"status_code",
"==",
"200",
":",
"errors",
"=",
"0",
"return",
"resp",
"elif",
"resp",
".",
"status_code",
"==",
"401",
":",
"# Hack to retain the original exception, but augment it with",
"# additional context for the user to interpret it. In a Python",
"# 3 only future we can raise a new exception of the same type",
"# with a new message from the old error.",
"try",
":",
"resp",
".",
"raise_for_status",
"(",
")",
"except",
"requests",
".",
"HTTPError",
"as",
"e",
":",
"message",
"=",
"\"\\nThis is a protected or locked account, or\"",
"+",
"\" the credentials provided are no longer valid.\"",
"e",
".",
"args",
"=",
"(",
"e",
".",
"args",
"[",
"0",
"]",
"+",
"message",
",",
")",
"+",
"e",
".",
"args",
"[",
"1",
":",
"]",
"log",
".",
"warning",
"(",
"\"401 Authentication required for %s\"",
",",
"resp",
".",
"url",
")",
"raise",
"elif",
"resp",
".",
"status_code",
"==",
"429",
":",
"reset",
"=",
"int",
"(",
"resp",
".",
"headers",
"[",
"'x-rate-limit-reset'",
"]",
")",
"now",
"=",
"time",
".",
"time",
"(",
")",
"seconds",
"=",
"reset",
"-",
"now",
"+",
"10",
"if",
"seconds",
"<",
"1",
":",
"seconds",
"=",
"10",
"log",
".",
"warning",
"(",
"\"rate limit exceeded: sleeping %s secs\"",
",",
"seconds",
")",
"time",
".",
"sleep",
"(",
"seconds",
")",
"elif",
"resp",
".",
"status_code",
">=",
"500",
":",
"errors",
"+=",
"1",
"if",
"errors",
">",
"30",
":",
"log",
".",
"warning",
"(",
"\"too many errors from Twitter, giving up\"",
")",
"resp",
".",
"raise_for_status",
"(",
")",
"seconds",
"=",
"60",
"*",
"errors",
"log",
".",
"warning",
"(",
"\"%s from Twitter API, sleeping %s\"",
",",
"resp",
".",
"status_code",
",",
"seconds",
")",
"time",
".",
"sleep",
"(",
"seconds",
")",
"else",
":",
"resp",
".",
"raise_for_status",
"(",
")",
"return",
"new_f"
] |
Move laggard tasks over | def finish ( self , status ) : retox_log . info ( "Completing %s with status %s" % ( self . name , status ) ) result = Screen . COLOUR_GREEN if not status else Screen . COLOUR_RED self . palette [ 'title' ] = ( Screen . COLOUR_WHITE , Screen . A_BOLD , result ) for item in list ( self . _task_view . options ) : self . _task_view . options . remove ( item ) self . _completed_view . options . append ( item ) self . refresh ( ) | 283 | https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L266-L279 | [
"def",
"_session_check",
"(",
"self",
")",
":",
"if",
"not",
"os",
".",
"path",
".",
"exists",
"(",
"SESSION_FILE",
")",
":",
"self",
".",
"_log",
".",
"debug",
"(",
"\"Session file does not exist\"",
")",
"return",
"False",
"with",
"open",
"(",
"SESSION_FILE",
",",
"'rb'",
")",
"as",
"f",
":",
"cookies",
"=",
"requests",
".",
"utils",
".",
"cookiejar_from_dict",
"(",
"pickle",
".",
"load",
"(",
"f",
")",
")",
"self",
".",
"_session",
".",
"cookies",
"=",
"cookies",
"self",
".",
"_log",
".",
"debug",
"(",
"\"Loaded cookies from session file\"",
")",
"response",
"=",
"self",
".",
"_session",
".",
"get",
"(",
"url",
"=",
"self",
".",
"TEST_URL",
",",
"headers",
"=",
"self",
".",
"HEADERS",
")",
"if",
"self",
".",
"TEST_KEY",
"in",
"str",
"(",
"response",
".",
"content",
")",
":",
"self",
".",
"_log",
".",
"debug",
"(",
"\"Session file appears invalid\"",
")",
"return",
"False",
"self",
".",
"_is_authenticated",
"=",
"True",
"self",
".",
"_process_state",
"(",
")",
"return",
"True"
] |
Reset the frame between jobs | def reset ( self ) : self . palette [ 'title' ] = ( Screen . COLOUR_WHITE , Screen . A_BOLD , Screen . COLOUR_BLUE ) self . _completed_view . options = [ ] self . _task_view . options = [ ] self . refresh ( ) | 284 | https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L281-L288 | [
"def",
"get_grid_district_polygon",
"(",
"config",
",",
"subst_id",
"=",
"None",
",",
"projection",
"=",
"4326",
")",
":",
"# make DB session",
"conn",
"=",
"connection",
"(",
"section",
"=",
"config",
"[",
"'db_connection'",
"]",
"[",
"'section'",
"]",
")",
"Session",
"=",
"sessionmaker",
"(",
"bind",
"=",
"conn",
")",
"session",
"=",
"Session",
"(",
")",
"# get polygon from versioned schema",
"if",
"config",
"[",
"'data_source'",
"]",
"[",
"'oedb_data_source'",
"]",
"==",
"'versioned'",
":",
"version",
"=",
"config",
"[",
"'versioned'",
"]",
"[",
"'version'",
"]",
"query",
"=",
"session",
".",
"query",
"(",
"EgoDpMvGriddistrict",
".",
"subst_id",
",",
"EgoDpMvGriddistrict",
".",
"geom",
")",
"Regions",
"=",
"[",
"(",
"subst_id",
",",
"shape",
".",
"to_shape",
"(",
"geom",
")",
")",
"for",
"subst_id",
",",
"geom",
"in",
"query",
".",
"filter",
"(",
"EgoDpMvGriddistrict",
".",
"version",
"==",
"version",
",",
"EgoDpMvGriddistrict",
".",
"subst_id",
"==",
"subst_id",
")",
".",
"all",
"(",
")",
"]",
"# get polygon from model_draft",
"else",
":",
"query",
"=",
"session",
".",
"query",
"(",
"EgoGridMvGriddistrict",
".",
"subst_id",
",",
"EgoGridMvGriddistrict",
".",
"geom",
")",
"Regions",
"=",
"[",
"(",
"subst_id",
",",
"shape",
".",
"to_shape",
"(",
"geom",
")",
")",
"for",
"subst_id",
",",
"geom",
"in",
"query",
".",
"filter",
"(",
"EgoGridMvGriddistrict",
".",
"subst_id",
".",
"in_",
"(",
"subst_id",
")",
")",
".",
"all",
"(",
")",
"]",
"crs",
"=",
"{",
"'init'",
":",
"'epsg:3035'",
"}",
"region",
"=",
"gpd",
".",
"GeoDataFrame",
"(",
"Regions",
",",
"columns",
"=",
"[",
"'subst_id'",
",",
"'geometry'",
"]",
",",
"crs",
"=",
"crs",
")",
"region",
"=",
"region",
".",
"to_crs",
"(",
"epsg",
"=",
"projection",
")",
"return",
"region"
] |
Returns the available kwargs of the called class | def default_arguments ( cls ) : func = cls . __init__ args = func . __code__ . co_varnames defaults = func . __defaults__ index = - len ( defaults ) return { k : v for k , v in zip ( args [ index : ] , defaults ) } | 285 | https://github.com/ryukinix/decorating/blob/df78c3f87800205701704c0bc0fb9b6bb908ba7e/decorating/decorator.py#L134-L140 | [
"def",
"_get_image_paths",
"(",
"im1",
",",
"im2",
")",
":",
"paths",
"=",
"[",
"]",
"for",
"im",
"in",
"[",
"im1",
",",
"im2",
"]",
":",
"if",
"im",
"is",
"None",
":",
"# Groupwise registration: only one image (ndim+1 dimensions)",
"paths",
".",
"append",
"(",
"paths",
"[",
"0",
"]",
")",
"continue",
"if",
"isinstance",
"(",
"im",
",",
"str",
")",
":",
"# Given a location",
"if",
"os",
".",
"path",
".",
"isfile",
"(",
"im1",
")",
":",
"paths",
".",
"append",
"(",
"im",
")",
"else",
":",
"raise",
"ValueError",
"(",
"'Image location does not exist.'",
")",
"elif",
"isinstance",
"(",
"im",
",",
"np",
".",
"ndarray",
")",
":",
"# Given a numpy array",
"id",
"=",
"len",
"(",
"paths",
")",
"+",
"1",
"p",
"=",
"_write_image_data",
"(",
"im",
",",
"id",
")",
"paths",
".",
"append",
"(",
"p",
")",
"else",
":",
"# Given something else ...",
"raise",
"ValueError",
"(",
"'Invalid input image.'",
")",
"# Done",
"return",
"tuple",
"(",
"paths",
")"
] |
Recreate the class based in your args multiple uses | def recreate ( cls , * args , * * kwargs ) : cls . check_arguments ( kwargs ) first_is_callable = True if any ( args ) and callable ( args [ 0 ] ) else False signature = cls . default_arguments ( ) allowed_arguments = { k : v for k , v in kwargs . items ( ) if k in signature } if ( any ( allowed_arguments ) or any ( args ) ) and not first_is_callable : if any ( args ) and not first_is_callable : return cls ( args [ 0 ] , * * allowed_arguments ) elif any ( allowed_arguments ) : return cls ( * * allowed_arguments ) return cls . instances [ - 1 ] if any ( cls . instances ) else cls ( ) | 286 | https://github.com/ryukinix/decorating/blob/df78c3f87800205701704c0bc0fb9b6bb908ba7e/decorating/decorator.py#L143-L155 | [
"def",
"_PrintProcessingTime",
"(",
"self",
",",
"processing_status",
")",
":",
"if",
"not",
"processing_status",
":",
"processing_time",
"=",
"'00:00:00'",
"else",
":",
"processing_time",
"=",
"time",
".",
"time",
"(",
")",
"-",
"processing_status",
".",
"start_time",
"time_struct",
"=",
"time",
".",
"gmtime",
"(",
"processing_time",
")",
"processing_time",
"=",
"time",
".",
"strftime",
"(",
"'%H:%M:%S'",
",",
"time_struct",
")",
"self",
".",
"_output_writer",
".",
"Write",
"(",
"'Processing time\\t\\t: {0:s}\\n'",
".",
"format",
"(",
"processing_time",
")",
")"
] |
Put warnings of arguments whose can t be handle by the class | def check_arguments ( cls , passed ) : defaults = list ( cls . default_arguments ( ) . keys ( ) ) template = ( "Pass arg {argument:!r} in {cname:!r}, can be a typo? " "Supported key arguments: {defaults}" ) fails = [ ] for arg in passed : if arg not in defaults : warn ( template . format ( argument = arg , cname = cls . __name__ , defaults = defaults ) ) fails . append ( arg ) return any ( fails ) | 287 | https://github.com/ryukinix/decorating/blob/df78c3f87800205701704c0bc0fb9b6bb908ba7e/decorating/decorator.py#L158-L171 | [
"def",
"queries",
"(",
"self",
",",
"request",
")",
":",
"queries",
"=",
"self",
".",
"get_queries",
"(",
"request",
")",
"worlds",
"=",
"[",
"]",
"with",
"self",
".",
"mapper",
".",
"begin",
"(",
")",
"as",
"session",
":",
"for",
"_",
"in",
"range",
"(",
"queries",
")",
":",
"world",
"=",
"session",
".",
"query",
"(",
"World",
")",
".",
"get",
"(",
"randint",
"(",
"1",
",",
"MAXINT",
")",
")",
"worlds",
".",
"append",
"(",
"self",
".",
"get_json",
"(",
"world",
")",
")",
"return",
"Json",
"(",
"worlds",
")",
".",
"http_response",
"(",
"request",
")"
] |
process the specified type then process its children | def process ( self , data , type , history ) : if type in history : return if type . enum ( ) : return history . append ( type ) resolved = type . resolve ( ) value = None if type . multi_occurrence ( ) : value = [ ] else : if len ( resolved ) > 0 : if resolved . mixed ( ) : value = Factory . property ( resolved . name ) md = value . __metadata__ md . sxtype = resolved else : value = Factory . object ( resolved . name ) md = value . __metadata__ md . sxtype = resolved md . ordering = self . ordering ( resolved ) setattr ( data , type . name , value ) if value is not None : data = value if not isinstance ( data , list ) : self . add_attributes ( data , resolved ) for child , ancestry in resolved . children ( ) : if self . skip_child ( child , ancestry ) : continue self . process ( data , child , history [ : ] ) | 288 | https://github.com/ovnicraft/suds2/blob/e5b540792206a41efc22f5d5b9cfac2dbe7a7992/suds/builder.py#L60-L90 | [
"def",
"gc_velocity_update",
"(",
"particle",
",",
"social",
",",
"state",
")",
":",
"gbest",
"=",
"state",
".",
"swarm",
"[",
"gbest_idx",
"(",
"state",
".",
"swarm",
")",
"]",
".",
"position",
"if",
"not",
"np",
".",
"array_equal",
"(",
"gbest",
",",
"particle",
".",
"position",
")",
":",
"return",
"std_velocity",
"(",
"particle",
",",
"social",
",",
"state",
")",
"rho",
"=",
"state",
".",
"params",
"[",
"'rho'",
"]",
"inertia",
"=",
"state",
".",
"params",
"[",
"'inertia'",
"]",
"v_max",
"=",
"state",
".",
"params",
"[",
"'v_max'",
"]",
"size",
"=",
"particle",
".",
"position",
".",
"size",
"r2",
"=",
"state",
".",
"rng",
".",
"uniform",
"(",
"0.0",
",",
"1.0",
",",
"size",
")",
"velocity",
"=",
"__gc_velocity_equation__",
"(",
"inertia",
",",
"rho",
",",
"r2",
",",
"particle",
",",
"gbest",
")",
"return",
"__clamp__",
"(",
"velocity",
",",
"v_max",
")"
] |
get whether or not to skip the specified child | def skip_child ( self , child , ancestry ) : if child . any ( ) : return True for x in ancestry : if x . choice ( ) : return True return False | 289 | https://github.com/ovnicraft/suds2/blob/e5b540792206a41efc22f5d5b9cfac2dbe7a7992/suds/builder.py#L99-L105 | [
"def",
"_load_cache",
"(",
"self",
")",
":",
"# If the cached file exist, read-it",
"max_refresh_date",
"=",
"timedelta",
"(",
"days",
"=",
"7",
")",
"cached_data",
"=",
"{",
"}",
"try",
":",
"with",
"open",
"(",
"self",
".",
"cache_file",
",",
"'rb'",
")",
"as",
"f",
":",
"cached_data",
"=",
"pickle",
".",
"load",
"(",
"f",
")",
"except",
"Exception",
"as",
"e",
":",
"logger",
".",
"debug",
"(",
"\"Cannot read version from cache file: {} ({})\"",
".",
"format",
"(",
"self",
".",
"cache_file",
",",
"e",
")",
")",
"else",
":",
"logger",
".",
"debug",
"(",
"\"Read version from cache file\"",
")",
"if",
"(",
"cached_data",
"[",
"'installed_version'",
"]",
"!=",
"self",
".",
"installed_version",
"(",
")",
"or",
"datetime",
".",
"now",
"(",
")",
"-",
"cached_data",
"[",
"'refresh_date'",
"]",
">",
"max_refresh_date",
")",
":",
"# Reset the cache if:",
"# - the installed version is different",
"# - the refresh_date is > max_refresh_date",
"cached_data",
"=",
"{",
"}",
"return",
"cached_data"
] |
Checks whether knocks are enabled for the model given as argument | def active_knocks ( obj ) : if not hasattr ( _thread_locals , 'knock_enabled' ) : return True return _thread_locals . knock_enabled . get ( obj . __class__ , True ) | 290 | https://github.com/nephila/django-knocker/blob/d25380d43a1f91285f1581dcf9db8510fe87f354/knocker/signals.py#L34-L43 | [
"def",
"_parse_array_bitmap",
"(",
"self",
",",
"block",
")",
":",
"array_bitmap_regexp",
"=",
"re",
".",
"compile",
"(",
"'^ *bitmap: (?P<allocated_pages>[0-9]*)/'",
"'(?P<total_pages>[0-9]*) pages '",
"'\\[(?P<page_size>[0-9]*)KB\\], '",
"'(?P<chunk_size>[0-9]*)KB chunk.*$'",
",",
"re",
".",
"MULTILINE",
")",
"regexp_res",
"=",
"array_bitmap_regexp",
".",
"search",
"(",
"block",
")",
"# bitmap is optionally in mdstat",
"if",
"not",
"regexp_res",
":",
"return",
"None",
"array_bitmap_dict",
"=",
"regexp_res",
".",
"groupdict",
"(",
")",
"array_bitmap_dict_sanitizied",
"=",
"{",
"}",
"# convert all values to int",
"for",
"key",
",",
"value",
"in",
"array_bitmap_dict",
".",
"iteritems",
"(",
")",
":",
"if",
"not",
"value",
":",
"continue",
"array_bitmap_dict_sanitizied",
"[",
"key",
"]",
"=",
"int",
"(",
"value",
")",
"# convert page_size to bytes",
"array_bitmap_dict_sanitizied",
"[",
"'page_size'",
"]",
"*=",
"1024",
"# convert chunk_size to bytes",
"array_bitmap_dict_sanitizied",
"[",
"'chunk_size'",
"]",
"*=",
"1024",
"return",
"array_bitmap_dict"
] |
Context manager to suspend sending knocks for the given model | def pause_knocks ( obj ) : if not hasattr ( _thread_locals , 'knock_enabled' ) : _thread_locals . knock_enabled = { } obj . __class__ . _disconnect ( ) _thread_locals . knock_enabled [ obj . __class__ ] = False yield _thread_locals . knock_enabled [ obj . __class__ ] = True obj . __class__ . _connect ( ) | 291 | https://github.com/nephila/django-knocker/blob/d25380d43a1f91285f1581dcf9db8510fe87f354/knocker/signals.py#L47-L59 | [
"def",
"stats",
"(",
"args",
")",
":",
"from",
"jcvi",
".",
"utils",
".",
"cbook",
"import",
"percentage",
"p",
"=",
"OptionParser",
"(",
"stats",
".",
"__doc__",
")",
"opts",
",",
"args",
"=",
"p",
".",
"parse_args",
"(",
"args",
")",
"if",
"len",
"(",
"args",
")",
"!=",
"1",
":",
"sys",
".",
"exit",
"(",
"not",
"p",
".",
"print_help",
"(",
")",
")",
"blocksfile",
",",
"=",
"args",
"fp",
"=",
"open",
"(",
"blocksfile",
")",
"counts",
"=",
"defaultdict",
"(",
"int",
")",
"total",
"=",
"orthologous",
"=",
"0",
"for",
"row",
"in",
"fp",
":",
"atoms",
"=",
"row",
".",
"rstrip",
"(",
")",
".",
"split",
"(",
"\"\\t\"",
")",
"hits",
"=",
"[",
"x",
"for",
"x",
"in",
"atoms",
"[",
"1",
":",
"]",
"if",
"x",
"!=",
"'.'",
"]",
"counts",
"[",
"len",
"(",
"hits",
")",
"]",
"+=",
"1",
"total",
"+=",
"1",
"if",
"atoms",
"[",
"1",
"]",
"!=",
"'.'",
":",
"orthologous",
"+=",
"1",
"print",
"(",
"\"Total lines: {0}\"",
".",
"format",
"(",
"total",
")",
",",
"file",
"=",
"sys",
".",
"stderr",
")",
"for",
"i",
",",
"n",
"in",
"sorted",
"(",
"counts",
".",
"items",
"(",
")",
")",
":",
"print",
"(",
"\"Count {0}: {1}\"",
".",
"format",
"(",
"i",
",",
"percentage",
"(",
"n",
",",
"total",
")",
")",
",",
"file",
"=",
"sys",
".",
"stderr",
")",
"print",
"(",
"file",
"=",
"sys",
".",
"stderr",
")",
"matches",
"=",
"sum",
"(",
"n",
"for",
"i",
",",
"n",
"in",
"counts",
".",
"items",
"(",
")",
"if",
"i",
"!=",
"0",
")",
"print",
"(",
"\"Total lines with matches: {0}\"",
".",
"format",
"(",
"percentage",
"(",
"matches",
",",
"total",
")",
")",
",",
"file",
"=",
"sys",
".",
"stderr",
")",
"for",
"i",
",",
"n",
"in",
"sorted",
"(",
"counts",
".",
"items",
"(",
")",
")",
":",
"if",
"i",
"==",
"0",
":",
"continue",
"print",
"(",
"\"Count {0}: {1}\"",
".",
"format",
"(",
"i",
",",
"percentage",
"(",
"n",
",",
"matches",
")",
")",
",",
"file",
"=",
"sys",
".",
"stderr",
")",
"print",
"(",
"file",
"=",
"sys",
".",
"stderr",
")",
"print",
"(",
"\"Orthologous matches: {0}\"",
".",
"format",
"(",
"percentage",
"(",
"orthologous",
",",
"matches",
")",
")",
",",
"file",
"=",
"sys",
".",
"stderr",
")"
] |
Loop over the report progress | def _loopreport ( self ) : while 1 : eventlet . sleep ( 0.2 ) ac2popenlist = { } for action in self . session . _actions : for popen in action . _popenlist : if popen . poll ( ) is None : lst = ac2popenlist . setdefault ( action . activity , [ ] ) lst . append ( popen ) if not action . _popenlist and action in self . _actionmayfinish : super ( RetoxReporter , self ) . logaction_finish ( action ) self . _actionmayfinish . remove ( action ) self . screen . draw_next_frame ( repeat = False ) | 292 | https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/reporter.py#L49-L65 | [
"def",
"union",
"(",
"self",
",",
"rdds",
")",
":",
"first_jrdd_deserializer",
"=",
"rdds",
"[",
"0",
"]",
".",
"_jrdd_deserializer",
"if",
"any",
"(",
"x",
".",
"_jrdd_deserializer",
"!=",
"first_jrdd_deserializer",
"for",
"x",
"in",
"rdds",
")",
":",
"rdds",
"=",
"[",
"x",
".",
"_reserialize",
"(",
")",
"for",
"x",
"in",
"rdds",
"]",
"cls",
"=",
"SparkContext",
".",
"_jvm",
".",
"org",
".",
"apache",
".",
"spark",
".",
"api",
".",
"java",
".",
"JavaRDD",
"jrdds",
"=",
"SparkContext",
".",
"_gateway",
".",
"new_array",
"(",
"cls",
",",
"len",
"(",
"rdds",
")",
")",
"for",
"i",
"in",
"range",
"(",
"0",
",",
"len",
"(",
"rdds",
")",
")",
":",
"jrdds",
"[",
"i",
"]",
"=",
"rdds",
"[",
"i",
"]",
".",
"_jrdd",
"return",
"RDD",
"(",
"self",
".",
"_jsc",
".",
"union",
"(",
"jrdds",
")",
",",
"self",
",",
"rdds",
"[",
"0",
"]",
".",
"_jrdd_deserializer",
")"
] |
Send markdown email | def send ( email , subject = None , from_email = None , to_email = None , cc = None , bcc = None , reply_to = None , smtp = None ) : if is_string ( email ) : email = EmailContent ( email ) from_email = sanitize_email_address ( from_email or email . headers . get ( 'from' ) ) to_email = sanitize_email_address ( to_email or email . headers . get ( 'to' ) ) cc = sanitize_email_address ( cc or email . headers . get ( 'cc' ) ) bcc = sanitize_email_address ( bcc or email . headers . get ( 'bcc' ) ) reply_to = sanitize_email_address ( reply_to or email . headers . get ( 'reply-to' ) ) message_args = { 'html' : email . html , 'text' : email . text , 'subject' : ( subject or email . headers . get ( 'subject' , '' ) ) , 'mail_from' : from_email , 'mail_to' : to_email } if cc : message_args [ 'cc' ] = cc if bcc : message_args [ 'bcc' ] = bcc if reply_to : message_args [ 'headers' ] = { 'reply-to' : reply_to } message = emails . Message ( * * message_args ) for filename , data in email . inline_images : message . attach ( filename = filename , content_disposition = 'inline' , data = data ) message . send ( smtp = smtp ) | 293 | https://github.com/yejianye/mdmail/blob/ef03da8d5836b5ae0a4ad8c44f2fe4936a896644/mdmail/api.py#L11-L63 | [
"def",
"set_size",
"(",
"self",
",",
"size",
",",
"surface_size",
")",
":",
"self",
".",
"size",
"=",
"size",
"self",
".",
"position",
"=",
"(",
"0",
",",
"surface_size",
"[",
"1",
"]",
"-",
"self",
".",
"size",
"[",
"1",
"]",
")",
"y",
"=",
"self",
".",
"position",
"[",
"1",
"]",
"+",
"self",
".",
"padding",
"max_length",
"=",
"self",
".",
"max_length",
"for",
"row",
"in",
"self",
".",
"rows",
":",
"r",
"=",
"len",
"(",
"row",
")",
"width",
"=",
"(",
"r",
"*",
"self",
".",
"key_size",
")",
"+",
"(",
"(",
"r",
"+",
"1",
")",
"*",
"self",
".",
"padding",
")",
"x",
"=",
"(",
"surface_size",
"[",
"0",
"]",
"-",
"width",
")",
"/",
"2",
"if",
"row",
".",
"space",
"is",
"not",
"None",
":",
"x",
"-=",
"(",
"(",
"row",
".",
"space",
".",
"length",
"-",
"1",
")",
"*",
"self",
".",
"key_size",
")",
"/",
"2",
"row",
".",
"set_size",
"(",
"(",
"x",
",",
"y",
")",
",",
"self",
".",
"key_size",
",",
"self",
".",
"padding",
")",
"y",
"+=",
"self",
".",
"padding",
"+",
"self",
".",
"key_size"
] |
Process timezone casting and conversion . | def _process_tz ( self , dt , naive , tz ) : def _tz ( t ) : if t in ( None , 'naive' ) : return t if t == 'local' : if __debug__ and not localtz : raise ValueError ( "Requested conversion to local timezone, but `localtz` not installed." ) t = localtz if not isinstance ( t , tzinfo ) : if __debug__ and not localtz : raise ValueError ( "The `pytz` package must be installed to look up timezone: " + repr ( t ) ) t = get_tz ( t ) if not hasattr ( t , 'normalize' ) and get_tz : # Attempt to handle non-pytz tzinfo. t = get_tz ( t . tzname ( dt ) ) return t naive = _tz ( naive ) tz = _tz ( tz ) if not dt . tzinfo and naive : if hasattr ( naive , 'localize' ) : dt = naive . localize ( dt ) else : dt = dt . replace ( tzinfo = naive ) if not tz : return dt if hasattr ( tz , 'normalize' ) : dt = tz . normalize ( dt . astimezone ( tz ) ) elif tz == 'naive' : dt = dt . replace ( tzinfo = None ) else : dt = dt . astimezone ( tz ) # Warning: this might not always be entirely correct! return dt | 294 | https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/field/date.py#L59-L102 | [
"def",
"get_context_data",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"context",
"=",
"super",
"(",
"SmartView",
",",
"self",
")",
".",
"get_context_data",
"(",
"*",
"*",
"kwargs",
")",
"# derive our field config",
"self",
".",
"field_config",
"=",
"self",
".",
"derive_field_config",
"(",
")",
"# add our fields",
"self",
".",
"fields",
"=",
"self",
".",
"derive_fields",
"(",
")",
"# build up our current parameter string, EXCLUSIVE of our page. These",
"# are used to build pagination URLs",
"url_params",
"=",
"\"?\"",
"order_params",
"=",
"\"\"",
"for",
"key",
"in",
"self",
".",
"request",
".",
"GET",
".",
"keys",
"(",
")",
":",
"if",
"key",
"!=",
"'page'",
"and",
"key",
"!=",
"'pjax'",
"and",
"(",
"len",
"(",
"key",
")",
"==",
"0",
"or",
"key",
"[",
"0",
"]",
"!=",
"'_'",
")",
":",
"for",
"value",
"in",
"self",
".",
"request",
".",
"GET",
".",
"getlist",
"(",
"key",
")",
":",
"url_params",
"+=",
"\"%s=%s&\"",
"%",
"(",
"key",
",",
"urlquote",
"(",
"value",
")",
")",
"elif",
"key",
"==",
"'_order'",
":",
"order_params",
"=",
"\"&\"",
".",
"join",
"(",
"[",
"\"%s=%s\"",
"%",
"(",
"key",
",",
"_",
")",
"for",
"_",
"in",
"self",
".",
"request",
".",
"GET",
".",
"getlist",
"(",
"key",
")",
"]",
")",
"context",
"[",
"'url_params'",
"]",
"=",
"url_params",
"context",
"[",
"'order_params'",
"]",
"=",
"order_params",
"+",
"\"&\"",
"context",
"[",
"'pjax'",
"]",
"=",
"self",
".",
"pjax",
"# set our blocks",
"context",
"[",
"'blocks'",
"]",
"=",
"dict",
"(",
")",
"# stuff it all in our context",
"context",
"[",
"'fields'",
"]",
"=",
"self",
".",
"fields",
"context",
"[",
"'view'",
"]",
"=",
"self",
"context",
"[",
"'field_config'",
"]",
"=",
"self",
".",
"field_config",
"context",
"[",
"'title'",
"]",
"=",
"self",
".",
"derive_title",
"(",
")",
"# and any extra context the user specified",
"context",
".",
"update",
"(",
"self",
".",
"extra_context",
")",
"# by default, our base is 'base.html', but we might be pjax",
"base_template",
"=",
"\"base.html\"",
"if",
"'pjax'",
"in",
"self",
".",
"request",
".",
"GET",
"or",
"'pjax'",
"in",
"self",
".",
"request",
".",
"POST",
":",
"base_template",
"=",
"\"smartmin/pjax.html\"",
"if",
"'HTTP_X_PJAX'",
"in",
"self",
".",
"request",
".",
"META",
":",
"base_template",
"=",
"\"smartmin/pjax.html\"",
"context",
"[",
"'base_template'",
"]",
"=",
"base_template",
"# set our refresh if we have one",
"refresh",
"=",
"self",
".",
"derive_refresh",
"(",
")",
"if",
"refresh",
":",
"context",
"[",
"'refresh'",
"]",
"=",
"refresh",
"return",
"context"
] |
Trigger assignment of default values . | def _prepare_defaults ( self ) : for name , field in self . __fields__ . items ( ) : if field . assign : getattr ( self , name ) | 295 | https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/document.py#L71-L76 | [
"def",
"trace_integration",
"(",
"tracer",
"=",
"None",
")",
":",
"log",
".",
"info",
"(",
"'Integrated module: {}'",
".",
"format",
"(",
"MODULE_NAME",
")",
")",
"# Wrap the httplib request function",
"request_func",
"=",
"getattr",
"(",
"httplib",
".",
"HTTPConnection",
",",
"HTTPLIB_REQUEST_FUNC",
")",
"wrapped_request",
"=",
"wrap_httplib_request",
"(",
"request_func",
")",
"setattr",
"(",
"httplib",
".",
"HTTPConnection",
",",
"request_func",
".",
"__name__",
",",
"wrapped_request",
")",
"# Wrap the httplib response function",
"response_func",
"=",
"getattr",
"(",
"httplib",
".",
"HTTPConnection",
",",
"HTTPLIB_RESPONSE_FUNC",
")",
"wrapped_response",
"=",
"wrap_httplib_response",
"(",
"response_func",
")",
"setattr",
"(",
"httplib",
".",
"HTTPConnection",
",",
"response_func",
".",
"__name__",
",",
"wrapped_response",
")"
] |
Convert data coming in from the MongoDB wire driver into a Document instance . | def from_mongo ( cls , doc ) : if doc is None : # To support simplified iterative use, None should return None. return None if isinstance ( doc , Document ) : # No need to perform processing on existing Document instances. return doc if cls . __type_store__ and cls . __type_store__ in doc : # Instantiate specific class mentioned in the data. cls = load ( doc [ cls . __type_store__ ] , 'marrow.mongo.document' ) # Prepare a new instance in such a way that changes to the instance will be reflected in the originating doc. instance = cls ( _prepare_defaults = False ) # Construct an instance, but delay default value processing. instance . __data__ = doc # I am Popeye of Borg (pattern); you will be askimilgrated. instance . _prepare_defaults ( ) # pylint:disable=protected-access -- deferred default value processing. return instance | 296 | https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/document.py#L81-L98 | [
"def",
"variance",
"(",
"self",
")",
":",
"alpha",
"=",
"self",
".",
"__success",
"+",
"self",
".",
"__default_alpha",
"beta",
"=",
"self",
".",
"__failure",
"+",
"self",
".",
"__default_beta",
"try",
":",
"variance",
"=",
"alpha",
"*",
"beta",
"/",
"(",
"(",
"alpha",
"+",
"beta",
")",
"**",
"2",
")",
"*",
"(",
"alpha",
"+",
"beta",
"+",
"1",
")",
"except",
"ZeroDivisionError",
":",
"variance",
"=",
"0.0",
"return",
"variance"
] |
Retrieve and remove a value from the backing store optionally with a default . | def pop ( self , name , default = SENTINEL ) : if default is SENTINEL : return self . __data__ . pop ( name ) return self . __data__ . pop ( name , default ) | 297 | https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/document.py#L246-L252 | [
"def",
"update_table",
"(",
"event",
")",
":",
"update_number",
"=",
"0",
"for",
"update",
"in",
"event",
".",
"get",
"(",
"'updates'",
",",
"[",
"]",
")",
":",
"header",
"=",
"\"======= Update #%s on %s =======\"",
"%",
"(",
"update_number",
",",
"utils",
".",
"clean_time",
"(",
"update",
".",
"get",
"(",
"'startDate'",
")",
")",
")",
"click",
".",
"secho",
"(",
"header",
",",
"fg",
"=",
"'green'",
")",
"update_number",
"=",
"update_number",
"+",
"1",
"text",
"=",
"update",
".",
"get",
"(",
"'contents'",
")",
"# deals with all the \\r\\n from the API",
"click",
".",
"secho",
"(",
"utils",
".",
"clean_splitlines",
"(",
"text",
")",
")"
] |
A basic operation operating on a single value . | def _op ( self , operation , other , * allowed ) : f = self . _field if self . _combining : # We are a field-compound query fragment, e.g. (Foo.bar & Foo.baz). return reduce ( self . _combining , ( q . _op ( operation , other , * allowed ) for q in f ) ) # pylint:disable=protected-access # Optimize this away in production; diagnosic aide. if __debug__ and _complex_safety_check ( f , { operation } | set ( allowed ) ) : # pragma: no cover raise NotImplementedError ( "{self!r} does not allow {op} comparison." . format ( self = self , op = operation ) ) if other is not None : other = f . transformer . foreign ( other , ( f , self . _document ) ) return Filter ( { self . _name : { operation : other } } ) | 298 | https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/query/query.py#L154-L170 | [
"def",
"create",
"(",
"cls",
",",
"destination",
")",
":",
"mdb_gz_b64",
"=",
"\"\"\"\\\n H4sICIenn1gC/25ldzIwMDMubWRiAO2de2wcRx3Hf7O7Pt/d3u6eLyEtVaOaqg+EkjQvuVVDwa9a\n jWXHdZxQQlCJ7fOrfp3OTpqkhVxTItFWIhVQVFBRVNIKRaColVpAUKGKRwwFqUAhKiBIpUaoVWP+\n qKgIIHL8Znb39u72znWJiWP3+9l473fzm/nNY3cdf2fmbBJEPdO9E+nebLq+fWC6vrWZOImen9D7\n 9sR+vPPNE0PZxo/TE5879mj+yNc3/OzAD2bXv3DmV9/o/8PZnxxr+/fDL2w79ulzN7e+/sS/zvzz\n w3+N1z28p3PTfQ3nfn/m2YmeFS2no89uWnvqwO5HUvd/5Phr938tes3j/zm5+qT41J8/P/iZx87/\n +qHrjgyduubG1t/+7eWB2XztTNuT+1clZt9c2/e7HRGizevWEwAAAAAAAACAhUEIwvE+PoRIO8K7\n FzT6obPPwTMBAAAAAAAAAABcfpzPXwya+Ispo1xlEO2KEEX9eaGyWnrqyKQ60tQ0AcNZRcR1RYuy\n +XZCxoqRzmaMI6cKGRJuJVrIEZUOQ9UrHStUYpyzKkdNmSPFDkM6aguhXMdVHCMuHXE2Suu4IFQJ\n l6CErNWUDouDlbdKOZIcrKLD4S5WdNhqIEodqlVaofKgVTHpiBQ6uLG0uaKsuYbf3IS8BmV1qFAm\n j1Z5Hbp06GWDKC+DTS00SRN8DFA/TXNfW6mXX3upj7+mOHWllzLAObN8du0gdSdlKO3ZcWqjMbaH\n uOQqtidViRF+P0HbOH2c3xm0lfMb1EH7uHZ5vp32c+ks+5PqfSeXS9NejjTAvZQpd7J3kuuJFqLE\n qYvuVa3Ocqk7OVXWNMFxZPRVtJ1zSXuCBrlkh+rjEF1Zlt5Dw6qN0xx5Bx3gGgbowVo56EIjkc9T\n xX9Jdd+5PKDOD6q3VQvwv7qiZ8st419cdYHlo6iuriF8X4HA590AsodXhvrsj0yMDPnAuI+ZvOrq\n 1o7K51Hdy7a8cdXNm5AedbfG5W3j3lOybxFZKb6zAgAAAAAAsNzQxAlbvnYJV3VcUU3/S2luBIKF\n ha+IlWp+wxW4IiRXRSXxKeNU1eOxUuUbSOIINbEM7WT506ZE3LASgCOeYJWCMcnCsI/u8eSsFEYR\n lnlbWa6+u0jTYqSkvuQL9G5CLFwTRBMAAAAAAAAAgMtW/79lyVdLKxW7oqDF3bXOniib0UD/m/xq\n loWqvFwt3DX/mrLNALIu3V35NkpK1JDmL+2XOmr9pf1gKiFY4I672wc0mveaf6zaenyKmljPT6t5\n hT7a6y13y0XqjFpwneJjRC0oRwvL3eUL2fHCcuyGIntjhTkDuZCd5Vc5j+HNUMyx+myYcpHW5YG5\n ZijUdbg2VFu4ZzzcHFM3seQLAAAAAAAAAMtc//9S6cm1emX97ytK1v81rHelhtfVfAFnseZXRdV9\n Ad7+dhGS5kbl3eqe/K8pU/nnYwX5X2VeoLbCZwHi7txD6aTELabnoLJ5AfPFC8JmFd3Pun+MlfM4\n q/846/4s62i5+8Dmc7EvSVN0UG2tL00p1uPXqZTt/G5QqX+5lbufz+mSctVzFce6upBrTG3Fd+cn\n pmiYrUyw8+GNfL4hn8/k83qZrVlyGzgPeqbhjcOqx7KMEZRpU/MPQ+rsldEtuYm8vExkznoMS+6b\n KC5TZRt8wVf4xEkFX4V5D/X2vYz1/EcR8yMAAAAAAACAJY0Qf/d3vLPUlb//b4Nzzv6W3Wevtl+1\n vmxts2LWTxOHErcm3jGfMUfNG0yMGQAAAAAAeJ/8rLwAMXIYRgCARFv8IIaYtKpGqCdqlN/2kupD\n /ob67qXhsi0lDh2Vp6728faO9tHuUflfWJ1wE0e6724f35XuG71r16Dr0FwH573by6rKi0N7RveN\n tnd6aTVBWrpjd3fnuJtsBMnDk90ju7zckSA5XGGtdGrK2dWhUnRcMgAAAAAAAAD4v2CIV6vqf82I\n Jusbcwsy7wkWSf/n1JQNq/Oc+uQGq/ecmsphYZ6Tn6XwRLjwxb7mTxDoakLgURUFshwAAAAAAAAA\n ljpCrHZ8W/f2/2NUAAAAAAAAAAAAhXH5RLm4IIbotqot7hbW/0MGWCp46/+pgpHwjZS3IyAlfMPy\n tgakNN+wfcPxNgukdN9I+kadt30gZfhGjW+s8I2V3s6CVNTbWZCK+Eatb3zAN1Z5mw5SMd+I+wZ+\n +QQAAAAAAAAA/K8IcdT27Zqi3/+HkQEAAAAAAAAAsGgkMQQLjSHqbQPDAAAAAAAAAAAALGuw/g8A\n AAAAAAAA4DJUqwsQI7cQDWlcLiMq1/9rcGMBAAAAAAAAAADLGuh/AAAAAAAAAAAA+h8AAAAAAAAA\n AABLHyHusDTPjtLzTtoxnRftUftqe8YatDA+AAAAAAAAAPDeqJN/KVt+et0R9PYnzz7W8PrZRv+V\n HblO6qEDNEXbaYDGqJemaYQmaYJThtnK8Gvzb1opfDRTPZmUlxUY86qgm/ZyFVkOOqCC3kLhoyEI\n qs8raBO10O0q3EYKH+uDcNq8wnVRH93D7evnYZhHG5kkB3a0OYO2ctCWV9ZR+FhT0l2HCzl6xVBz\n XZyPUvi4taTjcwRuVUF7uYW9HMy9MJspfGwMAoo5A+5Qwca8UHN2WogeU/fu0ito1vmjM+M85zzp\n fNG5zxl2djrNzk3O9+0m+yWrx2q0fpH4buJ4Yk3ig4lvmkfxx9gBAAAAAAC4OAylQfJ5h5pfSVCc\n f853gqSmWPSZux6xjUznltH2HT/flNu7++0NZ7/07cg/vnPbVu30y6d/NLvlabPh+j81v/Xc5g9l\n 1h2f+epn9+VPdN90OHHvU50fm94y/ZXvWQ/tP/yJG/NH3llz8A79tlNPG72DHSePHdzz2s3XPzVj\n vzSUvSHjVys1Rv5CSUv8pEvcEqkbV/KX35JaQ+npikmRS9o4rtYIt8RYnJa4Ou6SV6stTm+l7rcX\n q9qSy+23pCVIcgV/SZKuJj5CSRc4Y/PpkiesLJcI53J37NvFuQzv4peGL0/SypP+C+45xVAAMAEA\n \"\"\"",
"pristine",
"=",
"StringIO",
"(",
")",
"pristine",
".",
"write",
"(",
"base64",
".",
"b64decode",
"(",
"mdb_gz_b64",
")",
")",
"pristine",
".",
"seek",
"(",
"0",
")",
"pristine",
"=",
"gzip",
".",
"GzipFile",
"(",
"fileobj",
"=",
"pristine",
",",
"mode",
"=",
"'rb'",
")",
"with",
"open",
"(",
"destination",
",",
"'wb'",
")",
"as",
"handle",
":",
"shutil",
".",
"copyfileobj",
"(",
"pristine",
",",
"handle",
")",
"return",
"cls",
"(",
"destination",
")"
] |
An iterative operation operating on multiple values . Consumes iterators to construct a concrete list at time of execution . | def _iop ( self , operation , other , * allowed ) : f = self . _field if self . _combining : # We are a field-compound query fragment, e.g. (Foo.bar & Foo.baz). return reduce ( self . _combining , ( q . _iop ( operation , other , * allowed ) for q in f ) ) # pylint:disable=protected-access # Optimize this away in production; diagnosic aide. if __debug__ and _complex_safety_check ( f , { operation } | set ( allowed ) ) : # pragma: no cover raise NotImplementedError ( "{self!r} does not allow {op} comparison." . format ( self = self , op = operation ) ) def _t ( o ) : for value in o : yield None if value is None else f . transformer . foreign ( value , ( f , self . _document ) ) other = other if len ( other ) > 1 else other [ 0 ] values = list ( _t ( other ) ) return Filter ( { self . _name : { operation : values } } ) | 299 | https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/query/query.py#L172-L196 | [
"def",
"reset_flags",
"(",
"self",
")",
":",
"self",
".",
"C",
"=",
"None",
"self",
".",
"Z",
"=",
"None",
"self",
".",
"P",
"=",
"None",
"self",
".",
"S",
"=",
"None"
] |