id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1 value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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242,500 | tanghaibao/goatools | goatools/gosubdag/plot/go_name_shorten.py | ShortenText.get_short_plot_name | def get_short_plot_name(self, goobj):
"""Shorten some GO names so plots are smaller."""
name = goobj.name
if self._keep_this(name):
return self.replace_greek(name)
name = name.replace("cellular response to chemical stimulus",
"cellular rsp. to chemical stim.")
depth = goobj.depth
if depth > 1:
name = name.replace("regulation of ", "reg. of ")
name = name.replace("positive reg", "+reg")
name = name.replace("negative reg", "-reg")
name = name.replace("involved in", "in")
if depth > 2:
name = name.replace("antigen processing and presentation", "a.p.p")
name = name.replace("MHC class I", "MHC-I")
if depth == 4:
if goobj.id == "GO:0002460":
before = " ".join([
"adaptive immune response based on somatic recombination of",
"immune receptors built from immunoglobulin superfamily domains"])
name = name.replace(
before,
"rsp. based on somatic recombination of Ig immune receptors")
if depth > 3:
name = name.replace("signaling pathway", "sig. pw.")
name = name.replace("response", "rsp.")
name = name.replace("immunoglobulin superfamily domains", "Ig domains")
name = name.replace("immunoglobulin", "Ig")
if depth > 4:
name = name.replace("production", "prod.")
if depth == 6 or depth == 5:
name = name.replace("tumor necrosis factor", "TNF")
name = self.replace_greek(name)
return name | python | def get_short_plot_name(self, goobj):
name = goobj.name
if self._keep_this(name):
return self.replace_greek(name)
name = name.replace("cellular response to chemical stimulus",
"cellular rsp. to chemical stim.")
depth = goobj.depth
if depth > 1:
name = name.replace("regulation of ", "reg. of ")
name = name.replace("positive reg", "+reg")
name = name.replace("negative reg", "-reg")
name = name.replace("involved in", "in")
if depth > 2:
name = name.replace("antigen processing and presentation", "a.p.p")
name = name.replace("MHC class I", "MHC-I")
if depth == 4:
if goobj.id == "GO:0002460":
before = " ".join([
"adaptive immune response based on somatic recombination of",
"immune receptors built from immunoglobulin superfamily domains"])
name = name.replace(
before,
"rsp. based on somatic recombination of Ig immune receptors")
if depth > 3:
name = name.replace("signaling pathway", "sig. pw.")
name = name.replace("response", "rsp.")
name = name.replace("immunoglobulin superfamily domains", "Ig domains")
name = name.replace("immunoglobulin", "Ig")
if depth > 4:
name = name.replace("production", "prod.")
if depth == 6 or depth == 5:
name = name.replace("tumor necrosis factor", "TNF")
name = self.replace_greek(name)
return name | [
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242,501 | tanghaibao/goatools | goatools/gosubdag/plot/go_name_shorten.py | ShortenText.shorten_go_name_ptbl1 | def shorten_go_name_ptbl1(self, name):
"""Shorten GO name for tables in paper."""
if self._keep_this(name):
return name
name = name.replace("negative", "neg.")
name = name.replace("positive", "pos.")
name = name.replace("response", "rsp.")
name = name.replace("regulation", "reg.")
name = name.replace("antigen processing and presentation", "app.")
return name | python | def shorten_go_name_ptbl1(self, name):
if self._keep_this(name):
return name
name = name.replace("negative", "neg.")
name = name.replace("positive", "pos.")
name = name.replace("response", "rsp.")
name = name.replace("regulation", "reg.")
name = name.replace("antigen processing and presentation", "app.")
return name | [
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242,502 | tanghaibao/goatools | goatools/gosubdag/plot/go_name_shorten.py | ShortenText.shorten_go_name_ptbl3 | def shorten_go_name_ptbl3(self, name, dcnt):
"""Shorten GO description for Table 3 in manuscript."""
if self._keep_this(name):
return name
name = name.replace("positive regulation of immune system process",
"+ reg. of immune sys. process")
name = name.replace("positive regulation of immune response",
"+ reg. of immune response")
name = name.replace("positive regulation of cytokine production",
"+ reg. of cytokine production")
if dcnt < 40:
name = name.replace("antigen processing and presentation", "a.p.p.")
if dcnt < 10:
name = name.replace("negative", "-")
name = name.replace("positive", "+")
#name = name.replace("tumor necrosis factor production", "tumor necrosis factor prod.")
name = name.replace("tumor necrosis factor production", "TNF production")
if dcnt < 4:
name = name.replace("regulation", "reg.")
name = name.replace("exogenous ", "")
name = name.replace(" via ", " w/")
name = name.replace("T cell mediated cytotoxicity", "cytotoxicity via T cell")
name = name.replace('involved in', 'in')
name = name.replace('-positive', '+')
return name | python | def shorten_go_name_ptbl3(self, name, dcnt):
if self._keep_this(name):
return name
name = name.replace("positive regulation of immune system process",
"+ reg. of immune sys. process")
name = name.replace("positive regulation of immune response",
"+ reg. of immune response")
name = name.replace("positive regulation of cytokine production",
"+ reg. of cytokine production")
if dcnt < 40:
name = name.replace("antigen processing and presentation", "a.p.p.")
if dcnt < 10:
name = name.replace("negative", "-")
name = name.replace("positive", "+")
#name = name.replace("tumor necrosis factor production", "tumor necrosis factor prod.")
name = name.replace("tumor necrosis factor production", "TNF production")
if dcnt < 4:
name = name.replace("regulation", "reg.")
name = name.replace("exogenous ", "")
name = name.replace(" via ", " w/")
name = name.replace("T cell mediated cytotoxicity", "cytotoxicity via T cell")
name = name.replace('involved in', 'in')
name = name.replace('-positive', '+')
return name | [
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242,503 | tanghaibao/goatools | goatools/gosubdag/plot/go_name_shorten.py | ShortenText.shorten_go_name_all | def shorten_go_name_all(self, name):
"""Shorten GO name for tables in paper, supplemental materials, and plots."""
name = self.replace_greek(name)
name = name.replace("MHC class I", "MHC-I")
return name | python | def shorten_go_name_all(self, name):
name = self.replace_greek(name)
name = name.replace("MHC class I", "MHC-I")
return name | [
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242,504 | tanghaibao/goatools | goatools/gosubdag/plot/go_name_shorten.py | ShortenText._keep_this | def _keep_this(self, name):
"""Return True if there are to be no modifications to name."""
for keep_name in self.keep:
if name == keep_name:
return True
return False | python | def _keep_this(self, name):
for keep_name in self.keep:
if name == keep_name:
return True
return False | [
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242,505 | tanghaibao/goatools | goatools/gosubdag/rpt/wr_xlsx.py | read_d1_letter | def read_d1_letter(fin_txt):
"""Reads letter aliases from a text file created by GoDepth1LettersWr."""
go2letter = {}
re_goid = re.compile(r"(GO:\d{7})")
with open(fin_txt) as ifstrm:
for line in ifstrm:
mtch = re_goid.search(line)
if mtch and line[:1] != ' ':
# Alias is expected to be the first character
go2letter[mtch.group(1)] = line[:1]
return go2letter | python | def read_d1_letter(fin_txt):
go2letter = {}
re_goid = re.compile(r"(GO:\d{7})")
with open(fin_txt) as ifstrm:
for line in ifstrm:
mtch = re_goid.search(line)
if mtch and line[:1] != ' ':
# Alias is expected to be the first character
go2letter[mtch.group(1)] = line[:1]
return go2letter | [
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242,506 | tanghaibao/goatools | goatools/gosubdag/rpt/wr_xlsx.py | GoSubDagWr.get_goids_sections | def get_goids_sections(sections):
"""Return all the GO IDs in a 2-D sections list."""
goids_all = set()
for _, goids_sec in sections:
goids_all |= set(goids_sec)
return goids_all | python | def get_goids_sections(sections):
goids_all = set()
for _, goids_sec in sections:
goids_all |= set(goids_sec)
return goids_all | [
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242,507 | tanghaibao/goatools | goatools/gosubdag/rpt/wr_xlsx.py | GoDepth1LettersWr.prt_txt | def prt_txt(self, prt=sys.stdout, pre=''):
"""Print letters, descendant count, and GO information."""
data_nts = self.get_d1nts()
for ntdata in data_nts:
prt.write("{PRE}{L:1} {NS} {d:6,} D{D:02} {GO} {NAME}\n".format(
PRE=pre,
L=ntdata.D1,
d=ntdata.dcnt,
NS=ntdata.NS,
D=ntdata.depth,
GO=ntdata.GO,
NAME=ntdata.name))
return data_nts | python | def prt_txt(self, prt=sys.stdout, pre=''):
data_nts = self.get_d1nts()
for ntdata in data_nts:
prt.write("{PRE}{L:1} {NS} {d:6,} D{D:02} {GO} {NAME}\n".format(
PRE=pre,
L=ntdata.D1,
d=ntdata.dcnt,
NS=ntdata.NS,
D=ntdata.depth,
GO=ntdata.GO,
NAME=ntdata.name))
return data_nts | [
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242,508 | tanghaibao/goatools | goatools/gosubdag/rpt/wr_xlsx.py | GoDepth1LettersWr.wr_xlsx | def wr_xlsx(self, fout_xlsx="gos_depth01.xlsx", **kws):
"""Write xlsx table of depth-01 GO terms and their letter representation."""
data_nts = self.get_d1nts()
if 'fld2col_widths' not in kws:
kws['fld2col_widths'] = {'D1': 6, 'NS':3, 'depth': 5, 'GO': 12, 'name': 40}
if 'hdrs' not in kws:
kws['hdrs'] = self.hdrs
wr_xlsx_tbl(fout_xlsx, data_nts, **kws) | python | def wr_xlsx(self, fout_xlsx="gos_depth01.xlsx", **kws):
data_nts = self.get_d1nts()
if 'fld2col_widths' not in kws:
kws['fld2col_widths'] = {'D1': 6, 'NS':3, 'depth': 5, 'GO': 12, 'name': 40}
if 'hdrs' not in kws:
kws['hdrs'] = self.hdrs
wr_xlsx_tbl(fout_xlsx, data_nts, **kws) | [
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242,509 | tanghaibao/goatools | goatools/gosubdag/rpt/wr_xlsx.py | GoDepth1LettersWr.get_d1nts | def get_d1nts(self):
"""Get letters for depth-01 GO terms, descendants count, and GO information."""
data = []
ntdata = cx.namedtuple("NtPrt", "D1 NS dcnt depth GO name")
namespace = None
for ntlet in sorted(self.goone2ntletter.values(),
key=lambda nt: [nt.goobj.namespace, -1 * nt.dcnt, nt.D1]):
goobj = ntlet.goobj
goid = goobj.id
assert len(goobj.parents) == 1
if namespace != goobj.namespace:
namespace = goobj.namespace
ntns = self.ns2nt[namespace]
pobj = ntns.goobj
ns2 = self.str2ns[goobj.namespace]
data.append(ntdata._make([" ", ns2, ntns.dcnt, pobj.depth, pobj.id, pobj.name]))
data.append(ntdata._make(
[ntlet.D1, self.str2ns[namespace], ntlet.dcnt, goobj.depth, goid, goobj.name]))
return data | python | def get_d1nts(self):
data = []
ntdata = cx.namedtuple("NtPrt", "D1 NS dcnt depth GO name")
namespace = None
for ntlet in sorted(self.goone2ntletter.values(),
key=lambda nt: [nt.goobj.namespace, -1 * nt.dcnt, nt.D1]):
goobj = ntlet.goobj
goid = goobj.id
assert len(goobj.parents) == 1
if namespace != goobj.namespace:
namespace = goobj.namespace
ntns = self.ns2nt[namespace]
pobj = ntns.goobj
ns2 = self.str2ns[goobj.namespace]
data.append(ntdata._make([" ", ns2, ntns.dcnt, pobj.depth, pobj.id, pobj.name]))
data.append(ntdata._make(
[ntlet.D1, self.str2ns[namespace], ntlet.dcnt, goobj.depth, goid, goobj.name]))
return data | [
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242,510 | tanghaibao/goatools | goatools/gosubdag/rpt/wr_xlsx.py | GoDepth1LettersWr._init_ns2nt | def _init_ns2nt(rcntobj):
"""Save depth-00 GO terms ordered using descendants cnt."""
go2dcnt = rcntobj.go2dcnt
ntobj = cx.namedtuple("NtD1", "D1 dcnt goobj")
d0s = rcntobj.depth2goobjs[0]
ns_nt = [(o.namespace, ntobj(D1="", dcnt=go2dcnt[o.id], goobj=o)) for o in d0s]
return cx.OrderedDict(ns_nt) | python | def _init_ns2nt(rcntobj):
go2dcnt = rcntobj.go2dcnt
ntobj = cx.namedtuple("NtD1", "D1 dcnt goobj")
d0s = rcntobj.depth2goobjs[0]
ns_nt = [(o.namespace, ntobj(D1="", dcnt=go2dcnt[o.id], goobj=o)) for o in d0s]
return cx.OrderedDict(ns_nt) | [
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242,511 | tanghaibao/goatools | goatools/grouper/wrxlsx.py | WrXlsxSortedGos._get_xlsx_kws | def _get_xlsx_kws(self, **kws_usr):
"""Return keyword arguments relevant to writing an xlsx."""
kws_xlsx = {'fld2col_widths':self._get_fld2col_widths(**kws_usr), 'items':'GO IDs'}
remaining_keys = set(['title', 'hdrs', 'prt_flds', 'fld2fmt',
'ntval2wbfmtdict', 'ntfld_wbfmt'])
for usr_key, usr_val in kws_usr.items():
if usr_key in remaining_keys:
kws_xlsx[usr_key] = usr_val
return kws_xlsx | python | def _get_xlsx_kws(self, **kws_usr):
kws_xlsx = {'fld2col_widths':self._get_fld2col_widths(**kws_usr), 'items':'GO IDs'}
remaining_keys = set(['title', 'hdrs', 'prt_flds', 'fld2fmt',
'ntval2wbfmtdict', 'ntfld_wbfmt'])
for usr_key, usr_val in kws_usr.items():
if usr_key in remaining_keys:
kws_xlsx[usr_key] = usr_val
return kws_xlsx | [
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242,512 | tanghaibao/goatools | goatools/grouper/wrxlsx.py | WrXlsxSortedGos._adjust_prt_flds | def _adjust_prt_flds(self, kws_xlsx, desc2nts, shade_hdrgos):
"""Print user-requested fields or provided fields minus info fields."""
# Use xlsx prt_flds from the user, if provided
if "prt_flds" in kws_xlsx:
return kws_xlsx["prt_flds"]
# If the user did not provide specific fields to print in an xlsx file:
dont_print = set(['hdr_idx', 'is_hdrgo', 'is_usrgo'])
# Are we printing GO group headers?
# Build new list of xlsx print fields, excluding those which add no new information
prt_flds_adjusted = []
# Get all namedtuple fields
nt_flds = self.sortobj.get_fields(desc2nts)
# Keep fields intended for print and optionally gray-shade field (format_txt)
# print('FFFFFFFFFFFFFFF WrXlsxSortedGos::_adjust_prt_flds:', nt_flds)
for nt_fld in nt_flds:
if nt_fld not in dont_print:
# Only add grey-shade to hdrgo and section name rows if hdrgo_prt=True
if nt_fld == "format_txt":
if shade_hdrgos is True:
prt_flds_adjusted.append(nt_fld)
else:
prt_flds_adjusted.append(nt_fld)
kws_xlsx['prt_flds'] = prt_flds_adjusted | python | def _adjust_prt_flds(self, kws_xlsx, desc2nts, shade_hdrgos):
# Use xlsx prt_flds from the user, if provided
if "prt_flds" in kws_xlsx:
return kws_xlsx["prt_flds"]
# If the user did not provide specific fields to print in an xlsx file:
dont_print = set(['hdr_idx', 'is_hdrgo', 'is_usrgo'])
# Are we printing GO group headers?
# Build new list of xlsx print fields, excluding those which add no new information
prt_flds_adjusted = []
# Get all namedtuple fields
nt_flds = self.sortobj.get_fields(desc2nts)
# Keep fields intended for print and optionally gray-shade field (format_txt)
# print('FFFFFFFFFFFFFFF WrXlsxSortedGos::_adjust_prt_flds:', nt_flds)
for nt_fld in nt_flds:
if nt_fld not in dont_print:
# Only add grey-shade to hdrgo and section name rows if hdrgo_prt=True
if nt_fld == "format_txt":
if shade_hdrgos is True:
prt_flds_adjusted.append(nt_fld)
else:
prt_flds_adjusted.append(nt_fld)
kws_xlsx['prt_flds'] = prt_flds_adjusted | [
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242,513 | tanghaibao/goatools | goatools/grouper/wrxlsx.py | WrXlsxSortedGos._get_fld2col_widths | def _get_fld2col_widths(self, **kws):
"""Return xlsx column widths based on default and user-specified field-value pairs."""
fld2col_widths = self._init_fld2col_widths()
if 'fld2col_widths' not in kws:
return fld2col_widths
for fld, val in kws['fld2col_widths'].items():
fld2col_widths[fld] = val
return fld2col_widths | python | def _get_fld2col_widths(self, **kws):
fld2col_widths = self._init_fld2col_widths()
if 'fld2col_widths' not in kws:
return fld2col_widths
for fld, val in kws['fld2col_widths'].items():
fld2col_widths[fld] = val
return fld2col_widths | [
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242,514 | tanghaibao/goatools | goatools/grouper/wrxlsx.py | WrXlsxSortedGos._init_fld2col_widths | def _init_fld2col_widths(self):
"""Return default column widths for writing an Excel Spreadsheet."""
# GO info namedtuple fields: NS dcnt level depth GO D1 name
# GO header namedtuple fields: format_txt hdr_idx
fld2col_widths = GoSubDagWr.fld2col_widths.copy()
for fld, wid in self.oprtfmt.default_fld2col_widths.items():
fld2col_widths[fld] = wid
for fld in get_hdridx_flds():
fld2col_widths[fld] = 2
return fld2col_widths | python | def _init_fld2col_widths(self):
# GO info namedtuple fields: NS dcnt level depth GO D1 name
# GO header namedtuple fields: format_txt hdr_idx
fld2col_widths = GoSubDagWr.fld2col_widths.copy()
for fld, wid in self.oprtfmt.default_fld2col_widths.items():
fld2col_widths[fld] = wid
for fld in get_hdridx_flds():
fld2col_widths[fld] = 2
return fld2col_widths | [
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242,515 | tanghaibao/goatools | goatools/grouper/wrxlsx.py | WrXlsxSortedGos._get_shade_hdrgos | def _get_shade_hdrgos(**kws):
"""If no hdrgo_prt specified, and these conditions are present -> hdrgo_prt=F."""
# KWS: shade_hdrgos hdrgo_prt section_sortby top_n
if 'shade_hdrgos' in kws:
return kws['shade_hdrgos']
# Return user-sepcified hdrgo_prt, if provided
if 'hdrgo_prt' in kws:
return kws['hdrgo_prt']
# If no hdrgo_prt provided, set hdrgo_prt to False if:
# * section_sortby == True
# * section_sortby = user_sort
# * top_n == N
if 'section_sortby' in kws and kws['section_sortby']:
return False
if 'top_n' in kws and isinstance(kws['top_n'], int):
return False
return True | python | def _get_shade_hdrgos(**kws):
# KWS: shade_hdrgos hdrgo_prt section_sortby top_n
if 'shade_hdrgos' in kws:
return kws['shade_hdrgos']
# Return user-sepcified hdrgo_prt, if provided
if 'hdrgo_prt' in kws:
return kws['hdrgo_prt']
# If no hdrgo_prt provided, set hdrgo_prt to False if:
# * section_sortby == True
# * section_sortby = user_sort
# * top_n == N
if 'section_sortby' in kws and kws['section_sortby']:
return False
if 'top_n' in kws and isinstance(kws['top_n'], int):
return False
return True | [
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242,516 | tanghaibao/goatools | goatools/rpt/goea_nt_xfrm.py | MgrNtGOEAs.dflt_sortby_objgoea | def dflt_sortby_objgoea(goea_res):
"""Default sorting of GOEA results."""
return [getattr(goea_res, 'enrichment'),
getattr(goea_res, 'namespace'),
getattr(goea_res, 'p_uncorrected'),
getattr(goea_res, 'depth'),
getattr(goea_res, 'GO')] | python | def dflt_sortby_objgoea(goea_res):
return [getattr(goea_res, 'enrichment'),
getattr(goea_res, 'namespace'),
getattr(goea_res, 'p_uncorrected'),
getattr(goea_res, 'depth'),
getattr(goea_res, 'GO')] | [
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242,517 | tanghaibao/goatools | goatools/rpt/goea_nt_xfrm.py | MgrNtGOEAs.dflt_sortby_ntgoea | def dflt_sortby_ntgoea(ntgoea):
"""Default sorting of GOEA results stored in namedtuples."""
return [ntgoea.enrichment,
ntgoea.namespace,
ntgoea.p_uncorrected,
ntgoea.depth,
ntgoea.GO] | python | def dflt_sortby_ntgoea(ntgoea):
return [ntgoea.enrichment,
ntgoea.namespace,
ntgoea.p_uncorrected,
ntgoea.depth,
ntgoea.GO] | [
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242,518 | tanghaibao/goatools | goatools/rpt/goea_nt_xfrm.py | MgrNtGOEAs.get_goea_nts_prt | def get_goea_nts_prt(self, fldnames=None, **usr_kws):
"""Return list of namedtuples removing fields which are redundant or verbose."""
kws = usr_kws.copy()
if 'not_fldnames' not in kws:
kws['not_fldnames'] = ['goterm', 'parents', 'children', 'id']
if 'rpt_fmt' not in kws:
kws['rpt_fmt'] = True
return self.get_goea_nts_all(fldnames, **kws) | python | def get_goea_nts_prt(self, fldnames=None, **usr_kws):
kws = usr_kws.copy()
if 'not_fldnames' not in kws:
kws['not_fldnames'] = ['goterm', 'parents', 'children', 'id']
if 'rpt_fmt' not in kws:
kws['rpt_fmt'] = True
return self.get_goea_nts_all(fldnames, **kws) | [
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242,519 | tanghaibao/goatools | goatools/rpt/goea_nt_xfrm.py | MgrNtGOEAs._get_field_values | def _get_field_values(item, fldnames, rpt_fmt=None, itemid2name=None):
"""Return fieldnames and values of either a namedtuple or GOEnrichmentRecord."""
if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord
return item.get_field_values(fldnames, rpt_fmt, itemid2name)
if hasattr(item, "_fields"): # Is a namedtuple
return [getattr(item, f) for f in fldnames] | python | def _get_field_values(item, fldnames, rpt_fmt=None, itemid2name=None):
if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord
return item.get_field_values(fldnames, rpt_fmt, itemid2name)
if hasattr(item, "_fields"): # Is a namedtuple
return [getattr(item, f) for f in fldnames] | [
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242,520 | tanghaibao/goatools | goatools/rpt/goea_nt_xfrm.py | MgrNtGOEAs._get_fieldnames | def _get_fieldnames(item):
"""Return fieldnames of either a namedtuple or GOEnrichmentRecord."""
if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord
return item.get_prtflds_all()
if hasattr(item, "_fields"): # Is a namedtuple
return item._fields | python | def _get_fieldnames(item):
if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord
return item.get_prtflds_all()
if hasattr(item, "_fields"): # Is a namedtuple
return item._fields | [
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242,521 | tanghaibao/goatools | goatools/grouper/colors.py | GrouperColors.get_bordercolor | def get_bordercolor(self):
"""Get bordercolor based on hdrgos and usergos."""
hdrgos_all = self.grprobj.hdrobj.get_hdrgos()
hdrgos_unused = hdrgos_all.difference(self.hdrgos_actual)
go2bordercolor = {}
# hdrgos that went unused
for hdrgo in hdrgos_unused:
go2bordercolor[hdrgo] = self.hdrcol_all
# hdrgos used in this grouping that are NOT usrgos
for hdrgo in self.grprobj.hdrgo2usrgos.keys():
go2bordercolor[hdrgo] = self.hdrcol_all
# hdrgos used in this grouping that ARE usrgos
for hdrgo in self.grprobj.hdrgo_is_usrgo:
go2bordercolor[hdrgo] = 'blue'
# usrgos which are NOT hdrgos
usrgos_rem = self.grprobj.usrgos.difference(self.grprobj.hdrgo_is_usrgo)
for usrgo in usrgos_rem:
go2bordercolor[usrgo] = '#029386' # teal
# print("{N:5} hdrgos actual".format(N=len(self.hdrgos_actual)))
# print("{N:5} hdrgos unused".format(N=len(hdrgos_unused)))
# print("{N:5} hdrgos only BLACK".format(N=len(self.grprobj.hdrgo2usrgos.keys())))
# print("{N:5} usrgos".format(N=len(self.grprobj.usrgos)))
# print("{N:5} usrgos AND hdrgos BLUE".format(N=len(self.grprobj.hdrgo_is_usrgo)))
# print("{N:5} usrgos Only".format(N=len(usrgos_rem)))
return go2bordercolor | python | def get_bordercolor(self):
hdrgos_all = self.grprobj.hdrobj.get_hdrgos()
hdrgos_unused = hdrgos_all.difference(self.hdrgos_actual)
go2bordercolor = {}
# hdrgos that went unused
for hdrgo in hdrgos_unused:
go2bordercolor[hdrgo] = self.hdrcol_all
# hdrgos used in this grouping that are NOT usrgos
for hdrgo in self.grprobj.hdrgo2usrgos.keys():
go2bordercolor[hdrgo] = self.hdrcol_all
# hdrgos used in this grouping that ARE usrgos
for hdrgo in self.grprobj.hdrgo_is_usrgo:
go2bordercolor[hdrgo] = 'blue'
# usrgos which are NOT hdrgos
usrgos_rem = self.grprobj.usrgos.difference(self.grprobj.hdrgo_is_usrgo)
for usrgo in usrgos_rem:
go2bordercolor[usrgo] = '#029386' # teal
# print("{N:5} hdrgos actual".format(N=len(self.hdrgos_actual)))
# print("{N:5} hdrgos unused".format(N=len(hdrgos_unused)))
# print("{N:5} hdrgos only BLACK".format(N=len(self.grprobj.hdrgo2usrgos.keys())))
# print("{N:5} usrgos".format(N=len(self.grprobj.usrgos)))
# print("{N:5} usrgos AND hdrgos BLUE".format(N=len(self.grprobj.hdrgo_is_usrgo)))
# print("{N:5} usrgos Only".format(N=len(usrgos_rem)))
return go2bordercolor | [
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] | 407682e573a108864a79031f8ca19ee3bf377626 | https://github.com/tanghaibao/goatools/blob/407682e573a108864a79031f8ca19ee3bf377626/goatools/grouper/colors.py#L18-L42 |
242,522 | tanghaibao/goatools | goatools/grouper/colors.py | GrouperColors.get_go2color_users | def get_go2color_users(self,
usrgo_color='#feffa3', # yellow
hdrusrgo_color='#d4ffea', # green
hdrgo_color='#eee6f6'): # purple
"""Get go2color for GO DAG plots."""
go2color = {}
# Color user GO IDs
for goid in self.usrgos:
go2color[goid] = usrgo_color
# Color header GO IDs. Headers which are also GO IDs get their own color.
for goid_hdr in self.hdrgos_actual:
go2color[goid_hdr] = hdrusrgo_color if goid_hdr in self.usrgos else hdrgo_color
return go2color | python | def get_go2color_users(self,
usrgo_color='#feffa3', # yellow
hdrusrgo_color='#d4ffea', # green
hdrgo_color='#eee6f6'): # purple
go2color = {}
# Color user GO IDs
for goid in self.usrgos:
go2color[goid] = usrgo_color
# Color header GO IDs. Headers which are also GO IDs get their own color.
for goid_hdr in self.hdrgos_actual:
go2color[goid_hdr] = hdrusrgo_color if goid_hdr in self.usrgos else hdrgo_color
return go2color | [
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242,523 | tanghaibao/goatools | goatools/grouper/aart_geneproducts_all.py | AArtGeneProductSetsAll.run | def run(self, name, goea_nts, log):
"""Run gene product ASCII art."""
objaart = AArtGeneProductSetsOne(name, goea_nts, self)
if self.hdrobj.sections:
return objaart.prt_report_grp1(log)
else:
return objaart.prt_report_grp0(log) | python | def run(self, name, goea_nts, log):
objaart = AArtGeneProductSetsOne(name, goea_nts, self)
if self.hdrobj.sections:
return objaart.prt_report_grp1(log)
else:
return objaart.prt_report_grp0(log) | [
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242,524 | tanghaibao/goatools | goatools/grouper/aart_geneproducts_all.py | AArtGeneProductSetsAll.get_chr2idx | def get_chr2idx(self):
"""Return a dict with the ASCII art character as key and its index as value."""
return {chr(ascii_int):idx for idx, ascii_int in enumerate(self.all_chrints)} | python | def get_chr2idx(self):
return {chr(ascii_int):idx for idx, ascii_int in enumerate(self.all_chrints)} | [
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242,525 | tanghaibao/goatools | goatools/grouper/aart_geneproducts_all.py | AArtGeneProductSetsAll._init_kws | def _init_kws(self):
"""Fill default values for keyword args, if necessary."""
# Return user-specified GO formatting, if specfied:
if 'fmtgo' not in self.kws:
self.kws['fmtgo'] = self.grprdflt.gosubdag.prt_attr['fmt'] + "\n"
if 'fmtgo2' not in self.kws:
self.kws['fmtgo2'] = self.grprdflt.gosubdag.prt_attr['fmt'] + "\n"
if 'fmtgene' not in self.kws:
if 'itemid2name' not in self.kws:
self.kws['fmtgene'] = "{AART} {ID}\n"
else:
self.kws['fmtgene'] = "{AART} {ID} {NAME}\n"
if 'fmtgene2' not in self.kws:
self.kws['fmtgene2'] = self.kws['fmtgene'] | python | def _init_kws(self):
# Return user-specified GO formatting, if specfied:
if 'fmtgo' not in self.kws:
self.kws['fmtgo'] = self.grprdflt.gosubdag.prt_attr['fmt'] + "\n"
if 'fmtgo2' not in self.kws:
self.kws['fmtgo2'] = self.grprdflt.gosubdag.prt_attr['fmt'] + "\n"
if 'fmtgene' not in self.kws:
if 'itemid2name' not in self.kws:
self.kws['fmtgene'] = "{AART} {ID}\n"
else:
self.kws['fmtgene'] = "{AART} {ID} {NAME}\n"
if 'fmtgene2' not in self.kws:
self.kws['fmtgene2'] = self.kws['fmtgene'] | [
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242,526 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitGOs._init_relationships | def _init_relationships(self, relationships_arg):
"""Return a set of relationships found in all subset GO Terms."""
if relationships_arg:
relationships_all = self._get_all_relationships()
if relationships_arg is True:
return relationships_all
else:
return relationships_all.intersection(relationships_arg)
return set() | python | def _init_relationships(self, relationships_arg):
if relationships_arg:
relationships_all = self._get_all_relationships()
if relationships_arg is True:
return relationships_all
else:
return relationships_all.intersection(relationships_arg)
return set() | [
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242,527 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitGOs._get_all_relationships | def _get_all_relationships(self):
"""Return all relationships seen in GO Dag subset."""
relationships_all = set()
for goterm in self.go2obj.values():
if goterm.relationship:
relationships_all.update(goterm.relationship)
if goterm.relationship_rev:
relationships_all.update(goterm.relationship_rev)
return relationships_all | python | def _get_all_relationships(self):
relationships_all = set()
for goterm in self.go2obj.values():
if goterm.relationship:
relationships_all.update(goterm.relationship)
if goterm.relationship_rev:
relationships_all.update(goterm.relationship_rev)
return relationships_all | [
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242,528 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitGOs._init_gos | def _init_gos(self, go_sources_arg, relationships_arg):
"""Initialize GO sources."""
# No GO sources provided
if not go_sources_arg:
assert self.go2obj_orig, "go2obj MUST BE PRESENT IF go_sources IS NOT"
self.go_sources = set(self.go2obj_orig)
self.go2obj = self.go2obj_orig
sys.stdout.write("**NOTE: {N:,} SOURCE GO IDS\n".format(N=len(self.go_sources)))
return
# GO sources provided
go_sources = self._init_go_sources(go_sources_arg, self.go2obj_orig)
# Create new go2obj_user subset matching GO sources
# Fill with source and parent GO IDs and alternate GO IDs
go2obj_user = {}
objrel = CurNHigher(relationships_arg, self.go2obj_orig)
objrel.get_id2obj_cur_n_high(go2obj_user, go_sources)
# Add additional GOTerm information, if needed for user task
kws_gos = {k:v for k, v in self.kws.items() if k in self.kws_aux_gos}
if kws_gos:
self._add_goterms_kws(go2obj_user, kws_gos)
self.go_sources = go_sources
self.go2obj = go2obj_user | python | def _init_gos(self, go_sources_arg, relationships_arg):
# No GO sources provided
if not go_sources_arg:
assert self.go2obj_orig, "go2obj MUST BE PRESENT IF go_sources IS NOT"
self.go_sources = set(self.go2obj_orig)
self.go2obj = self.go2obj_orig
sys.stdout.write("**NOTE: {N:,} SOURCE GO IDS\n".format(N=len(self.go_sources)))
return
# GO sources provided
go_sources = self._init_go_sources(go_sources_arg, self.go2obj_orig)
# Create new go2obj_user subset matching GO sources
# Fill with source and parent GO IDs and alternate GO IDs
go2obj_user = {}
objrel = CurNHigher(relationships_arg, self.go2obj_orig)
objrel.get_id2obj_cur_n_high(go2obj_user, go_sources)
# Add additional GOTerm information, if needed for user task
kws_gos = {k:v for k, v in self.kws.items() if k in self.kws_aux_gos}
if kws_gos:
self._add_goterms_kws(go2obj_user, kws_gos)
self.go_sources = go_sources
self.go2obj = go2obj_user | [
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242,529 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitGOs._add_goterms_kws | def _add_goterms_kws(self, go2obj_user, kws_gos):
"""Add more GOTerms to go2obj_user, if requested and relevant."""
if 'go2color' in kws_gos:
for goid in kws_gos['go2color'].keys():
self._add_goterms(go2obj_user, goid) | python | def _add_goterms_kws(self, go2obj_user, kws_gos):
if 'go2color' in kws_gos:
for goid in kws_gos['go2color'].keys():
self._add_goterms(go2obj_user, goid) | [
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242,530 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitGOs._add_goterms | def _add_goterms(self, go2obj_user, goid):
"""Add alt GO IDs to go2obj subset, if requested and relevant."""
goterm = self.go2obj_orig[goid]
if goid != goterm.id and goterm.id in go2obj_user and goid not in go2obj_user:
go2obj_user[goid] = goterm | python | def _add_goterms(self, go2obj_user, goid):
goterm = self.go2obj_orig[goid]
if goid != goterm.id and goterm.id in go2obj_user and goid not in go2obj_user:
go2obj_user[goid] = goterm | [
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242,531 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitGOs._init_go_sources | def _init_go_sources(self, go_sources_arg, go2obj_arg):
"""Return GO sources which are present in GODag."""
gos_user = set(go_sources_arg)
if 'children' in self.kws and self.kws['children']:
gos_user |= get_leaf_children(gos_user, go2obj_arg)
gos_godag = set(go2obj_arg)
gos_source = gos_user.intersection(gos_godag)
gos_missing = gos_user.difference(gos_godag)
if not gos_missing:
return gos_source
sys.stdout.write("{N} GO IDs NOT FOUND IN GO DAG: {GOs}\n".format(
N=len(gos_missing), GOs=" ".join([str(e) for e in gos_missing])))
return gos_source | python | def _init_go_sources(self, go_sources_arg, go2obj_arg):
gos_user = set(go_sources_arg)
if 'children' in self.kws and self.kws['children']:
gos_user |= get_leaf_children(gos_user, go2obj_arg)
gos_godag = set(go2obj_arg)
gos_source = gos_user.intersection(gos_godag)
gos_missing = gos_user.difference(gos_godag)
if not gos_missing:
return gos_source
sys.stdout.write("{N} GO IDs NOT FOUND IN GO DAG: {GOs}\n".format(
N=len(gos_missing), GOs=" ".join([str(e) for e in gos_missing])))
return gos_source | [
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242,532 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitFields.get_rcntobj | def get_rcntobj(self):
"""Return None or user-provided CountRelatives object."""
# rcntobj value in kws can be: None, False, True, CountRelatives object
if 'rcntobj' in self.kws:
rcntobj = self.kws['rcntobj']
if isinstance(rcntobj, CountRelatives):
return rcntobj
return CountRelatives(
self.go2obj, # Subset go2obj contains only items needed by go_sources
self.relationships,
dcnt='dcnt' in self.kw_elems,
go2letter=self.kws.get('go2letter')) | python | def get_rcntobj(self):
# rcntobj value in kws can be: None, False, True, CountRelatives object
if 'rcntobj' in self.kws:
rcntobj = self.kws['rcntobj']
if isinstance(rcntobj, CountRelatives):
return rcntobj
return CountRelatives(
self.go2obj, # Subset go2obj contains only items needed by go_sources
self.relationships,
dcnt='dcnt' in self.kw_elems,
go2letter=self.kws.get('go2letter')) | [
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242,533 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitFields.get_prt_fmt | def get_prt_fmt(self, alt=False):
"""Return the format for printing GO named tuples and their related information."""
# prt_fmt = [ # rcnt
# '{GO} # {NS} L{level:02} D{depth:02} {GO_name}',
# '{GO} # {NS} {dcnt:6,} L{level:02} D{depth:02} {D1:5} {GO_name}']
prt_fmt = []
if alt:
prt_fmt.append('{GO}{alt:1}')
else:
prt_fmt.append('{GO}')
prt_fmt.append('# {NS}')
if 'dcnt' in self.prt_flds:
prt_fmt.append('{dcnt:5}')
if 'childcnt' in self.prt_flds:
prt_fmt.append('{childcnt:3}')
if 'tcnt' in self.prt_flds:
prt_fmt.append("{tcnt:7,}")
if 'tfreq' in self.prt_flds:
prt_fmt.append("{tfreq:8.6f}")
if 'tinfo' in self.prt_flds:
prt_fmt.append("{tinfo:5.2f}")
prt_fmt.append('L{level:02} D{depth:02}')
if self.relationships:
prt_fmt.append('R{reldepth:02}')
if 'D1' in self.prt_flds:
prt_fmt.append('{D1:5}')
if 'REL' in self.prt_flds:
prt_fmt.append('{REL}')
prt_fmt.append('{rel}')
prt_fmt.append('{GO_name}')
return " ".join(prt_fmt) | python | def get_prt_fmt(self, alt=False):
# prt_fmt = [ # rcnt
# '{GO} # {NS} L{level:02} D{depth:02} {GO_name}',
# '{GO} # {NS} {dcnt:6,} L{level:02} D{depth:02} {D1:5} {GO_name}']
prt_fmt = []
if alt:
prt_fmt.append('{GO}{alt:1}')
else:
prt_fmt.append('{GO}')
prt_fmt.append('# {NS}')
if 'dcnt' in self.prt_flds:
prt_fmt.append('{dcnt:5}')
if 'childcnt' in self.prt_flds:
prt_fmt.append('{childcnt:3}')
if 'tcnt' in self.prt_flds:
prt_fmt.append("{tcnt:7,}")
if 'tfreq' in self.prt_flds:
prt_fmt.append("{tfreq:8.6f}")
if 'tinfo' in self.prt_flds:
prt_fmt.append("{tinfo:5.2f}")
prt_fmt.append('L{level:02} D{depth:02}')
if self.relationships:
prt_fmt.append('R{reldepth:02}')
if 'D1' in self.prt_flds:
prt_fmt.append('{D1:5}')
if 'REL' in self.prt_flds:
prt_fmt.append('{REL}')
prt_fmt.append('{rel}')
prt_fmt.append('{GO_name}')
return " ".join(prt_fmt) | [
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242,534 | tanghaibao/goatools | goatools/gosubdag/gosubdag_init.py | InitFields._init_kwelems | def _init_kwelems(self):
"""Init set elements."""
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ret.add('dcnt')
ret.add('D1')
if 'tcntobj' in self.kws:
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ret.add('tfreq')
ret.add('tinfo')
return ret | python | def _init_kwelems(self):
ret = set()
if 'rcntobj' in self.kws:
ret.add('dcnt')
ret.add('D1')
if 'tcntobj' in self.kws:
ret.add('tcnt')
ret.add('tfreq')
ret.add('tinfo')
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242,535 | tanghaibao/goatools | goatools/anno/extensions/extensions.py | AnnotationExtensions.get_relations_cnt | def get_relations_cnt(self):
"""Get the set of all relations."""
return cx.Counter([e.relation for es in self.exts for e in es]) | python | def get_relations_cnt(self):
return cx.Counter([e.relation for es in self.exts for e in es]) | [
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242,536 | tanghaibao/goatools | goatools/gosubdag/plot/go2color.py | Go2Color._init_equiv | def _init_equiv(self):
"""Add equivalent GO IDs to go2color, if necessary."""
gocolored_all = set(self.go2color)
go2obj_usr = self.gosubdag.go2obj
go2color_add = {}
for gocolored_cur, color in self.go2color.items():
# Ignore GOs in go2color that are not in the user set
if gocolored_cur in go2obj_usr:
goobj = go2obj_usr[gocolored_cur]
goids_equiv = goobj.alt_ids.union([goobj.id])
# mrk_alt = "*" if gocolored_cur != goobj.id else ""
# print("COLORED({}) KEY({}){:1} ALL({})".format(
# gocolored_cur, goobj.id, mrk_alt, goids_equiv))
# Loop through GO IDs which are not colored, but are equivalent to colored GO IDs.
for goid_add in goids_equiv.difference(gocolored_all):
if goid_add in go2color_add:
print('**TBD: TWO DIFFERENT COLORS FOR EQUIV GO ID') # pylint: disable=superfluous-parens
go2color_add[goid_add] = color
# print("ADDING {N} GO IDs TO go2color".format(N=len(go2color_add)))
for goid, color in go2color_add.items():
self.go2color[goid] = color | python | def _init_equiv(self):
gocolored_all = set(self.go2color)
go2obj_usr = self.gosubdag.go2obj
go2color_add = {}
for gocolored_cur, color in self.go2color.items():
# Ignore GOs in go2color that are not in the user set
if gocolored_cur in go2obj_usr:
goobj = go2obj_usr[gocolored_cur]
goids_equiv = goobj.alt_ids.union([goobj.id])
# mrk_alt = "*" if gocolored_cur != goobj.id else ""
# print("COLORED({}) KEY({}){:1} ALL({})".format(
# gocolored_cur, goobj.id, mrk_alt, goids_equiv))
# Loop through GO IDs which are not colored, but are equivalent to colored GO IDs.
for goid_add in goids_equiv.difference(gocolored_all):
if goid_add in go2color_add:
print('**TBD: TWO DIFFERENT COLORS FOR EQUIV GO ID') # pylint: disable=superfluous-parens
go2color_add[goid_add] = color
# print("ADDING {N} GO IDs TO go2color".format(N=len(go2color_add)))
for goid, color in go2color_add.items():
self.go2color[goid] = color | [
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242,537 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord.get_pvalue | def get_pvalue(self):
"""Returns pval for 1st method, if it exists. Else returns uncorrected pval."""
if self.method_flds:
return getattr(self, "p_{m}".format(m=self.get_method_name()))
return getattr(self, "p_uncorrected") | python | def get_pvalue(self):
if self.method_flds:
return getattr(self, "p_{m}".format(m=self.get_method_name()))
return getattr(self, "p_uncorrected") | [
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242,538 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord.set_corrected_pval | def set_corrected_pval(self, nt_method, pvalue):
"""Add object attribute based on method name."""
self.method_flds.append(nt_method)
fieldname = "".join(["p_", nt_method.fieldname])
setattr(self, fieldname, pvalue) | python | def set_corrected_pval(self, nt_method, pvalue):
self.method_flds.append(nt_method)
fieldname = "".join(["p_", nt_method.fieldname])
setattr(self, fieldname, pvalue) | [
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242,539 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord._chk_fields | def _chk_fields(field_data, field_formatter):
"""Check that expected fields are present."""
if len(field_data) == len(field_formatter):
return
len_dat = len(field_data)
len_fmt = len(field_formatter)
msg = [
"FIELD DATA({d}) != FORMATTER({f})".format(d=len_dat, f=len_fmt),
"DAT({N}): {D}".format(N=len_dat, D=field_data),
"FMT({N}): {F}".format(N=len_fmt, F=field_formatter)]
raise Exception("\n".join(msg)) | python | def _chk_fields(field_data, field_formatter):
if len(field_data) == len(field_formatter):
return
len_dat = len(field_data)
len_fmt = len(field_formatter)
msg = [
"FIELD DATA({d}) != FORMATTER({f})".format(d=len_dat, f=len_fmt),
"DAT({N}): {D}".format(N=len_dat, D=field_data),
"FMT({N}): {F}".format(N=len_fmt, F=field_formatter)]
raise Exception("\n".join(msg)) | [
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242,540 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord.set_goterm | def set_goterm(self, go2obj):
"""Set goterm and copy GOTerm's name and namespace."""
if self.GO in go2obj:
goterm = go2obj[self.GO]
self.goterm = goterm
self.name = goterm.name
self.depth = goterm.depth
self.NS = self.namespace2NS[self.goterm.namespace] | python | def set_goterm(self, go2obj):
if self.GO in go2obj:
goterm = go2obj[self.GO]
self.goterm = goterm
self.name = goterm.name
self.depth = goterm.depth
self.NS = self.namespace2NS[self.goterm.namespace] | [
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242,541 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord._init_enrichment | def _init_enrichment(self):
"""Mark as 'enriched' or 'purified'."""
if self.study_n:
return 'e' if ((1.0 * self.study_count / self.study_n) >
(1.0 * self.pop_count / self.pop_n)) else 'p'
return 'p' | python | def _init_enrichment(self):
if self.study_n:
return 'e' if ((1.0 * self.study_count / self.study_n) >
(1.0 * self.pop_count / self.pop_n)) else 'p'
return 'p' | [
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242,542 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord.get_prtflds_default | def get_prtflds_default(self):
"""Get default fields."""
return self._fldsdefprt[:-1] + \
["p_{M}".format(M=m.fieldname) for m in self.method_flds] + \
[self._fldsdefprt[-1]] | python | def get_prtflds_default(self):
return self._fldsdefprt[:-1] + \
["p_{M}".format(M=m.fieldname) for m in self.method_flds] + \
[self._fldsdefprt[-1]] | [
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242,543 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord.get_prtflds_all | def get_prtflds_all(self):
"""When converting to a namedtuple, get all possible fields in their original order."""
flds = []
dont_add = set(['_parents', 'method_flds', 'relationship_rev', 'relationship'])
# Fields: GO NS enrichment name ratio_in_study ratio_in_pop p_uncorrected
# depth study_count p_sm_bonferroni p_fdr_bh study_items
self._flds_append(flds, self.get_prtflds_default(), dont_add)
# Fields: GO NS goterm
# ratio_in_pop pop_n pop_count pop_items name
# ratio_in_study study_n study_count study_items
# method_flds enrichment p_uncorrected p_sm_bonferroni p_fdr_bh
self._flds_append(flds, vars(self).keys(), dont_add)
# Fields: name level is_obsolete namespace id depth parents children _parents alt_ids
self._flds_append(flds, vars(self.goterm).keys(), dont_add)
return flds | python | def get_prtflds_all(self):
flds = []
dont_add = set(['_parents', 'method_flds', 'relationship_rev', 'relationship'])
# Fields: GO NS enrichment name ratio_in_study ratio_in_pop p_uncorrected
# depth study_count p_sm_bonferroni p_fdr_bh study_items
self._flds_append(flds, self.get_prtflds_default(), dont_add)
# Fields: GO NS goterm
# ratio_in_pop pop_n pop_count pop_items name
# ratio_in_study study_n study_count study_items
# method_flds enrichment p_uncorrected p_sm_bonferroni p_fdr_bh
self._flds_append(flds, vars(self).keys(), dont_add)
# Fields: name level is_obsolete namespace id depth parents children _parents alt_ids
self._flds_append(flds, vars(self.goterm).keys(), dont_add)
return flds | [
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242,544 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord._flds_append | def _flds_append(flds, addthese, dont_add):
"""Retain order of fields as we add them once to the list."""
for fld in addthese:
if fld not in flds and fld not in dont_add:
flds.append(fld) | python | def _flds_append(flds, addthese, dont_add):
for fld in addthese:
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242,545 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord.get_field_values | def get_field_values(self, fldnames, rpt_fmt=True, itemid2name=None):
"""Get flat namedtuple fields for one GOEnrichmentRecord."""
row = []
# Loop through each user field desired
for fld in fldnames:
# 1. Check the GOEnrichmentRecord's attributes
val = getattr(self, fld, None)
if val is not None:
if rpt_fmt:
val = self._get_rpt_fmt(fld, val, itemid2name)
row.append(val)
else:
# 2. Check the GO object for the field
val = getattr(self.goterm, fld, None)
if rpt_fmt:
val = self._get_rpt_fmt(fld, val, itemid2name)
if val is not None:
row.append(val)
else:
# 3. Field not found, raise Exception
self._err_fld(fld, fldnames)
if rpt_fmt:
assert not isinstance(val, list), \
"UNEXPECTED LIST: FIELD({F}) VALUE({V}) FMT({P})".format(
P=rpt_fmt, F=fld, V=val)
return row | python | def get_field_values(self, fldnames, rpt_fmt=True, itemid2name=None):
row = []
# Loop through each user field desired
for fld in fldnames:
# 1. Check the GOEnrichmentRecord's attributes
val = getattr(self, fld, None)
if val is not None:
if rpt_fmt:
val = self._get_rpt_fmt(fld, val, itemid2name)
row.append(val)
else:
# 2. Check the GO object for the field
val = getattr(self.goterm, fld, None)
if rpt_fmt:
val = self._get_rpt_fmt(fld, val, itemid2name)
if val is not None:
row.append(val)
else:
# 3. Field not found, raise Exception
self._err_fld(fld, fldnames)
if rpt_fmt:
assert not isinstance(val, list), \
"UNEXPECTED LIST: FIELD({F}) VALUE({V}) FMT({P})".format(
P=rpt_fmt, F=fld, V=val)
return row | [
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242,546 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord._get_rpt_fmt | def _get_rpt_fmt(fld, val, itemid2name=None):
"""Return values in a format amenable to printing in a table."""
if fld.startswith("ratio_"):
return "{N}/{TOT}".format(N=val[0], TOT=val[1])
elif fld in set(['study_items', 'pop_items', 'alt_ids']):
if itemid2name is not None:
val = [itemid2name.get(v, v) for v in val]
return ", ".join([str(v) for v in sorted(val)])
return val | python | def _get_rpt_fmt(fld, val, itemid2name=None):
if fld.startswith("ratio_"):
return "{N}/{TOT}".format(N=val[0], TOT=val[1])
elif fld in set(['study_items', 'pop_items', 'alt_ids']):
if itemid2name is not None:
val = [itemid2name.get(v, v) for v in val]
return ", ".join([str(v) for v in sorted(val)])
return val | [
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242,547 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentRecord._err_fld | def _err_fld(self, fld, fldnames):
"""Unrecognized field. Print detailed Failure message."""
msg = ['ERROR. UNRECOGNIZED FIELD({F})'.format(F=fld)]
actual_flds = set(self.get_prtflds_default() + self.goterm.__dict__.keys())
bad_flds = set(fldnames).difference(set(actual_flds))
if bad_flds:
msg.append("\nGOEA RESULT FIELDS: {}".format(" ".join(self._fldsdefprt)))
msg.append("GO FIELDS: {}".format(" ".join(self.goterm.__dict__.keys())))
msg.append("\nFATAL: {N} UNEXPECTED FIELDS({F})\n".format(
N=len(bad_flds), F=" ".join(bad_flds)))
msg.append(" {N} User-provided fields:".format(N=len(fldnames)))
for idx, fld in enumerate(fldnames, 1):
mrk = "ERROR -->" if fld in bad_flds else ""
msg.append(" {M:>9} {I:>2}) {F}".format(M=mrk, I=idx, F=fld))
raise Exception("\n".join(msg)) | python | def _err_fld(self, fld, fldnames):
msg = ['ERROR. UNRECOGNIZED FIELD({F})'.format(F=fld)]
actual_flds = set(self.get_prtflds_default() + self.goterm.__dict__.keys())
bad_flds = set(fldnames).difference(set(actual_flds))
if bad_flds:
msg.append("\nGOEA RESULT FIELDS: {}".format(" ".join(self._fldsdefprt)))
msg.append("GO FIELDS: {}".format(" ".join(self.goterm.__dict__.keys())))
msg.append("\nFATAL: {N} UNEXPECTED FIELDS({F})\n".format(
N=len(bad_flds), F=" ".join(bad_flds)))
msg.append(" {N} User-provided fields:".format(N=len(fldnames)))
for idx, fld in enumerate(fldnames, 1):
mrk = "ERROR -->" if fld in bad_flds else ""
msg.append(" {M:>9} {I:>2}) {F}".format(M=mrk, I=idx, F=fld))
raise Exception("\n".join(msg)) | [
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242,548 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.run_study_nts | def run_study_nts(self, study, **kws):
"""Run GOEA on study ids. Return results as a list of namedtuples."""
goea_results = self.run_study(study, **kws)
return MgrNtGOEAs(goea_results).get_goea_nts_all() | python | def run_study_nts(self, study, **kws):
goea_results = self.run_study(study, **kws)
return MgrNtGOEAs(goea_results).get_goea_nts_all() | [
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242,549 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.get_results_msg | def get_results_msg(self, results, study):
"""Return summary for GOEA results."""
# To convert msg list to string: "\n".join(msg)
msg = []
if results:
fmt = "{M:6,} GO terms are associated with {N:6,} of {NT:6,}"
stu_items, num_gos_stu = self.get_item_cnt(results, "study_items")
pop_items, num_gos_pop = self.get_item_cnt(results, "pop_items")
stu_txt = fmt.format(N=len(stu_items), M=num_gos_stu, NT=len(set(study)))
pop_txt = fmt.format(N=len(pop_items), M=num_gos_pop, NT=self.pop_n)
msg.append("{POP} population items".format(POP=pop_txt))
msg.append("{STU} study items".format(STU=stu_txt))
return msg | python | def get_results_msg(self, results, study):
# To convert msg list to string: "\n".join(msg)
msg = []
if results:
fmt = "{M:6,} GO terms are associated with {N:6,} of {NT:6,}"
stu_items, num_gos_stu = self.get_item_cnt(results, "study_items")
pop_items, num_gos_pop = self.get_item_cnt(results, "pop_items")
stu_txt = fmt.format(N=len(stu_items), M=num_gos_stu, NT=len(set(study)))
pop_txt = fmt.format(N=len(pop_items), M=num_gos_pop, NT=self.pop_n)
msg.append("{POP} population items".format(POP=pop_txt))
msg.append("{STU} study items".format(STU=stu_txt))
return msg | [
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242,550 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.get_pval_uncorr | def get_pval_uncorr(self, study, log=sys.stdout):
"""Calculate the uncorrected pvalues for study items."""
results = []
study_in_pop = self.pop.intersection(study)
# " 99% 378 of 382 study items found in population"
go2studyitems = get_terms("study", study_in_pop, self.assoc, self.obo_dag, log)
pop_n, study_n = self.pop_n, len(study_in_pop)
allterms = set(go2studyitems).union(set(self.go2popitems))
if log is not None:
# Some study genes may not have been found in the population. Report from orig
study_n_orig = len(study)
perc = 100.0*study_n/study_n_orig if study_n_orig != 0 else 0.0
log.write("{R:3.0f}% {N:>6,} of {M:>6,} study items found in population({P})\n".format(
N=study_n, M=study_n_orig, P=pop_n, R=perc))
if study_n:
log.write("Calculating {N:,} uncorrected p-values using {PFNC}\n".format(
N=len(allterms), PFNC=self.pval_obj.name))
# If no study genes were found in the population, return empty GOEA results
if not study_n:
return []
calc_pvalue = self.pval_obj.calc_pvalue
for goid in allterms:
study_items = go2studyitems.get(goid, set())
study_count = len(study_items)
pop_items = self.go2popitems.get(goid, set())
pop_count = len(pop_items)
one_record = GOEnrichmentRecord(
goid,
p_uncorrected=calc_pvalue(study_count, study_n, pop_count, pop_n),
study_items=study_items,
pop_items=pop_items,
ratio_in_study=(study_count, study_n),
ratio_in_pop=(pop_count, pop_n))
results.append(one_record)
return results | python | def get_pval_uncorr(self, study, log=sys.stdout):
results = []
study_in_pop = self.pop.intersection(study)
# " 99% 378 of 382 study items found in population"
go2studyitems = get_terms("study", study_in_pop, self.assoc, self.obo_dag, log)
pop_n, study_n = self.pop_n, len(study_in_pop)
allterms = set(go2studyitems).union(set(self.go2popitems))
if log is not None:
# Some study genes may not have been found in the population. Report from orig
study_n_orig = len(study)
perc = 100.0*study_n/study_n_orig if study_n_orig != 0 else 0.0
log.write("{R:3.0f}% {N:>6,} of {M:>6,} study items found in population({P})\n".format(
N=study_n, M=study_n_orig, P=pop_n, R=perc))
if study_n:
log.write("Calculating {N:,} uncorrected p-values using {PFNC}\n".format(
N=len(allterms), PFNC=self.pval_obj.name))
# If no study genes were found in the population, return empty GOEA results
if not study_n:
return []
calc_pvalue = self.pval_obj.calc_pvalue
for goid in allterms:
study_items = go2studyitems.get(goid, set())
study_count = len(study_items)
pop_items = self.go2popitems.get(goid, set())
pop_count = len(pop_items)
one_record = GOEnrichmentRecord(
goid,
p_uncorrected=calc_pvalue(study_count, study_n, pop_count, pop_n),
study_items=study_items,
pop_items=pop_items,
ratio_in_study=(study_count, study_n),
ratio_in_pop=(pop_count, pop_n))
results.append(one_record)
return results | [
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242,551 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.get_study_items | def get_study_items(results):
"""Return a list of study items associated with the given results."""
study_items = set()
for obj in results:
study_items.update(obj.study_items)
return study_items | python | def get_study_items(results):
study_items = set()
for obj in results:
study_items.update(obj.study_items)
return study_items | [
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242,552 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy._update_pvalcorr | def _update_pvalcorr(ntmt, corrected_pvals):
"""Add data members to store multiple test corrections."""
if corrected_pvals is None:
return
for rec, val in zip(ntmt.results, corrected_pvals):
rec.set_corrected_pval(ntmt.nt_method, val) | python | def _update_pvalcorr(ntmt, corrected_pvals):
if corrected_pvals is None:
return
for rec, val in zip(ntmt.results, corrected_pvals):
rec.set_corrected_pval(ntmt.nt_method, val) | [
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242,553 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.wr_txt | def wr_txt(self, fout_txt, goea_results, prtfmt=None, **kws):
"""Print GOEA results to text file."""
if not goea_results:
sys.stdout.write(" 0 GOEA results. NOT WRITING {FOUT}\n".format(FOUT=fout_txt))
return
with open(fout_txt, 'w') as prt:
if 'title' in kws:
prt.write("{TITLE}\n".format(TITLE=kws['title']))
data_nts = self.prt_txt(prt, goea_results, prtfmt, **kws)
log = self.log if self.log is not None else sys.stdout
log.write(" {N:>5} GOEA results for {CUR:5} study items. WROTE: {F}\n".format(
N=len(data_nts),
CUR=len(MgrNtGOEAs(goea_results).get_study_items()),
F=fout_txt)) | python | def wr_txt(self, fout_txt, goea_results, prtfmt=None, **kws):
if not goea_results:
sys.stdout.write(" 0 GOEA results. NOT WRITING {FOUT}\n".format(FOUT=fout_txt))
return
with open(fout_txt, 'w') as prt:
if 'title' in kws:
prt.write("{TITLE}\n".format(TITLE=kws['title']))
data_nts = self.prt_txt(prt, goea_results, prtfmt, **kws)
log = self.log if self.log is not None else sys.stdout
log.write(" {N:>5} GOEA results for {CUR:5} study items. WROTE: {F}\n".format(
N=len(data_nts),
CUR=len(MgrNtGOEAs(goea_results).get_study_items()),
F=fout_txt)) | [
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242,554 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.prt_txt | def prt_txt(prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
objprt = PrtFmt()
if prtfmt is None:
flds = ['GO', 'NS', 'p_uncorrected',
'ratio_in_study', 'ratio_in_pop', 'depth', 'name', 'study_items']
prtfmt = objprt.get_prtfmt_str(flds)
prtfmt = objprt.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts | python | def prt_txt(prt, goea_results, prtfmt=None, **kws):
objprt = PrtFmt()
if prtfmt is None:
flds = ['GO', 'NS', 'p_uncorrected',
'ratio_in_study', 'ratio_in_pop', 'depth', 'name', 'study_items']
prtfmt = objprt.get_prtfmt_str(flds)
prtfmt = objprt.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts | [
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242,555 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.wr_xlsx | def wr_xlsx(self, fout_xlsx, goea_results, **kws):
"""Write a xlsx file."""
# kws: prt_if indent itemid2name(study_items)
objprt = PrtFmt()
prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
xlsx_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
if 'fld2col_widths' not in kws:
kws['fld2col_widths'] = {f:objprt.default_fld2col_widths.get(f, 8) for f in prt_flds}
RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws) | python | def wr_xlsx(self, fout_xlsx, goea_results, **kws):
# kws: prt_if indent itemid2name(study_items)
objprt = PrtFmt()
prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
xlsx_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
if 'fld2col_widths' not in kws:
kws['fld2col_widths'] = {f:objprt.default_fld2col_widths.get(f, 8) for f in prt_flds}
RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws) | [
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242,556 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.wr_tsv | def wr_tsv(self, fout_tsv, goea_results, **kws):
"""Write tab-separated table data to file"""
prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.wr_tsv(fout_tsv, tsv_data, **kws) | python | def wr_tsv(self, fout_tsv, goea_results, **kws):
prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.wr_tsv(fout_tsv, tsv_data, **kws) | [
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242,557 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.prt_tsv | def prt_tsv(self, prt, goea_results, **kws):
"""Write tab-separated table data"""
prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_tsv(prt, tsv_data, **kws) | python | def prt_tsv(self, prt, goea_results, **kws):
prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_tsv(prt, tsv_data, **kws) | [
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242,558 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.get_ns2nts | def get_ns2nts(results, fldnames=None, **kws):
"""Get namedtuples of GOEA results, split into BP, MF, CC."""
ns2nts = cx.defaultdict(list)
nts = MgrNtGOEAs(results).get_goea_nts_all(fldnames, **kws)
for ntgoea in nts:
ns2nts[ntgoea.NS].append(ntgoea)
return ns2nts | python | def get_ns2nts(results, fldnames=None, **kws):
ns2nts = cx.defaultdict(list)
nts = MgrNtGOEAs(results).get_goea_nts_all(fldnames, **kws)
for ntgoea in nts:
ns2nts[ntgoea.NS].append(ntgoea)
return ns2nts | [
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242,559 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.print_date | def print_date(min_ratio=None, pval=0.05):
"""Print GOATOOLS version and the date the GOEA was run."""
import goatools
# Header contains provenance and parameters
date = datetime.date.today()
print("# Generated by GOATOOLS v{0} ({1})".format(goatools.__version__, date))
print("# min_ratio={0} pval={1}".format(min_ratio, pval)) | python | def print_date(min_ratio=None, pval=0.05):
import goatools
# Header contains provenance and parameters
date = datetime.date.today()
print("# Generated by GOATOOLS v{0} ({1})".format(goatools.__version__, date))
print("# min_ratio={0} pval={1}".format(min_ratio, pval)) | [
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242,560 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.print_results | def print_results(self, results, min_ratio=None, indent=False, pval=0.05, prt=sys.stdout):
"""Print GOEA results with some additional statistics calculated."""
results_adj = self.get_adj_records(results, min_ratio, pval)
self.print_results_adj(results_adj, indent, prt) | python | def print_results(self, results, min_ratio=None, indent=False, pval=0.05, prt=sys.stdout):
results_adj = self.get_adj_records(results, min_ratio, pval)
self.print_results_adj(results_adj, indent, prt) | [
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242,561 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.get_adj_records | def get_adj_records(results, min_ratio=None, pval=0.05):
"""Return GOEA results with some additional statistics calculated."""
records = []
for rec in results:
# calculate some additional statistics
# (over_under, is_ratio_different)
rec.update_remaining_fldsdefprt(min_ratio=min_ratio)
if pval is not None and rec.p_uncorrected >= pval:
continue
if rec.is_ratio_different:
records.append(rec)
return records | python | def get_adj_records(results, min_ratio=None, pval=0.05):
records = []
for rec in results:
# calculate some additional statistics
# (over_under, is_ratio_different)
rec.update_remaining_fldsdefprt(min_ratio=min_ratio)
if pval is not None and rec.p_uncorrected >= pval:
continue
if rec.is_ratio_different:
records.append(rec)
return records | [
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242,562 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.print_results_adj | def print_results_adj(results, indent=False, prt=sys.stdout):
"""Print GOEA results."""
# Print column headers if there are results to be printed
if results:
prt.write("{R}\n".format(R="\t".join(GOEnrichmentStudy.get_prtflds_default(results))))
# Print the GOEA results
for rec in results:
prt.write("{R}\n".format(R=rec.__str__(indent=indent))) | python | def print_results_adj(results, indent=False, prt=sys.stdout):
# Print column headers if there are results to be printed
if results:
prt.write("{R}\n".format(R="\t".join(GOEnrichmentStudy.get_prtflds_default(results))))
# Print the GOEA results
for rec in results:
prt.write("{R}\n".format(R=rec.__str__(indent=indent))) | [
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242,563 | tanghaibao/goatools | goatools/go_enrichment.py | GOEnrichmentStudy.wr_py_goea_results | def wr_py_goea_results(self, fout_py, goea_results, **kws):
"""Save GOEA results into Python package containing list of namedtuples."""
var_name = kws.get("var_name", "goea_results")
docstring = kws.get("docstring", "")
sortby = kws.get("sortby", None)
if goea_results:
from goatools.nt_utils import wr_py_nts
nts_goea = goea_results
# If list has GOEnrichmentRecords or verbose namedtuples, exclude some fields.
if hasattr(goea_results[0], "_fldsdefprt") or hasattr(goea_results[0], 'goterm'):
# Exclude some attributes from the namedtuple when saving results
# to a Python file because the information is redundant or verbose.
nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
docstring = "\n".join([docstring, "# {VER}\n\n".format(VER=self.obo_dag.version)])
assert hasattr(nts_goea[0], '_fields')
if sortby is None:
sortby = MgrNtGOEAs.dflt_sortby_objgoea
nts_goea = sorted(nts_goea, key=sortby)
wr_py_nts(fout_py, nts_goea, docstring, var_name) | python | def wr_py_goea_results(self, fout_py, goea_results, **kws):
var_name = kws.get("var_name", "goea_results")
docstring = kws.get("docstring", "")
sortby = kws.get("sortby", None)
if goea_results:
from goatools.nt_utils import wr_py_nts
nts_goea = goea_results
# If list has GOEnrichmentRecords or verbose namedtuples, exclude some fields.
if hasattr(goea_results[0], "_fldsdefprt") or hasattr(goea_results[0], 'goterm'):
# Exclude some attributes from the namedtuple when saving results
# to a Python file because the information is redundant or verbose.
nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
docstring = "\n".join([docstring, "# {VER}\n\n".format(VER=self.obo_dag.version)])
assert hasattr(nts_goea[0], '_fields')
if sortby is None:
sortby = MgrNtGOEAs.dflt_sortby_objgoea
nts_goea = sorted(nts_goea, key=sortby)
wr_py_nts(fout_py, nts_goea, docstring, var_name) | [
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242,564 | tryolabs/requestium | requestium/requestium.py | _ensure_click | def _ensure_click(self):
"""Ensures a click gets made, because Selenium can be a bit buggy about clicks
This method gets added to the selenium element returned in '__ensure_element_by_xpath'.
We should probably add it to more selenium methods, such as all the 'find**' methods though.
I wrote this method out of frustration with chromedriver and its problems with clicking
items that need to be scrolled to in order to be clickable. In '__ensure_element_by_xpath' we
scroll to the item before returning it, but chrome has some problems if it doesn't get some
time to scroll to the item. This method ensures chromes gets enough time to scroll to the item
before clicking it. I tried SEVERAL more 'correct' methods to get around this, but none of them
worked 100% of the time (waiting for the element to be 'clickable' does not work).
"""
# We ensure the element is scrolled into the middle of the viewport to ensure that
# it is clickable. There are two main ways an element may not be clickable:
# - It is outside of the viewport
# - It is under a banner or toolbar
# This script solves both cases
script = ("var viewPortHeight = Math.max("
"document.documentElement.clientHeight, window.innerHeight || 0);"
"var elementTop = arguments[0].getBoundingClientRect().top;"
"window.scrollBy(0, elementTop-(viewPortHeight/2));")
self.parent.execute_script(script, self) # parent = the webdriver
for _ in range(10):
try:
self.click()
return
except WebDriverException as e:
exception_message = str(e)
time.sleep(0.2)
raise WebDriverException(
"Couldn't click item after trying 10 times, got error message: \n{}".format(
exception_message
)
) | python | def _ensure_click(self):
# We ensure the element is scrolled into the middle of the viewport to ensure that
# it is clickable. There are two main ways an element may not be clickable:
# - It is outside of the viewport
# - It is under a banner or toolbar
# This script solves both cases
script = ("var viewPortHeight = Math.max("
"document.documentElement.clientHeight, window.innerHeight || 0);"
"var elementTop = arguments[0].getBoundingClientRect().top;"
"window.scrollBy(0, elementTop-(viewPortHeight/2));")
self.parent.execute_script(script, self) # parent = the webdriver
for _ in range(10):
try:
self.click()
return
except WebDriverException as e:
exception_message = str(e)
time.sleep(0.2)
raise WebDriverException(
"Couldn't click item after trying 10 times, got error message: \n{}".format(
exception_message
)
) | [
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I wrote this method out of frustration with chromedriver and its problems with clicking
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242,565 | tryolabs/requestium | requestium/requestium.py | Session.transfer_session_cookies_to_driver | def transfer_session_cookies_to_driver(self, domain=None):
"""Copies the Session's cookies into the webdriver
Using the 'domain' parameter we choose the cookies we wish to transfer, we only
transfer the cookies which belong to that domain. The domain defaults to our last visited
site if not provided.
"""
if not domain and self._last_requests_url:
domain = tldextract.extract(self._last_requests_url).registered_domain
elif not domain and not self._last_requests_url:
raise Exception('Trying to transfer cookies to selenium without specifying a domain '
'and without having visited any page in the current session')
# Transfer cookies
for c in [c for c in self.cookies if domain in c.domain]:
self.driver.ensure_add_cookie({'name': c.name, 'value': c.value, 'path': c.path,
'expiry': c.expires, 'domain': c.domain}) | python | def transfer_session_cookies_to_driver(self, domain=None):
if not domain and self._last_requests_url:
domain = tldextract.extract(self._last_requests_url).registered_domain
elif not domain and not self._last_requests_url:
raise Exception('Trying to transfer cookies to selenium without specifying a domain '
'and without having visited any page in the current session')
# Transfer cookies
for c in [c for c in self.cookies if domain in c.domain]:
self.driver.ensure_add_cookie({'name': c.name, 'value': c.value, 'path': c.path,
'expiry': c.expires, 'domain': c.domain}) | [
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242,566 | tryolabs/requestium | requestium/requestium.py | Session.copy_user_agent_from_driver | def copy_user_agent_from_driver(self):
""" Updates requests' session user-agent with the driver's user agent
This method will start the browser process if its not already running.
"""
selenium_user_agent = self.driver.execute_script("return navigator.userAgent;")
self.headers.update({"user-agent": selenium_user_agent}) | python | def copy_user_agent_from_driver(self):
selenium_user_agent = self.driver.execute_script("return navigator.userAgent;")
self.headers.update({"user-agent": selenium_user_agent}) | [
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242,567 | tryolabs/requestium | requestium/requestium.py | DriverMixin.ensure_add_cookie | def ensure_add_cookie(self, cookie, override_domain=None):
"""Ensures a cookie gets added to the driver
Selenium needs the driver to be currently at the domain of the cookie
before allowing you to add it, so we need to get through this limitation.
The cookie parameter is a dict which must contain the keys (name, value, domain) and
may contain the keys (path, expiry).
We first check that we aren't currently in the cookie's domain, if we aren't, we GET
the cookie's domain and then add the cookies to the driver.
We can override the cookie's domain using 'override_domain'. The use for this
parameter is that sometimes GETting the cookie's domain redirects you to a different
sub domain, and therefore adding the cookie fails. So sometimes the user may
need to override the cookie's domain to a less strict one, Eg.: 'site.com' instead of
'home.site.com', in this way even if the site redirects us to a subdomain, the cookie will
stick. If you set the domain to '', the cookie gets added with whatever domain the browser
is currently at (at least in chrome it does), so this ensures the cookie gets added.
It also retries adding the cookie with a more permissive domain if it fails in the first
try, and raises an exception if that fails. The standard selenium behaviour in this case
was to not do anything, which was very hard to debug.
"""
if override_domain:
cookie['domain'] = override_domain
cookie_domain = cookie['domain'] if cookie['domain'][0] != '.' else cookie['domain'][1:]
try:
browser_domain = tldextract.extract(self.current_url).fqdn
except AttributeError:
browser_domain = ''
if cookie_domain not in browser_domain:
# TODO Check if hardcoding 'http' causes trouble
# TODO Consider using a new proxy for this next request to not cause an anomalous
# request. This way their server sees our ip address as continuously having the
# same cookies and not have a request mid-session with no cookies
self.get('http://' + cookie_domain)
# Fixes phantomjs bug, all domains must start with a period
if self.name == "phantomjs": cookie['domain'] = '.' + cookie['domain']
self.add_cookie(cookie)
# If we fail adding the cookie, retry with a more permissive domain
if not self.is_cookie_in_driver(cookie):
cookie['domain'] = tldextract.extract(cookie['domain']).registered_domain
self.add_cookie(cookie)
if not self.is_cookie_in_driver(cookie):
raise WebDriverException(
"Couldn't add the following cookie to the webdriver\n{}\n".format(cookie)
) | python | def ensure_add_cookie(self, cookie, override_domain=None):
if override_domain:
cookie['domain'] = override_domain
cookie_domain = cookie['domain'] if cookie['domain'][0] != '.' else cookie['domain'][1:]
try:
browser_domain = tldextract.extract(self.current_url).fqdn
except AttributeError:
browser_domain = ''
if cookie_domain not in browser_domain:
# TODO Check if hardcoding 'http' causes trouble
# TODO Consider using a new proxy for this next request to not cause an anomalous
# request. This way their server sees our ip address as continuously having the
# same cookies and not have a request mid-session with no cookies
self.get('http://' + cookie_domain)
# Fixes phantomjs bug, all domains must start with a period
if self.name == "phantomjs": cookie['domain'] = '.' + cookie['domain']
self.add_cookie(cookie)
# If we fail adding the cookie, retry with a more permissive domain
if not self.is_cookie_in_driver(cookie):
cookie['domain'] = tldextract.extract(cookie['domain']).registered_domain
self.add_cookie(cookie)
if not self.is_cookie_in_driver(cookie):
raise WebDriverException(
"Couldn't add the following cookie to the webdriver\n{}\n".format(cookie)
) | [
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242,568 | tryolabs/requestium | requestium/requestium.py | DriverMixin.is_cookie_in_driver | def is_cookie_in_driver(self, cookie):
"""We check that the cookie is correctly added to the driver
We only compare name, value and domain, as the rest can produce false negatives.
We are a bit lenient when comparing domains.
"""
for driver_cookie in self.get_cookies():
if (cookie['name'] == driver_cookie['name'] and
cookie['value'] == driver_cookie['value'] and
(cookie['domain'] == driver_cookie['domain'] or
'.' + cookie['domain'] == driver_cookie['domain'])):
return True
return False | python | def is_cookie_in_driver(self, cookie):
for driver_cookie in self.get_cookies():
if (cookie['name'] == driver_cookie['name'] and
cookie['value'] == driver_cookie['value'] and
(cookie['domain'] == driver_cookie['domain'] or
'.' + cookie['domain'] == driver_cookie['domain'])):
return True
return False | [
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242,569 | tryolabs/requestium | requestium/requestium.py | DriverMixin.ensure_element | def ensure_element(self, locator, selector, state="present", timeout=None):
"""This method allows us to wait till an element appears or disappears in the browser
The webdriver runs in parallel with our scripts, so we must wait for it everytime it
runs javascript. Selenium automatically waits till a page loads when GETing it,
but it doesn't do this when it runs javascript and makes AJAX requests.
So we must explicitly wait in that case.
The 'locator' argument defines what strategy we use to search for the element.
The 'state' argument allows us to chose between waiting for the element to be visible,
clickable, present, or invisible. Presence is more inclusive, but sometimes we want to
know if the element is visible. Careful, its not always intuitive what Selenium considers
to be a visible element. We can also wait for it to be clickable, although this method
is a bit buggy in selenium, an element can be 'clickable' according to selenium and
still fail when we try to click it.
More info at: http://selenium-python.readthedocs.io/waits.html
"""
locators = {'id': By.ID,
'name': By.NAME,
'xpath': By.XPATH,
'link_text': By.LINK_TEXT,
'partial_link_text': By.PARTIAL_LINK_TEXT,
'tag_name': By.TAG_NAME,
'class_name': By.CLASS_NAME,
'css_selector': By.CSS_SELECTOR}
locator = locators[locator]
if not timeout: timeout = self.default_timeout
if state == 'visible':
element = WebDriverWait(self, timeout).until(
EC.visibility_of_element_located((locator, selector))
)
elif state == 'clickable':
element = WebDriverWait(self, timeout).until(
EC.element_to_be_clickable((locator, selector))
)
elif state == 'present':
element = WebDriverWait(self, timeout).until(
EC.presence_of_element_located((locator, selector))
)
elif state == 'invisible':
WebDriverWait(self, timeout).until(
EC.invisibility_of_element_located((locator, selector))
)
element = None
else:
raise ValueError(
"The 'state' argument must be 'visible', 'clickable', 'present' "
"or 'invisible', not '{}'".format(state)
)
# We add this method to our element to provide a more robust click. Chromedriver
# sometimes needs some time before it can click an item, specially if it needs to
# scroll into it first. This method ensures clicks don't fail because of this.
if element:
element.ensure_click = partial(_ensure_click, element)
return element | python | def ensure_element(self, locator, selector, state="present", timeout=None):
locators = {'id': By.ID,
'name': By.NAME,
'xpath': By.XPATH,
'link_text': By.LINK_TEXT,
'partial_link_text': By.PARTIAL_LINK_TEXT,
'tag_name': By.TAG_NAME,
'class_name': By.CLASS_NAME,
'css_selector': By.CSS_SELECTOR}
locator = locators[locator]
if not timeout: timeout = self.default_timeout
if state == 'visible':
element = WebDriverWait(self, timeout).until(
EC.visibility_of_element_located((locator, selector))
)
elif state == 'clickable':
element = WebDriverWait(self, timeout).until(
EC.element_to_be_clickable((locator, selector))
)
elif state == 'present':
element = WebDriverWait(self, timeout).until(
EC.presence_of_element_located((locator, selector))
)
elif state == 'invisible':
WebDriverWait(self, timeout).until(
EC.invisibility_of_element_located((locator, selector))
)
element = None
else:
raise ValueError(
"The 'state' argument must be 'visible', 'clickable', 'present' "
"or 'invisible', not '{}'".format(state)
)
# We add this method to our element to provide a more robust click. Chromedriver
# sometimes needs some time before it can click an item, specially if it needs to
# scroll into it first. This method ensures clicks don't fail because of this.
if element:
element.ensure_click = partial(_ensure_click, element)
return element | [
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runs javascript. Selenium automatically waits till a page loads when GETing it,
but it doesn't do this when it runs javascript and makes AJAX requests.
So we must explicitly wait in that case.
The 'locator' argument defines what strategy we use to search for the element.
The 'state' argument allows us to chose between waiting for the element to be visible,
clickable, present, or invisible. Presence is more inclusive, but sometimes we want to
know if the element is visible. Careful, its not always intuitive what Selenium considers
to be a visible element. We can also wait for it to be clickable, although this method
is a bit buggy in selenium, an element can be 'clickable' according to selenium and
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242,570 | Belval/pdf2image | pdf2image/parsers.py | parse_buffer_to_ppm | def parse_buffer_to_ppm(data):
"""
Parse PPM file bytes to Pillow Image
"""
images = []
index = 0
while index < len(data):
code, size, rgb = tuple(data[index:index + 40].split(b'\n')[0:3])
size_x, size_y = tuple(size.split(b' '))
file_size = len(code) + len(size) + len(rgb) + 3 + int(size_x) * int(size_y) * 3
images.append(Image.open(BytesIO(data[index:index + file_size])))
index += file_size
return images | python | def parse_buffer_to_ppm(data):
images = []
index = 0
while index < len(data):
code, size, rgb = tuple(data[index:index + 40].split(b'\n')[0:3])
size_x, size_y = tuple(size.split(b' '))
file_size = len(code) + len(size) + len(rgb) + 3 + int(size_x) * int(size_y) * 3
images.append(Image.open(BytesIO(data[index:index + file_size])))
index += file_size
return images | [
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242,571 | Belval/pdf2image | pdf2image/parsers.py | parse_buffer_to_jpeg | def parse_buffer_to_jpeg(data):
"""
Parse JPEG file bytes to Pillow Image
"""
return [
Image.open(BytesIO(image_data + b'\xff\xd9'))
for image_data in data.split(b'\xff\xd9')[:-1] # Last element is obviously empty
] | python | def parse_buffer_to_jpeg(data):
return [
Image.open(BytesIO(image_data + b'\xff\xd9'))
for image_data in data.split(b'\xff\xd9')[:-1] # Last element is obviously empty
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242,572 | Belval/pdf2image | pdf2image/parsers.py | parse_buffer_to_png | def parse_buffer_to_png(data):
"""
Parse PNG file bytes to Pillow Image
"""
images = []
c1 = 0
c2 = 0
data_len = len(data)
while c1 < data_len:
# IEND can appear in a PNG without being the actual end
if data[c2:c2 + 4] == b'IEND' and (c2 + 8 == data_len or data[c2+9:c2+12] == b'PNG'):
images.append(Image.open(BytesIO(data[c1:c2 + 8])))
c1 = c2 + 8
c2 = c1
c2 += 1
return images | python | def parse_buffer_to_png(data):
images = []
c1 = 0
c2 = 0
data_len = len(data)
while c1 < data_len:
# IEND can appear in a PNG without being the actual end
if data[c2:c2 + 4] == b'IEND' and (c2 + 8 == data_len or data[c2+9:c2+12] == b'PNG'):
images.append(Image.open(BytesIO(data[c1:c2 + 8])))
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c2 = c1
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return images | [
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242,573 | wal-e/wal-e | wal_e/log_help.py | configure | def configure(*args, **kwargs):
"""
Configure logging.
Borrowed from logging.basicConfig
Uses the IndentFormatter instead of the regular Formatter
Also, opts the caller into Syslog output, unless syslog could not
be opened for some reason or another, in which case a warning will
be printed to the other log handlers.
"""
# Configuration must only happen once: no mechanism for avoiding
# duplication of handlers exists.
assert len(HANDLERS) == 0
log_destinations = get_log_destinations()
if 'stderr' in log_destinations:
# Add stderr output.
HANDLERS.append(logging.StreamHandler())
def terrible_log_output(s):
import sys
print(s, file=sys.stderr)
places = [
# Linux
'/dev/log',
# FreeBSD
'/var/run/log',
# Macintosh
'/var/run/syslog',
]
default_syslog_address = places[0]
for p in places:
if path.exists(p):
default_syslog_address = p
break
syslog_address = kwargs.setdefault('syslog_address',
default_syslog_address)
valid_facility = False
if 'syslog' in log_destinations:
facility, valid_facility = get_syslog_facility()
if not valid_facility:
terrible_log_output('invalid syslog facility level specified')
try:
# Add syslog output.
HANDLERS.append(handlers.SysLogHandler(syslog_address,
facility=facility))
except EnvironmentError as e:
if e.errno in [errno.EACCES, errno.ECONNREFUSED]:
message = ('wal-e: Could not set up syslog, '
'continuing anyway. '
'Reason: {0}').format(errno.errorcode[e.errno])
terrible_log_output(message)
fs = kwargs.get("format", logging.BASIC_FORMAT)
dfs = kwargs.get("datefmt", None)
fmt = IndentFormatter(fs, dfs)
for handler in HANDLERS:
handler.setFormatter(fmt)
logging.root.addHandler(handler)
# Default to INFO level logging.
set_level(kwargs.get('level', logging.INFO)) | python | def configure(*args, **kwargs):
# Configuration must only happen once: no mechanism for avoiding
# duplication of handlers exists.
assert len(HANDLERS) == 0
log_destinations = get_log_destinations()
if 'stderr' in log_destinations:
# Add stderr output.
HANDLERS.append(logging.StreamHandler())
def terrible_log_output(s):
import sys
print(s, file=sys.stderr)
places = [
# Linux
'/dev/log',
# FreeBSD
'/var/run/log',
# Macintosh
'/var/run/syslog',
]
default_syslog_address = places[0]
for p in places:
if path.exists(p):
default_syslog_address = p
break
syslog_address = kwargs.setdefault('syslog_address',
default_syslog_address)
valid_facility = False
if 'syslog' in log_destinations:
facility, valid_facility = get_syslog_facility()
if not valid_facility:
terrible_log_output('invalid syslog facility level specified')
try:
# Add syslog output.
HANDLERS.append(handlers.SysLogHandler(syslog_address,
facility=facility))
except EnvironmentError as e:
if e.errno in [errno.EACCES, errno.ECONNREFUSED]:
message = ('wal-e: Could not set up syslog, '
'continuing anyway. '
'Reason: {0}').format(errno.errorcode[e.errno])
terrible_log_output(message)
fs = kwargs.get("format", logging.BASIC_FORMAT)
dfs = kwargs.get("datefmt", None)
fmt = IndentFormatter(fs, dfs)
for handler in HANDLERS:
handler.setFormatter(fmt)
logging.root.addHandler(handler)
# Default to INFO level logging.
set_level(kwargs.get('level', logging.INFO)) | [
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242,574 | wal-e/wal-e | wal_e/log_help.py | get_syslog_facility | def get_syslog_facility():
"""Get syslog facility from ENV var"""
facil = os.getenv('WALE_SYSLOG_FACILITY', 'user')
valid_facility = True
try:
facility = handlers.SysLogHandler.facility_names[facil.lower()]
except KeyError:
valid_facility = False
facility = handlers.SysLogHandler.LOG_USER
return facility, valid_facility | python | def get_syslog_facility():
facil = os.getenv('WALE_SYSLOG_FACILITY', 'user')
valid_facility = True
try:
facility = handlers.SysLogHandler.facility_names[facil.lower()]
except KeyError:
valid_facility = False
facility = handlers.SysLogHandler.LOG_USER
return facility, valid_facility | [
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242,575 | wal-e/wal-e | wal_e/log_help.py | set_level | def set_level(level):
"""Adjust the logging level of WAL-E"""
for handler in HANDLERS:
handler.setLevel(level)
logging.root.setLevel(level) | python | def set_level(level):
for handler in HANDLERS:
handler.setLevel(level)
logging.root.setLevel(level) | [
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242,576 | wal-e/wal-e | wal_e/log_help.py | IndentFormatter.format | def format(self, record, *args, **kwargs):
"""
Format a message in the log
Act like the normal format, but indent anything that is a
newline within the message.
"""
return logging.Formatter.format(
self, record, *args, **kwargs).replace('\n', '\n' + ' ' * 8) | python | def format(self, record, *args, **kwargs):
return logging.Formatter.format(
self, record, *args, **kwargs).replace('\n', '\n' + ' ' * 8) | [
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"log"
] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/log_help.py#L20-L29 |
242,577 | wal-e/wal-e | wal_e/tar_partition.py | _segmentation_guts | def _segmentation_guts(root, file_paths, max_partition_size):
"""Segment a series of file paths into TarPartition values
These TarPartitions are disjoint and roughly below the prescribed
size.
"""
# Canonicalize root to include the trailing slash, since root is
# intended to be a directory anyway.
if not root.endswith(os.path.sep):
root += os.path.sep
# Ensure that the root path is a directory before continuing.
if not os.path.isdir(root):
raise TarBadRootError(root=root)
bogus_tar = None
try:
# Create a bogus TarFile as a contrivance to be able to run
# gettarinfo and produce such instances. Some of the settings
# on the TarFile are important, like whether to de-reference
# symlinks.
bogus_tar = tarfile.TarFile(os.devnull, 'w', dereference=False)
# Bookkeeping for segmentation of tar members into partitions.
partition_number = 0
partition_bytes = 0
partition_members = 0
partition = TarPartition(partition_number)
for file_path in file_paths:
# Ensure tar members exist within a shared root before
# continuing.
if not file_path.startswith(root):
raise TarBadPathError(root=root, offensive_path=file_path)
# Create an ExtendedTarInfo to represent the tarfile.
try:
et_info = ExtendedTarInfo(
tarinfo=bogus_tar.gettarinfo(
file_path, arcname=file_path[len(root):]),
submitted_path=file_path)
except EnvironmentError as e:
if (e.errno == errno.ENOENT and
e.filename == file_path):
# log a NOTICE/INFO that the file was unlinked.
# Ostensibly harmless (such unlinks should be replayed
# in the WAL) but good to know.
logger.debug(
msg='tar member additions skipping an unlinked file',
detail='Skipping {0}.'.format(et_info.submitted_path))
continue
else:
raise
# Ensure tar members are within an expected size before
# continuing.
if et_info.tarinfo.size > max_partition_size:
raise TarMemberTooBigError(
et_info.tarinfo.name, max_partition_size,
et_info.tarinfo.size)
if (partition_bytes + et_info.tarinfo.size >= max_partition_size
or partition_members >= PARTITION_MAX_MEMBERS):
# Partition is full and cannot accept another member,
# so yield the complete one to the caller.
yield partition
# Prepare a fresh partition to accrue additional file
# paths into.
partition_number += 1
partition_bytes = et_info.tarinfo.size
partition_members = 1
partition = TarPartition(
partition_number, [et_info])
else:
# Partition is able to accept this member, so just add
# it and increment the size counters.
partition_bytes += et_info.tarinfo.size
partition_members += 1
partition.append(et_info)
# Partition size overflow must not to be possible
# here.
assert partition_bytes < max_partition_size
finally:
if bogus_tar is not None:
bogus_tar.close()
# Flush out the final partition should it be non-empty.
if partition:
yield partition | python | def _segmentation_guts(root, file_paths, max_partition_size):
# Canonicalize root to include the trailing slash, since root is
# intended to be a directory anyway.
if not root.endswith(os.path.sep):
root += os.path.sep
# Ensure that the root path is a directory before continuing.
if not os.path.isdir(root):
raise TarBadRootError(root=root)
bogus_tar = None
try:
# Create a bogus TarFile as a contrivance to be able to run
# gettarinfo and produce such instances. Some of the settings
# on the TarFile are important, like whether to de-reference
# symlinks.
bogus_tar = tarfile.TarFile(os.devnull, 'w', dereference=False)
# Bookkeeping for segmentation of tar members into partitions.
partition_number = 0
partition_bytes = 0
partition_members = 0
partition = TarPartition(partition_number)
for file_path in file_paths:
# Ensure tar members exist within a shared root before
# continuing.
if not file_path.startswith(root):
raise TarBadPathError(root=root, offensive_path=file_path)
# Create an ExtendedTarInfo to represent the tarfile.
try:
et_info = ExtendedTarInfo(
tarinfo=bogus_tar.gettarinfo(
file_path, arcname=file_path[len(root):]),
submitted_path=file_path)
except EnvironmentError as e:
if (e.errno == errno.ENOENT and
e.filename == file_path):
# log a NOTICE/INFO that the file was unlinked.
# Ostensibly harmless (such unlinks should be replayed
# in the WAL) but good to know.
logger.debug(
msg='tar member additions skipping an unlinked file',
detail='Skipping {0}.'.format(et_info.submitted_path))
continue
else:
raise
# Ensure tar members are within an expected size before
# continuing.
if et_info.tarinfo.size > max_partition_size:
raise TarMemberTooBigError(
et_info.tarinfo.name, max_partition_size,
et_info.tarinfo.size)
if (partition_bytes + et_info.tarinfo.size >= max_partition_size
or partition_members >= PARTITION_MAX_MEMBERS):
# Partition is full and cannot accept another member,
# so yield the complete one to the caller.
yield partition
# Prepare a fresh partition to accrue additional file
# paths into.
partition_number += 1
partition_bytes = et_info.tarinfo.size
partition_members = 1
partition = TarPartition(
partition_number, [et_info])
else:
# Partition is able to accept this member, so just add
# it and increment the size counters.
partition_bytes += et_info.tarinfo.size
partition_members += 1
partition.append(et_info)
# Partition size overflow must not to be possible
# here.
assert partition_bytes < max_partition_size
finally:
if bogus_tar is not None:
bogus_tar.close()
# Flush out the final partition should it be non-empty.
if partition:
yield partition | [
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242,578 | wal-e/wal-e | wal_e/tar_partition.py | TarPartition.tarfile_extract | def tarfile_extract(fileobj, dest_path):
"""Extract a tarfile described by a file object to a specified path.
Args:
fileobj (file): File object wrapping the target tarfile.
dest_path (str): Path to extract the contents of the tarfile to.
"""
# Though this method doesn't fit cleanly into the TarPartition object,
# tarballs are only ever extracted for partitions so the logic jives
# for the most part.
tar = tarfile.open(mode='r|', fileobj=fileobj,
bufsize=pipebuf.PIPE_BUF_BYTES)
# canonicalize dest_path so the prefix check below works
dest_path = os.path.realpath(dest_path)
# list of files that need fsyncing
extracted_files = []
# Iterate through each member of the tarfile individually. We must
# approach it this way because we are dealing with a pipe and the
# getmembers() method will consume it before we extract any data.
for member in tar:
assert not member.name.startswith('/')
relpath = os.path.join(dest_path, member.name)
# Workaround issue with tar handling of symlink, see:
# https://bugs.python.org/issue12800
if member.issym():
target_path = os.path.join(dest_path, member.name)
try:
os.symlink(member.linkname, target_path)
except OSError as e:
if e.errno == errno.EEXIST:
os.remove(target_path)
os.symlink(member.linkname, target_path)
else:
raise
continue
if member.isreg() and member.size >= pipebuf.PIPE_BUF_BYTES:
cat_extract(tar, member, relpath)
else:
tar.extract(member, path=dest_path)
filename = os.path.realpath(relpath)
extracted_files.append(filename)
# avoid accumulating an unbounded list of strings which
# could be quite large for a large database
if len(extracted_files) > 1000:
_fsync_files(extracted_files)
del extracted_files[:]
tar.close()
_fsync_files(extracted_files) | python | def tarfile_extract(fileobj, dest_path):
# Though this method doesn't fit cleanly into the TarPartition object,
# tarballs are only ever extracted for partitions so the logic jives
# for the most part.
tar = tarfile.open(mode='r|', fileobj=fileobj,
bufsize=pipebuf.PIPE_BUF_BYTES)
# canonicalize dest_path so the prefix check below works
dest_path = os.path.realpath(dest_path)
# list of files that need fsyncing
extracted_files = []
# Iterate through each member of the tarfile individually. We must
# approach it this way because we are dealing with a pipe and the
# getmembers() method will consume it before we extract any data.
for member in tar:
assert not member.name.startswith('/')
relpath = os.path.join(dest_path, member.name)
# Workaround issue with tar handling of symlink, see:
# https://bugs.python.org/issue12800
if member.issym():
target_path = os.path.join(dest_path, member.name)
try:
os.symlink(member.linkname, target_path)
except OSError as e:
if e.errno == errno.EEXIST:
os.remove(target_path)
os.symlink(member.linkname, target_path)
else:
raise
continue
if member.isreg() and member.size >= pipebuf.PIPE_BUF_BYTES:
cat_extract(tar, member, relpath)
else:
tar.extract(member, path=dest_path)
filename = os.path.realpath(relpath)
extracted_files.append(filename)
# avoid accumulating an unbounded list of strings which
# could be quite large for a large database
if len(extracted_files) > 1000:
_fsync_files(extracted_files)
del extracted_files[:]
tar.close()
_fsync_files(extracted_files) | [
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242,579 | wal-e/wal-e | wal_e/operator/backup.py | Backup.backup_list | def backup_list(self, query, detail):
"""
Lists base backups and basic information about them
"""
import csv
from wal_e.storage.base import BackupInfo
bl = self._backup_list(detail)
# If there is no query, return an exhaustive list, otherwise
# find a backup instead.
if query is None:
bl_iter = bl
else:
bl_iter = bl.find_all(query)
# TODO: support switchable formats for difference needs.
w_csv = csv.writer(sys.stdout, dialect='excel-tab')
w_csv.writerow(BackupInfo._fields)
for bi in bl_iter:
w_csv.writerow([getattr(bi, k) for k in BackupInfo._fields])
sys.stdout.flush() | python | def backup_list(self, query, detail):
import csv
from wal_e.storage.base import BackupInfo
bl = self._backup_list(detail)
# If there is no query, return an exhaustive list, otherwise
# find a backup instead.
if query is None:
bl_iter = bl
else:
bl_iter = bl.find_all(query)
# TODO: support switchable formats for difference needs.
w_csv = csv.writer(sys.stdout, dialect='excel-tab')
w_csv.writerow(BackupInfo._fields)
for bi in bl_iter:
w_csv.writerow([getattr(bi, k) for k in BackupInfo._fields])
sys.stdout.flush() | [
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242,580 | wal-e/wal-e | wal_e/operator/backup.py | Backup.database_backup | def database_backup(self, data_directory, *args, **kwargs):
"""Uploads a PostgreSQL file cluster to S3 or Windows Azure Blob
Service
Mechanism: just wraps _upload_pg_cluster_dir with
start/stop backup actions with exception handling.
In particular there is a 'finally' block to stop the backup in
most situations.
"""
upload_good = False
backup_stop_good = False
while_offline = False
start_backup_info = None
if 'while_offline' in kwargs:
while_offline = kwargs.pop('while_offline')
try:
if not while_offline:
start_backup_info = PgBackupStatements.run_start_backup()
version = PgBackupStatements.pg_version()['version']
else:
if os.path.exists(os.path.join(data_directory,
'postmaster.pid')):
hint = ('Shut down postgres. '
'If there is a stale lockfile, '
'then remove it after being very sure postgres '
'is not running.')
raise UserException(
msg='while_offline set, but pg looks to be running',
detail='Found a postmaster.pid lockfile, and aborting',
hint=hint)
ctrl_data = PgControlDataParser(data_directory)
start_backup_info = ctrl_data.last_xlog_file_name_and_offset()
version = ctrl_data.pg_version()
ret_tuple = self._upload_pg_cluster_dir(
start_backup_info, data_directory, version=version, *args,
**kwargs)
spec, uploaded_to, expanded_size_bytes = ret_tuple
upload_good = True
finally:
if not upload_good:
logger.warning(
'blocking on sending WAL segments',
detail=('The backup was not completed successfully, '
'but we have to wait anyway. '
'See README: TODO about pg_cancel_backup'))
if not while_offline:
stop_backup_info = PgBackupStatements.run_stop_backup()
else:
stop_backup_info = start_backup_info
backup_stop_good = True
# XXX: Ugly, this is more of a 'worker' task because it might
# involve retries and error messages, something that is not
# treated by the "operator" category of modules. So
# basically, if this small upload fails, the whole upload
# fails!
if upload_good and backup_stop_good:
# Try to write a sentinel file to the cluster backup
# directory that indicates that the base backup upload has
# definitely run its course and also communicates what WAL
# segments are needed to get to consistency.
sentinel_content = json.dumps(
{'wal_segment_backup_stop':
stop_backup_info['file_name'],
'wal_segment_offset_backup_stop':
stop_backup_info['file_offset'],
'expanded_size_bytes': expanded_size_bytes,
'spec': spec})
# XXX: should use the storage operators.
#
# XXX: distinguish sentinels by *PREFIX* not suffix,
# which makes searching harder. (For the next version
# bump).
uri_put_file(self.creds,
uploaded_to + '_backup_stop_sentinel.json',
BytesIO(sentinel_content.encode("utf8")),
content_type='application/json')
else:
# NB: Other exceptions should be raised before this that
# have more informative results, it is intended that this
# exception never will get raised.
raise UserCritical('could not complete backup process') | python | def database_backup(self, data_directory, *args, **kwargs):
upload_good = False
backup_stop_good = False
while_offline = False
start_backup_info = None
if 'while_offline' in kwargs:
while_offline = kwargs.pop('while_offline')
try:
if not while_offline:
start_backup_info = PgBackupStatements.run_start_backup()
version = PgBackupStatements.pg_version()['version']
else:
if os.path.exists(os.path.join(data_directory,
'postmaster.pid')):
hint = ('Shut down postgres. '
'If there is a stale lockfile, '
'then remove it after being very sure postgres '
'is not running.')
raise UserException(
msg='while_offline set, but pg looks to be running',
detail='Found a postmaster.pid lockfile, and aborting',
hint=hint)
ctrl_data = PgControlDataParser(data_directory)
start_backup_info = ctrl_data.last_xlog_file_name_and_offset()
version = ctrl_data.pg_version()
ret_tuple = self._upload_pg_cluster_dir(
start_backup_info, data_directory, version=version, *args,
**kwargs)
spec, uploaded_to, expanded_size_bytes = ret_tuple
upload_good = True
finally:
if not upload_good:
logger.warning(
'blocking on sending WAL segments',
detail=('The backup was not completed successfully, '
'but we have to wait anyway. '
'See README: TODO about pg_cancel_backup'))
if not while_offline:
stop_backup_info = PgBackupStatements.run_stop_backup()
else:
stop_backup_info = start_backup_info
backup_stop_good = True
# XXX: Ugly, this is more of a 'worker' task because it might
# involve retries and error messages, something that is not
# treated by the "operator" category of modules. So
# basically, if this small upload fails, the whole upload
# fails!
if upload_good and backup_stop_good:
# Try to write a sentinel file to the cluster backup
# directory that indicates that the base backup upload has
# definitely run its course and also communicates what WAL
# segments are needed to get to consistency.
sentinel_content = json.dumps(
{'wal_segment_backup_stop':
stop_backup_info['file_name'],
'wal_segment_offset_backup_stop':
stop_backup_info['file_offset'],
'expanded_size_bytes': expanded_size_bytes,
'spec': spec})
# XXX: should use the storage operators.
#
# XXX: distinguish sentinels by *PREFIX* not suffix,
# which makes searching harder. (For the next version
# bump).
uri_put_file(self.creds,
uploaded_to + '_backup_stop_sentinel.json',
BytesIO(sentinel_content.encode("utf8")),
content_type='application/json')
else:
# NB: Other exceptions should be raised before this that
# have more informative results, it is intended that this
# exception never will get raised.
raise UserCritical('could not complete backup process') | [
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242,581 | wal-e/wal-e | wal_e/operator/backup.py | Backup.wal_archive | def wal_archive(self, wal_path, concurrency=1):
"""
Uploads a WAL file to S3 or Windows Azure Blob Service
This code is intended to typically be called from Postgres's
archive_command feature.
"""
# Upload the segment expressly indicated. It's special
# relative to other uploads when parallel wal-push is enabled,
# in that it's not desirable to tweak its .ready/.done files
# in archive_status.
xlog_dir = os.path.dirname(wal_path)
segment = WalSegment(wal_path, explicit=True)
uploader = WalUploader(self.layout, self.creds, self.gpg_key_id)
group = WalTransferGroup(uploader)
group.start(segment)
# Upload any additional wal segments up to the specified
# concurrency by scanning the Postgres archive_status
# directory.
started = 1
seg_stream = WalSegment.from_ready_archive_status(xlog_dir)
while started < concurrency:
try:
other_segment = next(seg_stream)
except StopIteration:
break
if other_segment.path != wal_path:
group.start(other_segment)
started += 1
try:
# Wait for uploads to finish.
group.join()
except EnvironmentError as e:
if e.errno == errno.ENOENT:
print(e)
raise UserException(
msg='could not find file for wal-push',
detail=('The operating system reported: {0} {1}'
.format(e.strerror, repr(e.filename))))
raise | python | def wal_archive(self, wal_path, concurrency=1):
# Upload the segment expressly indicated. It's special
# relative to other uploads when parallel wal-push is enabled,
# in that it's not desirable to tweak its .ready/.done files
# in archive_status.
xlog_dir = os.path.dirname(wal_path)
segment = WalSegment(wal_path, explicit=True)
uploader = WalUploader(self.layout, self.creds, self.gpg_key_id)
group = WalTransferGroup(uploader)
group.start(segment)
# Upload any additional wal segments up to the specified
# concurrency by scanning the Postgres archive_status
# directory.
started = 1
seg_stream = WalSegment.from_ready_archive_status(xlog_dir)
while started < concurrency:
try:
other_segment = next(seg_stream)
except StopIteration:
break
if other_segment.path != wal_path:
group.start(other_segment)
started += 1
try:
# Wait for uploads to finish.
group.join()
except EnvironmentError as e:
if e.errno == errno.ENOENT:
print(e)
raise UserException(
msg='could not find file for wal-push',
detail=('The operating system reported: {0} {1}'
.format(e.strerror, repr(e.filename))))
raise | [
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242,582 | wal-e/wal-e | wal_e/operator/backup.py | Backup.wal_restore | def wal_restore(self, wal_name, wal_destination, prefetch_max):
"""
Downloads a WAL file from S3 or Windows Azure Blob Service
This code is intended to typically be called from Postgres's
restore_command feature.
NB: Postgres doesn't guarantee that wal_name ==
basename(wal_path), so both are required.
"""
url = '{0}://{1}/{2}'.format(
self.layout.scheme, self.layout.store_name(),
self.layout.wal_path(wal_name))
if prefetch_max > 0:
# Check for prefetch-hit.
base = os.path.dirname(os.path.realpath(wal_destination))
pd = prefetch.Dirs(base)
seg = WalSegment(wal_name)
started = start_prefetches(seg, pd, prefetch_max)
last_size = 0
while True:
if pd.contains(seg):
pd.promote(seg, wal_destination)
logger.info(
msg='promoted prefetched wal segment',
structured={'action': 'wal-fetch',
'key': url,
'seg': wal_name,
'prefix': self.layout.path_prefix})
pd.clear_except(started)
return True
# If there is a 'running' download, wait a bit for it
# to make progress or finish. However, if it doesn't
# make progress in some amount of time, assume that
# the prefetch process has died and go on with the
# in-band downloading code.
sz = pd.running_size(seg)
if sz <= last_size:
break
last_size = sz
gevent.sleep(0.5)
pd.clear_except(started)
logger.info(
msg='begin wal restore',
structured={'action': 'wal-fetch',
'key': url,
'seg': wal_name,
'prefix': self.layout.path_prefix,
'state': 'begin'})
ret = do_lzop_get(self.creds, url, wal_destination,
self.gpg_key_id is not None)
logger.info(
msg='complete wal restore',
structured={'action': 'wal-fetch',
'key': url,
'seg': wal_name,
'prefix': self.layout.path_prefix,
'state': 'complete'})
return ret | python | def wal_restore(self, wal_name, wal_destination, prefetch_max):
url = '{0}://{1}/{2}'.format(
self.layout.scheme, self.layout.store_name(),
self.layout.wal_path(wal_name))
if prefetch_max > 0:
# Check for prefetch-hit.
base = os.path.dirname(os.path.realpath(wal_destination))
pd = prefetch.Dirs(base)
seg = WalSegment(wal_name)
started = start_prefetches(seg, pd, prefetch_max)
last_size = 0
while True:
if pd.contains(seg):
pd.promote(seg, wal_destination)
logger.info(
msg='promoted prefetched wal segment',
structured={'action': 'wal-fetch',
'key': url,
'seg': wal_name,
'prefix': self.layout.path_prefix})
pd.clear_except(started)
return True
# If there is a 'running' download, wait a bit for it
# to make progress or finish. However, if it doesn't
# make progress in some amount of time, assume that
# the prefetch process has died and go on with the
# in-band downloading code.
sz = pd.running_size(seg)
if sz <= last_size:
break
last_size = sz
gevent.sleep(0.5)
pd.clear_except(started)
logger.info(
msg='begin wal restore',
structured={'action': 'wal-fetch',
'key': url,
'seg': wal_name,
'prefix': self.layout.path_prefix,
'state': 'begin'})
ret = do_lzop_get(self.creds, url, wal_destination,
self.gpg_key_id is not None)
logger.info(
msg='complete wal restore',
structured={'action': 'wal-fetch',
'key': url,
'seg': wal_name,
'prefix': self.layout.path_prefix,
'state': 'complete'})
return ret | [
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This code is intended to typically be called from Postgres's
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NB: Postgres doesn't guarantee that wal_name ==
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242,583 | wal-e/wal-e | wal_e/operator/backup.py | Backup._upload_pg_cluster_dir | def _upload_pg_cluster_dir(self, start_backup_info, pg_cluster_dir,
version, pool_size, rate_limit=None):
"""
Upload to url_prefix from pg_cluster_dir
This function ignores the directory pg_xlog, which contains WAL
files and are not generally part of a base backup.
Note that this is also lzo compresses the files: thus, the number
of pooled processes involves doing a full sequential scan of the
uncompressed Postgres heap file that is pipelined into lzo. Once
lzo is completely finished (necessary to have access to the file
size) the file is sent to S3 or WABS.
TODO: Investigate an optimization to decouple the compression and
upload steps to make sure that the most efficient possible use of
pipelining of network and disk resources occurs. Right now it
possible to bounce back and forth between bottlenecking on reading
from the database block device and subsequently the S3/WABS sending
steps should the processes be at the same stage of the upload
pipeline: this can have a very negative impact on being able to
make full use of system resources.
Furthermore, it desirable to overflowing the page cache: having
separate tunables for number of simultanious compression jobs
(which occupy /tmp space and page cache) and number of uploads
(which affect upload throughput) would help.
"""
spec, parts = tar_partition.partition(pg_cluster_dir)
# TODO :: Move arbitray path construction to StorageLayout Object
backup_prefix = '{0}/basebackups_{1}/base_{file_name}_{file_offset}'\
.format(self.layout.prefix.rstrip('/'), FILE_STRUCTURE_VERSION,
**start_backup_info)
if rate_limit is None:
per_process_limit = None
else:
per_process_limit = int(rate_limit / pool_size)
# Reject tiny per-process rate limits. They should be
# rejected more nicely elsewhere.
assert per_process_limit is None or per_process_limit > 0
total_size = 0
# Make an attempt to upload extended version metadata
extended_version_url = backup_prefix + '/extended_version.txt'
logger.info(
msg='start upload postgres version metadata',
detail=('Uploading to {extended_version_url}.'
.format(extended_version_url=extended_version_url)))
uri_put_file(self.creds,
extended_version_url, BytesIO(version.encode("utf8")),
content_type='text/plain')
logger.info(msg='postgres version metadata upload complete')
uploader = PartitionUploader(self.creds, backup_prefix,
per_process_limit, self.gpg_key_id)
pool = TarUploadPool(uploader, pool_size)
# Enqueue uploads for parallel execution
for tpart in parts:
total_size += tpart.total_member_size
# 'put' can raise an exception for a just-failed upload,
# aborting the process.
pool.put(tpart)
# Wait for remaining parts to upload. An exception can be
# raised to signal failure of the upload.
pool.join()
return spec, backup_prefix, total_size | python | def _upload_pg_cluster_dir(self, start_backup_info, pg_cluster_dir,
version, pool_size, rate_limit=None):
spec, parts = tar_partition.partition(pg_cluster_dir)
# TODO :: Move arbitray path construction to StorageLayout Object
backup_prefix = '{0}/basebackups_{1}/base_{file_name}_{file_offset}'\
.format(self.layout.prefix.rstrip('/'), FILE_STRUCTURE_VERSION,
**start_backup_info)
if rate_limit is None:
per_process_limit = None
else:
per_process_limit = int(rate_limit / pool_size)
# Reject tiny per-process rate limits. They should be
# rejected more nicely elsewhere.
assert per_process_limit is None or per_process_limit > 0
total_size = 0
# Make an attempt to upload extended version metadata
extended_version_url = backup_prefix + '/extended_version.txt'
logger.info(
msg='start upload postgres version metadata',
detail=('Uploading to {extended_version_url}.'
.format(extended_version_url=extended_version_url)))
uri_put_file(self.creds,
extended_version_url, BytesIO(version.encode("utf8")),
content_type='text/plain')
logger.info(msg='postgres version metadata upload complete')
uploader = PartitionUploader(self.creds, backup_prefix,
per_process_limit, self.gpg_key_id)
pool = TarUploadPool(uploader, pool_size)
# Enqueue uploads for parallel execution
for tpart in parts:
total_size += tpart.total_member_size
# 'put' can raise an exception for a just-failed upload,
# aborting the process.
pool.put(tpart)
# Wait for remaining parts to upload. An exception can be
# raised to signal failure of the upload.
pool.join()
return spec, backup_prefix, total_size | [
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This function ignores the directory pg_xlog, which contains WAL
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Note that this is also lzo compresses the files: thus, the number
of pooled processes involves doing a full sequential scan of the
uncompressed Postgres heap file that is pipelined into lzo. Once
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TODO: Investigate an optimization to decouple the compression and
upload steps to make sure that the most efficient possible use of
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possible to bounce back and forth between bottlenecking on reading
from the database block device and subsequently the S3/WABS sending
steps should the processes be at the same stage of the upload
pipeline: this can have a very negative impact on being able to
make full use of system resources.
Furthermore, it desirable to overflowing the page cache: having
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242,584 | wal-e/wal-e | wal_e/operator/backup.py | Backup._exception_gather_guard | def _exception_gather_guard(self, fn):
"""
A higher order function to trap UserExceptions and then log them.
This is to present nicer output to the user when failures are
occuring in another thread of execution that may not end up at
the catch-all try/except in main().
"""
@functools.wraps(fn)
def wrapper(*args, **kwargs):
try:
return fn(*args, **kwargs)
except UserException as e:
self.exceptions.append(e)
return wrapper | python | def _exception_gather_guard(self, fn):
@functools.wraps(fn)
def wrapper(*args, **kwargs):
try:
return fn(*args, **kwargs)
except UserException as e:
self.exceptions.append(e)
return wrapper | [
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242,585 | wal-e/wal-e | wal_e/worker/prefetch.py | Dirs.create | def create(self, segment):
"""A best-effort attempt to create directories.
Warnings are issued to the user if those directories could not
created or if they don't exist.
The caller should only call this function if the user
requested prefetching (i.e. concurrency) to avoid spurious
warnings.
"""
def lackadaisical_mkdir(place):
ok = False
place = path.realpath(place)
try:
os.makedirs(place, 0o700)
ok = True
except EnvironmentError as e:
if e.errno == errno.EEXIST:
# Has already been created: this is the most
# common situation, and is fine.
ok = True
else:
logger.warning(
msg='could not create prefetch directory',
detail=('Prefetch directory creation target: {0}, {1}'
.format(place, e.strerror)))
return ok
ok = True
for d in [self.prefetched_dir, self.running]:
ok &= lackadaisical_mkdir(d)
lackadaisical_mkdir(self.seg_dir(segment)) | python | def create(self, segment):
def lackadaisical_mkdir(place):
ok = False
place = path.realpath(place)
try:
os.makedirs(place, 0o700)
ok = True
except EnvironmentError as e:
if e.errno == errno.EEXIST:
# Has already been created: this is the most
# common situation, and is fine.
ok = True
else:
logger.warning(
msg='could not create prefetch directory',
detail=('Prefetch directory creation target: {0}, {1}'
.format(place, e.strerror)))
return ok
ok = True
for d in [self.prefetched_dir, self.running]:
ok &= lackadaisical_mkdir(d)
lackadaisical_mkdir(self.seg_dir(segment)) | [
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The caller should only call this function if the user
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242,586 | wal-e/wal-e | wal_e/pep3143daemon/pidfile.py | PidFile.acquire | def acquire(self):
"""Acquire the pidfile.
Create the pidfile, lock it, write the pid into it
and register the release with atexit.
:return: None
:raise: SystemExit
"""
try:
pidfile = open(self._pidfile, "a")
except IOError as err:
raise SystemExit(err)
try:
fcntl.flock(pidfile.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB)
except IOError:
raise SystemExit('Already running according to ' + self._pidfile)
pidfile.seek(0)
pidfile.truncate()
pidfile.write(str(os.getpid()) + '\n')
pidfile.flush()
self.pidfile = pidfile
atexit.register(self.release) | python | def acquire(self):
try:
pidfile = open(self._pidfile, "a")
except IOError as err:
raise SystemExit(err)
try:
fcntl.flock(pidfile.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB)
except IOError:
raise SystemExit('Already running according to ' + self._pidfile)
pidfile.seek(0)
pidfile.truncate()
pidfile.write(str(os.getpid()) + '\n')
pidfile.flush()
self.pidfile = pidfile
atexit.register(self.release) | [
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242,587 | wal-e/wal-e | wal_e/pep3143daemon/pidfile.py | PidFile.release | def release(self):
"""Release the pidfile.
Close and delete the Pidfile.
:return: None
"""
try:
self.pidfile.close()
os.remove(self._pidfile)
except OSError as err:
if err.errno != 2:
raise | python | def release(self):
try:
self.pidfile.close()
os.remove(self._pidfile)
except OSError as err:
if err.errno != 2:
raise | [
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242,588 | wal-e/wal-e | wal_e/pipebuf.py | _configure_buffer_sizes | def _configure_buffer_sizes():
"""Set up module globals controlling buffer sizes"""
global PIPE_BUF_BYTES
global OS_PIPE_SZ
PIPE_BUF_BYTES = 65536
OS_PIPE_SZ = None
# Teach the 'fcntl' module about 'F_SETPIPE_SZ', which is a Linux-ism,
# but a good one that can drastically reduce the number of syscalls
# when dealing with high-throughput pipes.
if not hasattr(fcntl, 'F_SETPIPE_SZ'):
import platform
if platform.system() == 'Linux':
fcntl.F_SETPIPE_SZ = 1031
# If Linux procfs (or something that looks like it) exposes its
# maximum F_SETPIPE_SZ, adjust the default buffer sizes.
try:
with open('/proc/sys/fs/pipe-max-size', 'r') as f:
# Figure out OS pipe size, but in case it is unusually large
# or small restrain it to sensible values.
OS_PIPE_SZ = min(int(f.read()), 1024 * 1024)
PIPE_BUF_BYTES = max(OS_PIPE_SZ, PIPE_BUF_BYTES)
except Exception:
pass | python | def _configure_buffer_sizes():
global PIPE_BUF_BYTES
global OS_PIPE_SZ
PIPE_BUF_BYTES = 65536
OS_PIPE_SZ = None
# Teach the 'fcntl' module about 'F_SETPIPE_SZ', which is a Linux-ism,
# but a good one that can drastically reduce the number of syscalls
# when dealing with high-throughput pipes.
if not hasattr(fcntl, 'F_SETPIPE_SZ'):
import platform
if platform.system() == 'Linux':
fcntl.F_SETPIPE_SZ = 1031
# If Linux procfs (or something that looks like it) exposes its
# maximum F_SETPIPE_SZ, adjust the default buffer sizes.
try:
with open('/proc/sys/fs/pipe-max-size', 'r') as f:
# Figure out OS pipe size, but in case it is unusually large
# or small restrain it to sensible values.
OS_PIPE_SZ = min(int(f.read()), 1024 * 1024)
PIPE_BUF_BYTES = max(OS_PIPE_SZ, PIPE_BUF_BYTES)
except Exception:
pass | [
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242,589 | wal-e/wal-e | wal_e/pipebuf.py | set_buf_size | def set_buf_size(fd):
"""Set up os pipe buffer size, if applicable"""
if OS_PIPE_SZ and hasattr(fcntl, 'F_SETPIPE_SZ'):
fcntl.fcntl(fd, fcntl.F_SETPIPE_SZ, OS_PIPE_SZ) | python | def set_buf_size(fd):
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242,590 | wal-e/wal-e | wal_e/worker/pg/wal_transfer.py | WalSegment.mark_done | def mark_done(self):
"""Mark the archive status of this segment as 'done'.
This is most useful when performing out-of-band parallel
uploads of segments, so that Postgres doesn't try to go and
upload them again.
This amounts to messing with an internal bookkeeping mechanism
of Postgres, but that mechanism is not changing too fast over
the last five years and seems simple enough.
"""
# Recheck that this is not an segment explicitly passed from Postgres
if self.explicit:
raise UserCritical(
msg='unexpected attempt to modify wal metadata detected',
detail=('Segments explicitly passed from postgres should not '
'engage in archiver metadata manipulation: {0}'
.format(self.path)),
hint='report a bug')
# Attempt a rename of archiver metadata, wrapping unexpected
# raised exceptions into a UserCritical.
try:
status_dir = path.join(path.dirname(self.path),
'archive_status')
ready_metadata = path.join(status_dir, self.name + '.ready')
done_metadata = path.join(status_dir, self.name + '.done')
os.rename(ready_metadata, done_metadata)
except Exception:
raise UserCritical(
msg='problem moving .ready archive status to .done',
detail='Traceback is: {0}'.format(traceback.format_exc()),
hint='report a bug') | python | def mark_done(self):
# Recheck that this is not an segment explicitly passed from Postgres
if self.explicit:
raise UserCritical(
msg='unexpected attempt to modify wal metadata detected',
detail=('Segments explicitly passed from postgres should not '
'engage in archiver metadata manipulation: {0}'
.format(self.path)),
hint='report a bug')
# Attempt a rename of archiver metadata, wrapping unexpected
# raised exceptions into a UserCritical.
try:
status_dir = path.join(path.dirname(self.path),
'archive_status')
ready_metadata = path.join(status_dir, self.name + '.ready')
done_metadata = path.join(status_dir, self.name + '.done')
os.rename(ready_metadata, done_metadata)
except Exception:
raise UserCritical(
msg='problem moving .ready archive status to .done',
detail='Traceback is: {0}'.format(traceback.format_exc()),
hint='report a bug') | [
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] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/worker/pg/wal_transfer.py#L30-L65 |
242,591 | wal-e/wal-e | wal_e/worker/pg/wal_transfer.py | WalTransferGroup.join | def join(self):
"""Wait for transfer to exit, raising errors as necessary."""
self.closed = True
while self.expect > 0:
val = self.wait_change.get()
self.expect -= 1
if val is not None:
# Wait a while for all running greenlets to exit, and
# then attempt to force them to exit so join()
# terminates in a reasonable amount of time.
gevent.joinall(list(self.greenlets), timeout=30)
gevent.killall(list(self.greenlets), block=True, timeout=30)
raise val | python | def join(self):
self.closed = True
while self.expect > 0:
val = self.wait_change.get()
self.expect -= 1
if val is not None:
# Wait a while for all running greenlets to exit, and
# then attempt to force them to exit so join()
# terminates in a reasonable amount of time.
gevent.joinall(list(self.greenlets), timeout=30)
gevent.killall(list(self.greenlets), block=True, timeout=30)
raise val | [
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242,592 | wal-e/wal-e | wal_e/worker/pg/wal_transfer.py | WalTransferGroup.start | def start(self, segment):
"""Begin transfer for an indicated wal segment."""
if self.closed:
raise UserCritical(msg='attempt to transfer wal after closing',
hint='report a bug')
g = gevent.Greenlet(self.transferer, segment)
g.link(self._complete_execution)
self.greenlets.add(g)
# Increment .expect before starting the greenlet, or else a
# very unlucky .join could be fooled as to when pool is
# complete.
self.expect += 1
g.start() | python | def start(self, segment):
if self.closed:
raise UserCritical(msg='attempt to transfer wal after closing',
hint='report a bug')
g = gevent.Greenlet(self.transferer, segment)
g.link(self._complete_execution)
self.greenlets.add(g)
# Increment .expect before starting the greenlet, or else a
# very unlucky .join could be fooled as to when pool is
# complete.
self.expect += 1
g.start() | [
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242,593 | wal-e/wal-e | wal_e/worker/pg/wal_transfer.py | WalTransferGroup._complete_execution | def _complete_execution(self, g):
"""Forward any raised exceptions across a channel."""
# Triggered via completion callback.
#
# Runs in its own greenlet, so take care to forward the
# exception, if any, to fail the entire transfer in event of
# trouble.
assert g.ready()
self.greenlets.remove(g)
placed = UserCritical(msg='placeholder bogus exception',
hint='report a bug')
if g.successful():
try:
segment = g.get()
if not segment.explicit:
segment.mark_done()
except BaseException as e:
# Absorb and forward exceptions across the channel.
placed = e
else:
placed = None
else:
placed = g.exception
self.wait_change.put(placed) | python | def _complete_execution(self, g):
# Triggered via completion callback.
#
# Runs in its own greenlet, so take care to forward the
# exception, if any, to fail the entire transfer in event of
# trouble.
assert g.ready()
self.greenlets.remove(g)
placed = UserCritical(msg='placeholder bogus exception',
hint='report a bug')
if g.successful():
try:
segment = g.get()
if not segment.explicit:
segment.mark_done()
except BaseException as e:
# Absorb and forward exceptions across the channel.
placed = e
else:
placed = None
else:
placed = g.exception
self.wait_change.put(placed) | [
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] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/worker/pg/wal_transfer.py#L164-L192 |
242,594 | wal-e/wal-e | wal_e/piper.py | pipe | def pipe(*args):
"""
Takes as parameters several dicts, each with the same
parameters passed to popen.
Runs the various processes in a pipeline, connecting
the stdout of every process except the last with the
stdin of the next process.
Adapted from http://www.enricozini.org/2009/debian/python-pipes/
"""
if len(args) < 2:
raise ValueError("pipe needs at least 2 processes")
# Set stdout=PIPE in every subprocess except the last
for i in args[:-1]:
i["stdout"] = subprocess.PIPE
# Runs all subprocesses connecting stdins and stdouts to create the
# pipeline. Closes stdouts to avoid deadlocks.
popens = [popen_sp(**args[0])]
for i in range(1, len(args)):
args[i]["stdin"] = popens[i - 1].stdout
popens.append(popen_sp(**args[i]))
popens[i - 1].stdout.close()
# Returns the array of subprocesses just created
return popens | python | def pipe(*args):
if len(args) < 2:
raise ValueError("pipe needs at least 2 processes")
# Set stdout=PIPE in every subprocess except the last
for i in args[:-1]:
i["stdout"] = subprocess.PIPE
# Runs all subprocesses connecting stdins and stdouts to create the
# pipeline. Closes stdouts to avoid deadlocks.
popens = [popen_sp(**args[0])]
for i in range(1, len(args)):
args[i]["stdin"] = popens[i - 1].stdout
popens.append(popen_sp(**args[i]))
popens[i - 1].stdout.close()
# Returns the array of subprocesses just created
return popens | [
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Runs the various processes in a pipeline, connecting
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Adapted from http://www.enricozini.org/2009/debian/python-pipes/ | [
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] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/piper.py#L94-L122 |
242,595 | wal-e/wal-e | wal_e/piper.py | pipe_wait | def pipe_wait(popens):
"""
Given an array of Popen objects returned by the
pipe method, wait for all processes to terminate
and return the array with their return values.
Taken from http://www.enricozini.org/2009/debian/python-pipes/
"""
# Avoid mutating the passed copy
popens = copy.copy(popens)
results = [0] * len(popens)
while popens:
last = popens.pop(-1)
results[len(popens)] = last.wait()
return results | python | def pipe_wait(popens):
# Avoid mutating the passed copy
popens = copy.copy(popens)
results = [0] * len(popens)
while popens:
last = popens.pop(-1)
results[len(popens)] = last.wait()
return results | [
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... | Given an array of Popen objects returned by the
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and return the array with their return values.
Taken from http://www.enricozini.org/2009/debian/python-pipes/ | [
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] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/piper.py#L125-L140 |
242,596 | wal-e/wal-e | wal_e/blobstore/wabs/calling_format.py | CallingInfo.connect | def connect(self, creds):
"""Return an azure BlockBlobService instance.
"""
return BlockBlobService(account_name=creds.account_name,
account_key=creds.account_key,
sas_token=creds.access_token,
protocol='https') | python | def connect(self, creds):
return BlockBlobService(account_name=creds.account_name,
account_key=creds.account_key,
sas_token=creds.access_token,
protocol='https') | [
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] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/blobstore/wabs/calling_format.py#L23-L29 |
242,597 | wal-e/wal-e | wal_e/blobstore/file/file_util.py | do_lzop_get | def do_lzop_get(creds, url, path, decrypt, do_retry):
"""
Get and decompress a URL
This streams the content directly to lzop; the compressed version
is never stored on disk.
"""
assert url.endswith('.lzo'), 'Expect an lzop-compressed file'
with files.DeleteOnError(path) as decomp_out:
key = _uri_to_key(creds, url)
with get_download_pipeline(PIPE, decomp_out.f, decrypt) as pl:
g = gevent.spawn(write_and_return_error, key, pl.stdin)
exc = g.get()
if exc is not None:
raise exc
logger.info(
msg='completed download and decompression',
detail='Downloaded and decompressed "{url}" to "{path}"'
.format(url=url, path=path))
return True | python | def do_lzop_get(creds, url, path, decrypt, do_retry):
assert url.endswith('.lzo'), 'Expect an lzop-compressed file'
with files.DeleteOnError(path) as decomp_out:
key = _uri_to_key(creds, url)
with get_download_pipeline(PIPE, decomp_out.f, decrypt) as pl:
g = gevent.spawn(write_and_return_error, key, pl.stdin)
exc = g.get()
if exc is not None:
raise exc
logger.info(
msg='completed download and decompression',
detail='Downloaded and decompressed "{url}" to "{path}"'
.format(url=url, path=path))
return True | [
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... | Get and decompress a URL
This streams the content directly to lzop; the compressed version
is never stored on disk. | [
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] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/blobstore/file/file_util.py#L36-L59 |
242,598 | wal-e/wal-e | wal_e/worker/pg/psql_worker.py | psql_csv_run | def psql_csv_run(sql_command, error_handler=None):
"""
Runs psql and returns a CSVReader object from the query
This CSVReader includes header names as the first record in all
situations. The output is fully buffered into Python.
"""
csv_query = ('COPY ({query}) TO STDOUT WITH CSV HEADER;'
.format(query=sql_command))
new_env = os.environ.copy()
new_env.setdefault('PGOPTIONS', '')
new_env["PGOPTIONS"] += ' --statement-timeout=0'
psql_proc = popen_nonblock([PSQL_BIN, '-d', 'postgres', '--no-password',
'--no-psqlrc', '-c', csv_query],
stdout=PIPE,
env=new_env)
stdout = psql_proc.communicate()[0].decode('utf-8')
if psql_proc.returncode != 0:
if error_handler is not None:
error_handler(psql_proc)
else:
assert error_handler is None
raise UserException(
'could not csv-execute a query successfully via psql',
'Query was "{query}".'.format(sql_command),
'You may have to set some libpq environment '
'variables if you are sure the server is running.')
# Previous code must raise any desired exceptions for non-zero
# exit codes
assert psql_proc.returncode == 0
# Fake enough iterator interface to get a CSV Reader object
# that works.
return csv.reader(iter(stdout.strip().split('\n'))) | python | def psql_csv_run(sql_command, error_handler=None):
csv_query = ('COPY ({query}) TO STDOUT WITH CSV HEADER;'
.format(query=sql_command))
new_env = os.environ.copy()
new_env.setdefault('PGOPTIONS', '')
new_env["PGOPTIONS"] += ' --statement-timeout=0'
psql_proc = popen_nonblock([PSQL_BIN, '-d', 'postgres', '--no-password',
'--no-psqlrc', '-c', csv_query],
stdout=PIPE,
env=new_env)
stdout = psql_proc.communicate()[0].decode('utf-8')
if psql_proc.returncode != 0:
if error_handler is not None:
error_handler(psql_proc)
else:
assert error_handler is None
raise UserException(
'could not csv-execute a query successfully via psql',
'Query was "{query}".'.format(sql_command),
'You may have to set some libpq environment '
'variables if you are sure the server is running.')
# Previous code must raise any desired exceptions for non-zero
# exit codes
assert psql_proc.returncode == 0
# Fake enough iterator interface to get a CSV Reader object
# that works.
return csv.reader(iter(stdout.strip().split('\n'))) | [
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] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/worker/pg/psql_worker.py#L34-L71 |
242,599 | wal-e/wal-e | wal_e/worker/pg/psql_worker.py | PgBackupStatements._wal_name | def _wal_name(cls):
"""
Sets and returns _WAL_NAME to 'wal' or 'xlog' depending on
version of postgres we are working with.
It is used for handling xlog -> wal rename in postgres v10
"""
if cls._WAL_NAME is None:
version = cls._dict_transform(psql_csv_run(
"SELECT current_setting('server_version_num')"))
if int(version['current_setting']) >= 100000:
cls._WAL_NAME = 'wal'
else:
cls._WAL_NAME = 'xlog'
return cls._WAL_NAME | python | def _wal_name(cls):
if cls._WAL_NAME is None:
version = cls._dict_transform(psql_csv_run(
"SELECT current_setting('server_version_num')"))
if int(version['current_setting']) >= 100000:
cls._WAL_NAME = 'wal'
else:
cls._WAL_NAME = 'xlog'
return cls._WAL_NAME | [
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It is used for handling xlog -> wal rename in postgres v10 | [
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] | 027263860e72a403bc0e1497bb3e67523138e7a2 | https://github.com/wal-e/wal-e/blob/027263860e72a403bc0e1497bb3e67523138e7a2/wal_e/worker/pg/psql_worker.py#L91-L106 |
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