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removes the parent of a child | def avl_release_parent ( node ) : parent = node . parent if parent is not None : if parent . right is node : parent . right = None elif parent . left is node : parent . left = None else : raise AssertionError ( 'impossible state' ) node . parent = None parent . balance = max ( height ( parent . right ) , height ( parent . left ) ) + 1 return node , parent | 9,201 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/experimental/euler_tour_tree_avl.py#L517-L531 | [
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Joins two trees t1 and t1 with an intermediate key - value pair | def avl_join ( t1 , t2 , node ) : if DEBUG_JOIN : print ( '-- JOIN node=%r' % ( node , ) ) if t1 is None and t2 is None : if DEBUG_JOIN : print ( 'Join Case 1' ) top = node elif t1 is None : # FIXME keep track of count if possible if DEBUG_JOIN : print ( 'Join Case 2' ) top = avl_insert_dir ( t2 , node , 0 ) elif t2 is None : if DEBUG_JOIN : print ( 'Join Case 3' ) top = avl_insert_dir ( t1 , node , 1 ) else : h1 = height ( t1 ) h2 = height ( t2 ) if h1 > h2 + 1 : if DEBUG_JOIN : print ( 'Join Case 4' ) top = avl_join_dir_recursive ( t1 , t2 , node , 1 ) if DEBUG_JOIN : ascii_tree ( t1 , 'top' ) elif h2 > h1 + 1 : if DEBUG_JOIN : print ( 'Join Case 5' ) ascii_tree ( t1 ) ascii_tree ( t2 ) top = avl_join_dir_recursive ( t1 , t2 , node , 0 ) if DEBUG_JOIN : ascii_tree ( top ) else : if DEBUG_JOIN : print ( 'Join Case 6' ) # Insert at the top of the tree top = avl_new_top ( t1 , t2 , node , 0 ) return top | 9,202 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/experimental/euler_tour_tree_avl.py#L667-L746 | [
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Removes the maximum element from the tree | def avl_split_last ( root ) : if root is None : raise IndexError ( 'Empty tree has no maximum element' ) root , left , right = avl_release_kids ( root ) if right is None : new_root , last_node = left , root else : new_right , last_node = avl_split_last ( right ) new_root = avl_join ( left , new_right , root ) return ( new_root , last_node ) | 9,203 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/experimental/euler_tour_tree_avl.py#L749-L766 | [
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Removes the minimum element from the tree | def avl_split_first ( root ) : if root is None : raise IndexError ( 'Empty tree has no maximum element' ) root , left , right = avl_release_kids ( root ) if left is None : new_root , first_node = right , root else : new_left , first_node = avl_split_first ( left ) new_root = avl_join ( new_left , right , root ) return ( new_root , first_node ) | 9,204 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/experimental/euler_tour_tree_avl.py#L769-L786 | [
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join two trees without any intermediate key | def avl_join2 ( t1 , t2 ) : if t1 is None and t2 is None : new_root = None elif t2 is None : new_root = t1 elif t1 is None : new_root = t2 else : new_left , last_node = avl_split_last ( t1 ) debug = 0 if debug : EulerTourTree ( root = new_left ) . _assert_nodes ( 'new_left' ) EulerTourTree ( root = last_node ) . _assert_nodes ( 'last_node' ) EulerTourTree ( root = t2 ) . _assert_nodes ( 't2' ) print ( 'new_left' ) EulerTourTree ( root = new_left ) . print_tree ( ) print ( 'last_node' ) EulerTourTree ( root = last_node ) . print_tree ( ) print ( 't2' ) EulerTourTree ( root = t2 ) . print_tree ( ) new_root = avl_join ( new_left , t2 , last_node ) if debug : print ( 'new_root' ) EulerTourTree ( root = new_root ) . print_tree ( ) EulerTourTree ( root = last_node ) . _assert_nodes ( 'new_root' ) return new_root | 9,205 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/experimental/euler_tour_tree_avl.py#L789-L831 | [
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Loops through peptides stores sequences mapped to PSM ids . | def create_merge_psm_map ( peptides , ns ) : psmmap = { } for peptide in peptides : seq = reader . get_peptide_seq ( peptide , ns ) psm_ids = reader . get_psm_ids_from_peptide ( peptide , ns ) for psm_id in psm_ids : try : psmmap [ seq ] [ psm_id . text ] = 1 except KeyError : psmmap [ seq ] = { psm_id . text : 2 } for seq , psm_id_dict in psmmap . items ( ) : psmmap [ seq ] = [ x for x in psm_id_dict ] return psmmap | 9,209 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/actions/pycolator/splitmerge.py#L8-L21 | [
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Create a connection pool . | def create_pool_b ( dsn = None , * , min_size = 10 , max_size = 10 , max_queries = 50000 , max_inactive_connection_lifetime = 300.0 , setup = None , init = None , loop = None , connection_class = BuildPgConnection , * * connect_kwargs , ) : return BuildPgPool ( dsn , connection_class = connection_class , min_size = min_size , max_size = max_size , max_queries = max_queries , loop = loop , setup = setup , init = init , max_inactive_connection_lifetime = max_inactive_connection_lifetime , * * connect_kwargs , ) | 9,210 | https://github.com/samuelcolvin/buildpg/blob/33cccff45279834d02ec7e97d8417da8fd2a875d/buildpg/asyncpg.py#L85-L119 | [
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Adds a runnable component to the list of runnable components in this simulation . | def add_runnable ( self , runnable ) : if runnable . id in self . runnables : raise SimError ( 'Duplicate runnable component {0}' . format ( runnable . id ) ) self . runnables [ runnable . id ] = runnable | 9,211 | https://github.com/LEMS/pylems/blob/4eeb719d2f23650fe16c38626663b69b5c83818b/lems/sim/sim.py#L37-L49 | [
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Name of the controller file to be created | def controller_creatr ( filename ) : if not check ( ) : click . echo ( Fore . RED + 'ERROR: Ensure you are in a bast app to run the create:controller command' ) return path = os . path . abspath ( '.' ) + '/controller' if not os . path . exists ( path ) : os . makedirs ( path ) # if os.path.isfile(path + ) file_name = str ( filename + '.py' ) if os . path . isfile ( path + "/" + file_name ) : click . echo ( Fore . WHITE + Back . RED + "ERROR: Controller file exists" ) return controller_file = open ( os . path . abspath ( '.' ) + '/controller/' + file_name , 'w+' ) compose = "from bast import Controller\n\nclass " + filename + "(Controller):\n pass" controller_file . write ( compose ) controller_file . close ( ) click . echo ( Fore . GREEN + "Controller " + filename + " created successfully" ) | 9,213 | https://github.com/moluwole/Bast/blob/eecf55ae72e6f24af7c101549be0422cd2c1c95a/bast/cli.py#L41-L61 | [
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Name of the View File to be created | def view_creatr ( filename ) : if not check ( ) : click . echo ( Fore . RED + 'ERROR: Ensure you are in a bast app to run the create:view command' ) return path = os . path . abspath ( '.' ) + '/public/templates' if not os . path . exists ( path ) : os . makedirs ( path ) filename_ = str ( filename + ".html" ) . lower ( ) view_file = open ( path + "/" + filename_ , 'w+' ) view_file . write ( "" ) view_file . close ( ) click . echo ( Fore . GREEN + "View file " + filename_ + "created in public/template folder" ) | 9,214 | https://github.com/moluwole/Bast/blob/eecf55ae72e6f24af7c101549be0422cd2c1c95a/bast/cli.py#L85-L99 | [
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Name of the migration file | def migration_creatr ( migration_file , create , table ) : if not check ( ) : click . echo ( Fore . RED + 'ERROR: Ensure you are in a bast app to run the create:migration command' ) return migration = CreateMigration ( ) if table is None : table = snake_case ( migration_file ) file = migration . create_file ( snake_case ( migration_file ) , table = table , create = create ) click . echo ( Fore . GREEN + 'Migration file created at %s' % file ) | 9,215 | https://github.com/moluwole/Bast/blob/eecf55ae72e6f24af7c101549be0422cd2c1c95a/bast/cli.py#L175-L185 | [
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Quit socket server | def quit ( self ) : logging . info ( "quiting sock server" ) if self . __quit is not None : self . __quit . set ( ) self . join ( ) return | 9,216 | https://github.com/mbunse/socket_client_server/blob/8e884925cf887d386554c1859f626d8f01bd0036/socket_client_server/socket_client_server.py#L146-L154 | [
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Searches for quantification columns using pattern and header list . Calls reader function to do regexp . Returns a single column for precursor quant . | def get_quantcols ( pattern , oldheader , coltype ) : if pattern is None : return False if coltype == 'precur' : return reader . get_cols_in_file ( pattern , oldheader , single_col = True ) | 9,217 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/actions/peptable/psmtopeptable.py#L10-L17 | [
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Parses lists of quantdata and returns maxvalue from them . Strips NA | def get_peptide_quant ( quantdata , quanttype ) : parsefnx = { 'precur' : max } quantfloats = [ ] for q in quantdata : try : quantfloats . append ( float ( q ) ) except ( TypeError , ValueError ) : pass if not quantfloats : return 'NA' return str ( parsefnx [ quanttype ] ( quantfloats ) ) | 9,218 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/actions/peptable/psmtopeptable.py#L50-L61 | [
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reads csv in unicode | def read_csv ( fpath ) : import csv import utool as ut #csvfile = open(fpath, 'rb') with open ( fpath , 'rb' ) as csvfile : row_iter = csv . reader ( csvfile , delimiter = str ( ',' ) , quotechar = str ( '|' ) ) row_list = [ ut . lmap ( ut . ensure_unicode , row ) for row in row_iter ] return row_list | 9,219 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_csv.py#L151-L159 | [
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Standalone version of get_caller_name | def get_caller_name ( N = 0 , strict = True ) : if isinstance ( N , ( list , tuple ) ) : name_list = [ ] for N_ in N : try : name_list . append ( get_caller_name ( N_ ) ) except AssertionError : name_list . append ( 'X' ) return '[' + '][' . join ( name_list ) + ']' # <get_parent_frame> parent_frame = get_stack_frame ( N = N + 2 , strict = strict ) # </get_parent_frame> caller_name = parent_frame . f_code . co_name if caller_name == '<module>' : co_filename = parent_frame . f_code . co_filename caller_name = splitext ( split ( co_filename ) [ 1 ] ) [ 0 ] if caller_name == '__init__' : co_filename = parent_frame . f_code . co_filename caller_name = basename ( dirname ( co_filename ) ) + '.' + caller_name return caller_name | 9,220 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/_internal/meta_util_dbg.py#L27-L47 | [
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Responds to pings from registry_client only if the node_ids present in the ping payload are registered | def _handle_ping ( self , packet , protocol ) : if 'payload' in packet : is_valid_node = True node_ids = list ( packet [ 'payload' ] . values ( ) ) for node_id in node_ids : if self . _repository . get_node ( node_id ) is None : is_valid_node = False break if is_valid_node : self . _pong ( packet , protocol ) else : self . _pong ( packet , protocol ) | 9,221 | https://github.com/quikmile/trellio/blob/e8b050077562acf32805fcbb9c0c162248a23c62/trellio/registry.py#L379-L395 | [
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Merge all psms and peptides | def set_features ( self ) : allpsms_str = readers . generate_psms_multiple_fractions_strings ( self . mergefiles , self . ns ) allpeps = preparation . merge_peptides ( self . mergefiles , self . ns ) self . features = { 'psm' : allpsms_str , 'peptide' : allpeps } | 9,222 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/drivers/pycolator/splitmerge.py#L94-L99 | [
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r squashes wip messages | def git_sequence_editor_squash ( fpath ) : # print(sys.argv) import utool as ut text = ut . read_from ( fpath ) # print('fpath = %r' % (fpath,)) print ( text ) # Doesnt work because of fixed witdth requirement # search = (ut.util_regex.positive_lookbehind('[a-z]* [a-z0-9]* wip\n') + 'pick ' + # ut.reponamed_field('hash', '[a-z0-9]*') + ' wip') # repl = ('squash ' + ut.bref_field('hash') + ' wip') # import re # new_text = re.sub(search, repl, text, flags=re.MULTILINE) # print(new_text) prev_msg = None prev_dt = None new_lines = [ ] def get_commit_date ( hashid ) : out , err , ret = ut . cmd ( 'git show -s --format=%ci ' + hashid , verbose = False , quiet = True , pad_stdout = False ) # from datetime import datetime from dateutil import parser # print('out = %r' % (out,)) stamp = out . strip ( '\n' ) # print('stamp = %r' % (stamp,)) dt = parser . parse ( stamp ) # dt = datetime.strptime(stamp, '%Y-%m-%d %H:%M:%S %Z') # print('dt = %r' % (dt,)) return dt for line in text . split ( '\n' ) : commit_line = line . split ( ' ' ) if len ( commit_line ) < 3 : prev_msg = None prev_dt = None new_lines += [ line ] continue action = commit_line [ 0 ] hashid = commit_line [ 1 ] msg = ' ' . join ( commit_line [ 2 : ] ) try : dt = get_commit_date ( hashid ) except ValueError : prev_msg = None prev_dt = None new_lines += [ line ] continue orig_msg = msg can_squash = action == 'pick' and msg == 'wip' and prev_msg == 'wip' if prev_dt is not None and prev_msg == 'wip' : tdelta = dt - prev_dt # Only squash closely consecutive commits threshold_minutes = 45 td_min = ( tdelta . total_seconds ( ) / 60. ) # print(tdelta) can_squash &= td_min < threshold_minutes msg = msg + ' -- tdelta=%r' % ( ut . get_timedelta_str ( tdelta ) , ) if can_squash : new_line = ' ' . join ( [ 'squash' , hashid , msg ] ) new_lines += [ new_line ] else : new_lines += [ line ] prev_msg = orig_msg prev_dt = dt new_text = '\n' . join ( new_lines ) def get_commit_date ( hashid ) : out = ut . cmd ( 'git show -s --format=%ci ' + hashid , verbose = False ) print ( 'out = %r' % ( out , ) ) # print('Dry run') # ut.dump_autogen_code(fpath, new_text) print ( new_text ) ut . write_to ( fpath , new_text , n = None ) | 9,223 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_git.py#L876-L1016 | [
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DEPRICATE My standard build script names . | def std_build_command ( repo = '.' ) : import utool as ut print ( '+**** stdbuild *******' ) print ( 'repo = %r' % ( repo , ) ) if sys . platform . startswith ( 'win32' ) : # vtool --rebuild-sver didnt work with this line #scriptname = './mingw_build.bat' scriptname = 'mingw_build.bat' else : scriptname = './unix_build.sh' if repo == '' : # default to cwd repo = '.' else : os . chdir ( repo ) ut . assert_exists ( scriptname ) normbuild_flag = '--no-rmbuild' if ut . get_argflag ( normbuild_flag ) : scriptname += ' ' + normbuild_flag # Execute build ut . cmd ( scriptname ) #os.system(scriptname) print ( 'L**** stdbuild *******' ) | 9,224 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_git.py#L1019-L1047 | [
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Wait until connection state is no longer IMPORT_CONFIGURATION . | def wait_for_import ( self , connection_id , wait_interval ) : self . stdout . write ( self . style . NOTICE ( 'Waiting for import' ) , ending = '' ) state = utils . ConnectionStates . IMPORT_CONFIGURATION while state == utils . ConnectionStates . IMPORT_CONFIGURATION : # before you get the first state, the API can be a bit behind self . stdout . write ( self . style . NOTICE ( '.' ) , ending = '' ) time . sleep ( wait_interval ) # take a breath try : connection = utils . get_connection ( connection_id ) except requests . HTTPError as e : raise CommandError ( "Failed to fetch connection information." ) from e else : state = connection [ 'state' ] self . stdout . write ( self . style . NOTICE ( ' Done!' ) ) | 9,225 | https://github.com/Thermondo/django-heroku-connect/blob/f390e0fbf256ee79b30bb88f9a8c9576c6c8d9b5/heroku_connect/management/commands/import_mappings.py#L76-L100 | [
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Method runs the plugin | def setup ( self ) : if self . dry_run is not True : self . client = self . _get_client ( ) self . _disable_access_key ( ) | 9,226 | https://github.com/ThreatResponse/aws_ir_plugins/blob/b5128ef5cbd91fc0b5d55615f1c14cb036ae7c73/aws_ir_plugins/disableaccess_key.py#L29-L33 | [
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Returns whether this plugin does what it claims to have done | def validate ( self ) : try : response = self . client . get_access_key_last_used ( AccessKeyId = self . access_key_id ) username = response [ 'UserName' ] access_keys = self . client . list_access_keys ( UserName = username ) for key in access_keys [ 'AccessKeyMetadata' ] : if ( key [ 'AccessKeyId' ] == self . access_key_id ) and ( key [ 'Status' ] == 'Inactive' ) : return True return False except Exception as e : logger . info ( "Failed to validate key disable for " "key {id} due to: {e}." . format ( e = e , id = self . access_key_id ) ) return False | 9,227 | https://github.com/ThreatResponse/aws_ir_plugins/blob/b5128ef5cbd91fc0b5d55615f1c14cb036ae7c73/aws_ir_plugins/disableaccess_key.py#L35-L61 | [
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This function first checks to see if the key is already disabled \ | def _disable_access_key ( self , force_disable_self = False ) : client = self . client if self . validate is True : return else : try : client . update_access_key ( UserName = self . _search_user_for_key ( ) , AccessKeyId = self . access_key_id , Status = 'Inactive' ) logger . info ( "Access key {id} has " "been disabled." . format ( id = self . access_key_id ) ) except Exception as e : logger . info ( "Access key {id} could not " "be disabled due to: {e}." . format ( e = e , id = self . access_key_id ) ) | 9,228 | https://github.com/ThreatResponse/aws_ir_plugins/blob/b5128ef5cbd91fc0b5d55615f1c14cb036ae7c73/aws_ir_plugins/disableaccess_key.py#L90-L115 | [
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Fed with a psms generator this returns the master proteins present in the PSM table . PSMs with multiple master proteins are excluded . | def generate_master_proteins ( psms , protcol ) : master_proteins = { } if not protcol : protcol = mzidtsvdata . HEADER_MASTER_PROT for psm in psms : protacc = psm [ protcol ] if ';' in protacc : continue master_proteins [ protacc ] = 1 if 'NA' in master_proteins : master_proteins . pop ( 'NA' ) if '' in master_proteins : master_proteins . pop ( '' ) for protacc in master_proteins : yield { prottabledata . HEADER_PROTEIN : protacc } | 9,229 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/actions/prottable/create_empty.py#L5-L21 | [
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Runs through a peptide table and adds quant data from ANOTHER peptide table that contains that data . | def add_isoquant_data ( peptides , quantpeptides , quantacc , quantfields ) : for peptide in base_add_isoquant_data ( peptides , quantpeptides , peptabledata . HEADER_PEPTIDE , quantacc , quantfields ) : yield peptide | 9,251 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/actions/peptable/isoquant.py#L5-L11 | [
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Run a map function across all y points in the series | def map ( self , fn ) : return TimeSeries ( [ ( x , fn ( y ) ) for x , y in self . points ] ) | 9,252 | https://github.com/chriso/gauged/blob/cda3bba2f3e92ce2fb4aa92132dcc0e689bf7976/gauged/results/time_series.py#L43-L45 | [
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Fetches proteins and quants from joined lookup table loops through them and when all of a protein s quants have been collected yields the protein quant information . | def build_proteintable ( pqdb , headerfields , mergecutoff , isobaric = False , precursor = False , probability = False , fdr = False , pep = False , genecentric = False ) : pdmap = create_featuredata_map ( pqdb , genecentric = genecentric , psm_fill_fun = pinfo . add_psms_to_proteindata , pgene_fill_fun = pinfo . add_protgene_to_protdata , count_fun = pinfo . count_peps_psms , get_uniques = True ) empty_return = lambda x , y , z : { } iso_fun = { True : get_isobaric_quant , False : empty_return } [ isobaric ] ms1_fun = { True : get_precursor_quant , False : empty_return } [ precursor ] prob_fun = { True : get_prot_probability , False : empty_return } [ probability ] fdr_fun = { True : get_prot_fdr , False : empty_return } [ fdr ] pep_fun = { True : get_prot_pep , False : empty_return } [ pep ] pdata_fun = { True : get_protein_data_genecentric , False : get_protein_data } [ genecentric is not False ] protein_sql , sqlfieldmap = pqdb . prepare_mergetable_sql ( precursor , isobaric , probability , fdr , pep ) accession_field = prottabledata . ACCESSIONS [ genecentric ] proteins = pqdb . get_merged_features ( protein_sql ) protein = next ( proteins ) outprotein = { accession_field : protein [ sqlfieldmap [ 'p_acc' ] ] } check_prot = { k : v for k , v in outprotein . items ( ) } if not mergecutoff or protein_pool_fdr_cutoff ( protein , sqlfieldmap , mergecutoff ) : fill_mergefeature ( outprotein , iso_fun , ms1_fun , prob_fun , fdr_fun , pep_fun , pdata_fun , protein , sqlfieldmap , headerfields , pdmap , accession_field ) for protein in proteins : if mergecutoff and not protein_pool_fdr_cutoff ( protein , sqlfieldmap , mergecutoff ) : continue p_acc = protein [ sqlfieldmap [ 'p_acc' ] ] if p_acc != outprotein [ accession_field ] : # check if protein has been filled, otherwise do not output # sometimes proteins have NA in all fields if outprotein != check_prot : yield outprotein outprotein = { accession_field : p_acc } check_prot = { k : v for k , v in outprotein . items ( ) } fill_mergefeature ( outprotein , iso_fun , ms1_fun , prob_fun , fdr_fun , pep_fun , pdata_fun , protein , sqlfieldmap , headerfields , pdmap , accession_field ) if outprotein != check_prot : yield outprotein | 9,253 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/actions/prottable/merge.py#L9-L60 | [
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Takes a list of protein accessions and a list of protein groups content from DB . Counts for each group in list how many proteins are found in lineproteins . Returns list of str amounts . | def count_protein_group_hits ( lineproteins , groups ) : hits = [ ] for group in groups : hits . append ( 0 ) for protein in lineproteins : if protein in group : hits [ - 1 ] += 1 return [ str ( x ) for x in hits ] | 9,254 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/actions/mzidtsv/proteingrouping.py#L57-L68 | [
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The default log dir is in the system resource directory But the utool global cache allows for the user to override where the logs for a specific app should be stored . | def get_logging_dir ( appname = 'default' ) : from utool . _internal import meta_util_cache from utool . _internal import meta_util_cplat from utool import util_cache if appname is None or appname == 'default' : appname = util_cache . get_default_appname ( ) resource_dpath = meta_util_cplat . get_resource_dir ( ) default = join ( resource_dpath , appname , 'logs' ) # Check global cache for a custom logging dir otherwise # use the default. log_dir = meta_util_cache . global_cache_read ( logdir_cacheid , appname = appname , default = default ) log_dir_realpath = realpath ( log_dir ) return log_dir_realpath | 9,255 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_logging.py#L186-L208 | [
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mostly for util_logging internals | def add_logging_handler ( handler , format_ = 'file' ) : global __UTOOL_ROOT_LOGGER__ if __UTOOL_ROOT_LOGGER__ is None : builtins . print ( '[WARNING] logger not started, cannot add handler' ) return # create formatter and add it to the handlers #logformat = '%Y-%m-%d %H:%M:%S' #logformat = '%(asctime)s - %(name)s - %(levelname)s - %(message)s' timeformat = '%H:%M:%S' if format_ == 'file' : logformat = '[%(asctime)s]%(message)s' elif format_ == 'stdout' : logformat = '%(message)s' else : raise AssertionError ( 'unknown logging format_: %r' % format_ ) # Create formatter for handlers formatter = logging . Formatter ( logformat , timeformat ) handler . setLevel ( logging . DEBUG ) handler . setFormatter ( formatter ) __UTOOL_ROOT_LOGGER__ . addHandler ( handler ) | 9,256 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_logging.py#L280-L302 | [
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r Overwrites utool print functions to use a logger | def start_logging ( log_fpath = None , mode = 'a' , appname = 'default' , log_dir = None ) : global __UTOOL_ROOT_LOGGER__ global __UTOOL_PRINT__ global __UTOOL_WRITE__ global __UTOOL_FLUSH__ global __CURRENT_LOG_FPATH__ if LOGGING_VERBOSE : print ( '[utool] start_logging()' ) # FIXME: The test for doctest may not work if __UTOOL_ROOT_LOGGER__ is None and __IN_MAIN_PROCESS__ and not __inside_doctest ( ) : if LOGGING_VERBOSE : print ( '[utool] start_logging()... rootcheck OK' ) #logging.config.dictConfig(LOGGING) if log_fpath is None : log_fpath = get_log_fpath ( num = 'next' , appname = appname , log_dir = log_dir ) __CURRENT_LOG_FPATH__ = log_fpath # Print what is about to happen if VERBOSE or LOGGING_VERBOSE : startmsg = ( 'logging to log_fpath=%r' % log_fpath ) _utool_print ( ) ( startmsg ) # Create root logger __UTOOL_ROOT_LOGGER__ = logging . getLogger ( 'root' ) __UTOOL_ROOT_LOGGER__ . setLevel ( 'DEBUG' ) # create file handler which logs even debug messages #fh = logging.handlers.WatchedFileHandler(log_fpath) logfile_handler = logging . FileHandler ( log_fpath , mode = mode ) #stdout_handler = logging.StreamHandler(__UTOOL_STDOUT__) stdout_handler = CustomStreamHandler ( __UTOOL_STDOUT__ ) stdout_handler . terminator = '' # http://stackoverflow.com/questions/7168790/suppress-newline-in-python-logging-module #stdout_handler.terminator = '' add_logging_handler ( logfile_handler , format_ = 'file' ) add_logging_handler ( stdout_handler , format_ = 'stdout' ) __UTOOL_ROOT_LOGGER__ . propagate = False __UTOOL_ROOT_LOGGER__ . setLevel ( logging . DEBUG ) # Overwrite utool functions with the logging functions def utool_flush ( * args ) : """ flushes whatever is in the current utool write buffer """ # Flushes only the stdout handler stdout_handler . flush ( ) #__UTOOL_ROOT_LOGGER__.flush() #global __UTOOL_WRITE_BUFFER__ #if len(__UTOOL_WRITE_BUFFER__) > 0: # msg = ''.join(__UTOOL_WRITE_BUFFER__) # #sys.stdout.write('FLUSHING %r\n' % (len(__UTOOL_WRITE_BUFFER__))) # __UTOOL_WRITE_BUFFER__ = [] # return __UTOOL_ROOT_LOGGER__.info(msg) #__PYTHON_FLUSH__() def utool_write ( * args ) : """ writes to current utool logs and to sys.stdout.write """ #global __UTOOL_WRITE_BUFFER__ #sys.stdout.write('WRITEING\n') msg = ', ' . join ( map ( six . text_type , args ) ) #__UTOOL_WRITE_BUFFER__.append(msg) __UTOOL_ROOT_LOGGER__ . info ( msg ) #if msg.endswith('\n'): # # Flush on newline, and remove newline # __UTOOL_WRITE_BUFFER__[-1] = __UTOOL_WRITE_BUFFER__[-1][:-1] # utool_flush() #elif len(__UTOOL_WRITE_BUFFER__) > 32: # # Flush if buffer is too large # utool_flush() if not PRINT_ALL_CALLERS : def utool_print ( * args ) : """ standard utool print function """ #sys.stdout.write('PRINT\n') endline = '\n' try : msg = ', ' . join ( map ( six . text_type , args ) ) return __UTOOL_ROOT_LOGGER__ . info ( msg + endline ) except UnicodeDecodeError : new_msg = ', ' . join ( map ( meta_util_six . ensure_unicode , args ) ) #print(new_msg) return __UTOOL_ROOT_LOGGER__ . info ( new_msg + endline ) else : def utool_print ( * args ) : """ debugging utool print function """ import utool as ut utool_flush ( ) endline = '\n' __UTOOL_ROOT_LOGGER__ . info ( '\n\n----------' ) __UTOOL_ROOT_LOGGER__ . info ( ut . get_caller_name ( range ( 0 , 20 ) ) ) return __UTOOL_ROOT_LOGGER__ . info ( ', ' . join ( map ( six . text_type , args ) ) + endline ) def utool_printdbg ( * args ) : """ DRPRICATE standard utool print debug function """ return __UTOOL_ROOT_LOGGER__ . debug ( ', ' . join ( map ( six . text_type , args ) ) ) # overwrite the utool printers __UTOOL_WRITE__ = utool_write __UTOOL_FLUSH__ = utool_flush __UTOOL_PRINT__ = utool_print # Test out our shiney new logger if VERBOSE or LOGGING_VERBOSE : __UTOOL_PRINT__ ( '<__LOG_START__>' ) __UTOOL_PRINT__ ( startmsg ) else : if LOGGING_VERBOSE : print ( '[utool] start_logging()... FAILED TO START' ) print ( 'DEBUG INFO' ) print ( '__inside_doctest() = %r' % ( __inside_doctest ( ) , ) ) print ( '__IN_MAIN_PROCESS__ = %r' % ( __IN_MAIN_PROCESS__ , ) ) print ( '__UTOOL_ROOT_LOGGER__ = %r' % ( __UTOOL_ROOT_LOGGER__ , ) ) | 9,257 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_logging.py#L375-L520 | [
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Restores utool print functions to python defaults | def stop_logging ( ) : global __UTOOL_ROOT_LOGGER__ global __UTOOL_PRINT__ global __UTOOL_WRITE__ global __UTOOL_FLUSH__ if __UTOOL_ROOT_LOGGER__ is not None : # Flush remaining buffer if VERBOSE or LOGGING_VERBOSE : _utool_print ( ) ( ) ( '<__LOG_STOP__>' ) _utool_flush ( ) ( ) # Remove handlers for h in __UTOOL_ROOT_LOGGER__ . handlers [ : ] : __UTOOL_ROOT_LOGGER__ . removeHandler ( h ) # Reset objects __UTOOL_ROOT_LOGGER__ = None __UTOOL_PRINT__ = None __UTOOL_WRITE__ = None __UTOOL_FLUSH__ = None | 9,258 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_logging.py#L523-L543 | [
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r Recursively removes target in all lists and sublists and replaces them with the repl variable | def recursive_replace ( list_ , target , repl = - 1 ) : repl_list = [ recursive_replace ( item , target , repl ) if isinstance ( item , ( list , np . ndarray ) ) else ( repl if item == target else item ) for item in list_ ] return repl_list | 9,260 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L116-L126 | [
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performs only one call to the underlying func with unique rowids the func must be some lookup function | def unflat_unique_rowid_map ( func , unflat_rowids , * * kwargs ) : import utool as ut # First flatten the list, and remember the original dimensions flat_rowids , reverse_list = ut . invertible_flatten2 ( unflat_rowids ) # Then make the input unique flat_rowids_arr = np . array ( flat_rowids ) unique_flat_rowids , inverse_unique = np . unique ( flat_rowids_arr , return_inverse = True ) # Then preform the lookup / implicit mapping unique_flat_vals = func ( unique_flat_rowids , * * kwargs ) # Then broadcast unique values back to original flat positions flat_vals_ = np . array ( unique_flat_vals ) [ inverse_unique ] #flat_vals_ = np.array(unique_flat_vals).take(inverse_unique, axis=0) output_shape = tuple ( list ( flat_rowids_arr . shape ) + list ( flat_vals_ . shape [ 1 : ] ) ) flat_vals = np . array ( flat_vals_ ) . reshape ( output_shape ) # Then _unflatten the results to the original input dimensions unflat_vals = ut . unflatten2 ( flat_vals , reverse_list ) return unflat_vals | 9,266 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L728-L796 | [
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checks to see if list is equal everywhere | def allsame ( list_ , strict = True ) : if len ( list_ ) == 0 : return True first_item = list_ [ 0 ] return list_all_eq_to ( list_ , first_item , strict ) | 9,267 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L832-L845 | [
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Returns each item in item_list where not flag in flag_list | def get_dirty_items ( item_list , flag_list ) : assert len ( item_list ) == len ( flag_list ) dirty_items = [ item for ( item , flag ) in zip ( item_list , flag_list ) if not flag ] #print('num_dirty_items = %r' % len(dirty_items)) #print('item_list = %r' % (item_list,)) #print('flag_list = %r' % (flag_list,)) return dirty_items | 9,269 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L877-L895 | [
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Map like function | def scalar_input_map ( func , input_ ) : if util_iter . isiterable ( input_ ) : return list ( map ( func , input_ ) ) else : return func ( input_ ) | 9,287 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2061-L2076 | [
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a bit messy | def partial_imap_1to1 ( func , si_func ) : @ functools . wraps ( si_func ) def wrapper ( input_ ) : if not util_iter . isiterable ( input_ ) : return func ( si_func ( input_ ) ) else : return list ( map ( func , si_func ( input_ ) ) ) set_funcname ( wrapper , util_str . get_callable_name ( func ) + '_mapper_' + get_funcname ( si_func ) ) return wrapper | 9,288 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2079-L2091 | [
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Helper for sampling | def sample_zip ( items_list , num_samples , allow_overflow = False , per_bin = 1 ) : # Prealloc a list of lists samples_list = [ [ ] for _ in range ( num_samples ) ] # Sample the ix-th value from every list samples_iter = zip_longest ( * items_list ) sx = 0 for ix , samples_ in zip ( range ( num_samples ) , samples_iter ) : samples = filter_Nones ( samples_ ) samples_list [ sx ] . extend ( samples ) # Put per_bin from each sublist into a sample if ( ix + 1 ) % per_bin == 0 : sx += 1 # Check for overflow if allow_overflow : overflow_samples = flatten ( [ filter_Nones ( samples_ ) for samples_ in samples_iter ] ) return samples_list , overflow_samples else : try : samples_iter . next ( ) except StopIteration : pass else : raise AssertionError ( 'Overflow occured' ) return samples_list | 9,289 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2094-L2152 | [
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Determines if a list is sorted | def issorted ( list_ , op = operator . le ) : return all ( op ( list_ [ ix ] , list_ [ ix + 1 ] ) for ix in range ( len ( list_ ) - 1 ) ) | 9,290 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2213-L2224 | [
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Returns the deepest level of nesting within a list of lists | def list_depth ( list_ , func = max , _depth = 0 ) : depth_list = [ list_depth ( item , func = func , _depth = _depth + 1 ) for item in list_ if util_type . is_listlike ( item ) ] if len ( depth_list ) > 0 : return func ( depth_list ) else : return _depth | 9,291 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2434-L2456 | [
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Find the nesting depth of a nested sequence | def depth ( sequence , func = max , _depth = 0 ) : if isinstance ( sequence , dict ) : sequence = list ( sequence . values ( ) ) depth_list = [ depth ( item , func = func , _depth = _depth + 1 ) for item in sequence if ( isinstance ( item , dict ) or util_type . is_listlike ( item ) ) ] if len ( depth_list ) > 0 : return func ( depth_list ) else : return _depth | 9,292 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2459-L2470 | [
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Returns all types in a deep list | def list_deep_types ( list_ ) : type_list = [ ] for item in list_ : if util_type . is_listlike ( item ) : type_list . extend ( list_deep_types ( item ) ) else : type_list . append ( type ( item ) ) return type_list | 9,293 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2473-L2483 | [
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r Returns a nested list corresponding the shape of the nested structures lists represent depth tuples represent shape . The values of the items do not matter . only the lengths . | def depth_profile ( list_ , max_depth = None , compress_homogenous = True , compress_consecutive = False , new_depth = False ) : if isinstance ( list_ , dict ) : list_ = list ( list_ . values ( ) ) # handle dict level_shape_list = [ ] # For a pure bottom level list return the length if not any ( map ( util_type . is_listlike , list_ ) ) : return len ( list_ ) if False and new_depth : pass # max_depth_ = None if max_depth is None else max_depth - 1 # if max_depth_ is None or max_depth_ > 0: # pass # else: # for item in list_: # if isinstance(item, dict): # item = list(item.values()) # handle dict # if util_type.is_listlike(item): # if max_depth is None: # level_shape_list.append(depth_profile(item, None)) # else: # if max_depth >= 0: # level_shape_list.append(depth_profile(item, max_depth - 1)) # else: # level_shape_list.append(str(len(item))) # else: # level_shape_list.append(1) else : for item in list_ : if isinstance ( item , dict ) : item = list ( item . values ( ) ) # handle dict if util_type . is_listlike ( item ) : if max_depth is None : level_shape_list . append ( depth_profile ( item , None ) ) else : if max_depth >= 0 : level_shape_list . append ( depth_profile ( item , max_depth - 1 ) ) else : level_shape_list . append ( str ( len ( item ) ) ) else : level_shape_list . append ( 1 ) if compress_homogenous : # removes redudant information by returning a shape duple if allsame ( level_shape_list ) : dim_ = level_shape_list [ 0 ] len_ = len ( level_shape_list ) if isinstance ( dim_ , tuple ) : level_shape_list = tuple ( [ len_ ] + list ( dim_ ) ) else : level_shape_list = tuple ( [ len_ , dim_ ] ) if compress_consecutive : hash_list = list ( map ( hash , map ( str , level_shape_list ) ) ) consec_list = group_consecutives ( hash_list , 0 ) if len ( consec_list ) != len ( level_shape_list ) : len_list = list ( map ( len , consec_list ) ) cumsum_list = np . cumsum ( len_list ) consec_str = '[' thresh = 1 for len_ , cumsum in zip ( len_list , cumsum_list ) : value = level_shape_list [ cumsum - 1 ] if len_ > thresh : consec_str += str ( value ) + '] * ' + str ( len_ ) consec_str += ' + [' else : consec_str += str ( value ) + ', ' if consec_str . endswith ( ', ' ) : consec_str = consec_str [ : - 2 ] #consec_str += ']' #consec_str = consec_str.rstrip(', ').rstrip(']') #consec_str = consec_str.rstrip(', ') #if consec_str.endswith(']'): # consec_str = consec_str[:-1] consec_str += ']' level_shape_list = consec_str return level_shape_list | 9,294 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2486-L2665 | [
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r returns boolean for each position in list1 if it is in list2 | def list_cover ( list1 , list2 ) : set2 = set ( list2 ) incover_list = [ item1 in set2 for item1 in list1 ] return incover_list | 9,295 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L2846-L2875 | [
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Assumes list items are unique | def list_alignment ( list1 , list2 , missing = False ) : import utool as ut item1_to_idx = make_index_lookup ( list1 ) if missing : sortx = ut . dict_take ( item1_to_idx , list2 , None ) else : sortx = ut . take ( item1_to_idx , list2 ) return sortx | 9,296 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L3008-L3052 | [
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Remove items from list_ at positions specified in index_list The original list_ is preserved if copy is True | def delete_items_by_index ( list_ , index_list , copy = False ) : if copy : list_ = list_ [ : ] # Rectify negative indicies index_list_ = [ ( len ( list_ ) + x if x < 0 else x ) for x in index_list ] # Remove largest indicies first index_list_ = sorted ( index_list_ , reverse = True ) for index in index_list_ : del list_ [ index ] return list_ | 9,298 | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_list.py#L3128-L3155 | [
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