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Merge pull request #9415 from mvdbeek/interval_viewport_fixes
[20.01] Fixes for get_estimated_display_viewport
This commit is contained in:
Marius van den Beek
+168
-181
@@ -167,40 +167,36 @@ class Interval(Tabular):
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start = sys.maxsize
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end = 0
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max_col = max(chrom_col, start_col, end_col)
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fh = open(dataset.file_name)
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while True:
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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# Stop if at end of file
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if not line:
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break
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# Skip comment lines
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if not line.startswith('#'):
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try:
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fields = line.rstrip().split('\t')
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if len(fields) > max_col:
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if chrom is None or chrom == fields[chrom_col]:
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start = min(start, int(fields[start_col]))
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end = max(end, int(fields[end_col]))
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# Set chrom last, in case start and end are not integers
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chrom = fields[chrom_col]
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viewport_feature_count -= 1
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except Exception:
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# Most likely a non-integer field has been encountered
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# for start / stop. Just ignore and make sure we finish
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# reading the line and decrementing the counters.
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pass
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# Make sure we are at the next new line
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readline_count = VIEWPORT_MAX_READS_PER_LINE
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while line.rstrip('\n\r') == line:
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assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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readline_count -= 1
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max_line_count -= 1
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if not viewport_feature_count or not max_line_count:
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# exceeded viewport or total line count to check
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break
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with open(dataset.file_name) as fh:
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for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
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# Skip comment lines
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if not line.startswith('#'):
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try:
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fields = line.rstrip().split('\t')
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if len(fields) > max_col:
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if chrom is None or chrom == fields[chrom_col]:
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start = min(start, int(fields[start_col]))
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end = max(end, int(fields[end_col]))
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# Set chrom last, in case start and end are not integers
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chrom = fields[chrom_col]
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viewport_feature_count -= 1
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except Exception:
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# Most likely a non-integer field has been encountered
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# for start / stop. Just ignore and make sure we finish
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# reading the line and decrementing the counters.
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pass
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# Make sure we are at the next new line
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readline_count = VIEWPORT_MAX_READS_PER_LINE
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while line.rstrip('\n\r') == line:
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assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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readline_count -= 1
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max_line_count -= 1
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if not viewport_feature_count or not max_line_count:
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# exceeded viewport or total line count to check
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break
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if chrom is not None:
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return (chrom, str(start), str(end)) # Necessary to return strings?
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except Exception:
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@@ -712,66 +708,63 @@ class Gff(Tabular, _RemoteCallMixin):
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seqid = None
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start = sys.maxsize
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stop = 0
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fh = open(dataset.file_name)
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while True:
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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try:
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if line.startswith('##sequence-region'): # ##sequence-region IV 6000000 6030000
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elems = line.rstrip('\n\r').split()
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if len(elems) > 3:
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# line looks like:
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# sequence-region ctg123 1 1497228
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seqid = elems[1] # IV
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start = int(elems[2]) # 6000000
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stop = int(elems[3]) # 6030000
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break # use location declared in file
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elif len(elems) == 2 and elems[1].find('..') > 0:
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# line looks like this:
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# sequence-region X:120000..140000
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elems = elems[1].split(':')
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seqid = elems[0]
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start = int(elems[1].split('..')[0])
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stop = int(elems[1].split('..')[1])
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break # use location declared in file
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else:
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log.exception("line (%s) uses an unsupported ##sequence-region definition." % str(line))
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# break #no break, if bad definition, we try another method
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elif line.startswith("browser position"):
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# Allow UCSC style browser and track info in the GFF file
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pos_info = line.split()[-1]
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seqid, startend = pos_info.split(":")
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start, stop = map(int, startend.split("-"))
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break # use location declared in file
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elif True not in map(line.startswith, ('#', 'track', 'browser')): # line.startswith() does not accept iterator in python2.4
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viewport_feature_count -= 1
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elems = line.rstrip('\n\r').split('\t')
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if len(elems) > 3:
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if not seqid:
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# We can only set the viewport for a single chromosome
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with open(dataset.file_name) as fh:
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for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
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try:
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if line.startswith('##sequence-region'): # ##sequence-region IV 6000000 6030000
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elems = line.rstrip('\n\r').split()
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if len(elems) > 3:
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# line looks like:
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# sequence-region ctg123 1 1497228
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seqid = elems[1] # IV
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start = int(elems[2]) # 6000000
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stop = int(elems[3]) # 6030000
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break # use location declared in file
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elif len(elems) == 2 and elems[1].find('..') > 0:
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# line looks like this:
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# sequence-region X:120000..140000
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elems = elems[1].split(':')
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seqid = elems[0]
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if seqid == elems[0]:
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# Make sure we have not spanned chromosomes
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start = min(start, int(elems[3]))
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stop = max(stop, int(elems[4]))
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except Exception:
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# most likely start/stop is not an int or not enough fields
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pass
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# make sure we are at the next new line
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readline_count = VIEWPORT_MAX_READS_PER_LINE
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while line.rstrip('\n\r') == line:
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assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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readline_count -= 1
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max_line_count -= 1
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if not viewport_feature_count or not max_line_count:
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# exceeded viewport or total line count to check
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break
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if seqid is not None:
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return (seqid, str(start), str(stop)) # Necessary to return strings?
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start = int(elems[1].split('..')[0])
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stop = int(elems[1].split('..')[1])
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break # use location declared in file
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else:
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log.debug("line (%s) uses an unsupported ##sequence-region definition." % str(line))
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# break #no break, if bad definition, we try another line
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elif line.startswith("browser position"):
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# Allow UCSC style browser and track info in the GFF file
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pos_info = line.split()[-1]
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seqid, startend = pos_info.split(":")
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start, stop = map(int, startend.split("-"))
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break # use location declared in file
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elif not line.startswith(('#', 'track', 'browser')):
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viewport_feature_count -= 1
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elems = line.rstrip('\n\r').split('\t')
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if len(elems) > 3:
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if not seqid:
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# We can only set the viewport for a single chromosome
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seqid = elems[0]
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if seqid == elems[0]:
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# Make sure we have not spanned chromosomes
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start = min(start, int(elems[3]))
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stop = max(stop, int(elems[4]))
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except Exception:
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# most likely start/stop is not an int or not enough fields
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pass
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# make sure we are at the next new line
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readline_count = VIEWPORT_MAX_READS_PER_LINE
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while line.rstrip('\n\r') == line:
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assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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readline_count -= 1
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max_line_count -= 1
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if not viewport_feature_count or not max_line_count:
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# exceeded viewport or total line count to check
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break
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if seqid is not None:
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return (seqid, str(start), str(stop)) # Necessary to return strings?
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except Exception:
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log.exception('Unexpected error')
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return (None, None, None) # could not determine viewport
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@@ -1091,53 +1084,50 @@ class Wiggle(Tabular, _RemoteCallMixin):
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end = 0
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span = 1
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step = None
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fh = open(dataset.file_name)
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while True:
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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try:
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if line.startswith("browser"):
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chr_info = line.rstrip('\n\r').split()[-1]
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chrom, coords = chr_info.split(":")
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start, end = map(int, coords.split("-"))
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break # use the browser line
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# variableStep chrom=chr20
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if line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
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if chrom is not None:
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break # different chrom or different section of the chrom
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chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
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if 'span=' in line:
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span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
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if 'step=' in line:
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step = int(line.rstrip('\n\r').split("step=")[1].split()[0])
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start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
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else:
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fields = line.rstrip('\n\r').split()
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if fields:
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if step is not None:
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if not end:
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end = start + span
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with open(dataset.file_name) as fh:
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for line in util.iter_readline_count(fh, VIEWPORT_READLINE_BUFFER_SIZE):
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try:
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if line.startswith("browser"):
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chr_info = line.rstrip('\n\r').split()[-1]
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chrom, coords = chr_info.split(":")
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start, end = map(int, coords.split("-"))
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break # use the browser line
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# variableStep chrom=chr20
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if line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
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if chrom is not None:
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break # different chrom or different section of the chrom
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chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
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if 'span=' in line:
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span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
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if 'step=' in line:
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step = int(line.rstrip('\n\r').split("step=")[1].split()[0])
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start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
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else:
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fields = line.rstrip('\n\r').split()
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if fields:
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if step is not None:
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if not end:
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end = start + span
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else:
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end += step
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else:
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end += step
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else:
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start = min(int(fields[0]), start)
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end = max(end, int(fields[0]) + span)
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viewport_feature_count -= 1
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except Exception:
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pass
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# make sure we are at the next new line
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readline_count = VIEWPORT_MAX_READS_PER_LINE
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while line.rstrip('\n\r') == line:
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assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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readline_count -= 1
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max_line_count -= 1
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if not viewport_feature_count or not max_line_count:
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# exceeded viewport or total line count to check
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break
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start = min(int(fields[0]), start)
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end = max(end, int(fields[0]) + span)
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viewport_feature_count -= 1
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except Exception:
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pass
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# make sure we are at the next new line
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readline_count = VIEWPORT_MAX_READS_PER_LINE
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while line.rstrip('\n\r') == line:
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assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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readline_count -= 1
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max_line_count -= 1
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if not viewport_feature_count or not max_line_count:
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# exceeded viewport or total line count to check
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break
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if chrom is not None:
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return (chrom, str(start), str(end)) # Necessary to return strings?
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except Exception:
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@@ -1278,49 +1268,46 @@ class CustomTrack(Tabular):
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span = 1
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if self.displayable(dataset):
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try:
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fh = open(dataset.file_name)
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while True:
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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if not line.startswith('#'):
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try:
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if variable_step_wig:
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fields = line.rstrip().split()
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if len(fields) == 2:
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start = int(fields[0])
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return (chrom, str(start), str(start + span))
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elif line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
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chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
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if 'span=' in line:
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span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
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if 'start=' in line:
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start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
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return (chrom, str(start), str(start + span))
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with open(dataset.file_name) as fh:
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for line in util.iter_start_of_line(fh, VIEWPORT_READLINE_BUFFER_SIZE):
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if not line.startswith('#'):
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try:
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if variable_step_wig:
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fields = line.rstrip().split()
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if len(fields) == 2:
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start = int(fields[0])
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return (chrom, str(start), str(start + span))
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elif line and (line.lower().startswith("variablestep") or line.lower().startswith("fixedstep")):
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chrom = line.rstrip('\n\r').split("chrom=")[1].split()[0]
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if 'span=' in line:
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span = int(line.rstrip('\n\r').split("span=")[1].split()[0])
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if 'start=' in line:
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start = int(line.rstrip('\n\r').split("start=")[1].split()[0])
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return (chrom, str(start), str(start + span))
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else:
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variable_step_wig = True
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else:
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variable_step_wig = True
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else:
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fields = line.rstrip().split('\t')
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if len(fields) >= 3:
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chrom = fields[0]
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start = int(fields[1])
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end = int(fields[2])
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return (chrom, str(start), str(end))
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except Exception:
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# most likely a non-integer field has been encountered for start / stop
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continue
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# make sure we are at the next new line
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readline_count = VIEWPORT_MAX_READS_PER_LINE
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while line.rstrip('\n\r') == line:
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assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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readline_count -= 1
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max_line_count -= 1
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if not max_line_count:
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# exceeded viewport or total line count to check
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break
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fields = line.rstrip().split('\t')
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if len(fields) >= 3:
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chrom = fields[0]
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start = int(fields[1])
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end = int(fields[2])
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return (chrom, str(start), str(end))
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except Exception:
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# most likely a non-integer field has been encountered for start / stop
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continue
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# make sure we are at the next new line
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readline_count = VIEWPORT_MAX_READS_PER_LINE
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while line.rstrip('\n\r') == line:
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assert readline_count > 0, Exception('Viewport readline count exceeded for dataset %s.' % dataset.id)
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line = fh.readline(VIEWPORT_READLINE_BUFFER_SIZE)
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if not line:
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break # EOF
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readline_count -= 1
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max_line_count -= 1
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if not max_line_count:
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# exceeded viewport or total line count to check
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break
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except Exception:
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log.exception('Unexpected error')
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return (None, None, None) # could not determine viewport
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@@ -66,12 +66,13 @@ def get_keys_from_dict(dl, keys_list):
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"""
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This function builds a list using the keys from nest dictionaries
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"""
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assert isinstance(keys_list, list)
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if isinstance(dl, dict):
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keys_list += list(dl.keys())
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list(map(lambda x: get_keys_from_dict(x, keys_list), dl.values()))
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keys_list.extend(dl.keys())
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for x in dl.values():
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get_keys_from_dict(x, keys_list)
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elif isinstance(dl, list):
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list(map(lambda x: get_keys_from_dict(x, keys_list), dl))
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for x in dl:
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get_keys_from_dict(x, keys_list)
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class RuleValidator(object):
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@@ -152,7 +152,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
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# precondition: user has been validated
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# allow user to be a list and call recursivly
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if isinstance(user, list):
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return list(map(lambda user: self.share_with(item, user, flush=False), user))
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return [self.share_with(item, _, flush=False) for _ in user]
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# get or create
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existing = self.get_share_assocs(item, user=user)
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if existing:
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@@ -181,7 +181,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
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Delete a user share (or list of shares) from the database.
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"""
|
||||
if isinstance(user, list):
|
||||
return list(map(lambda user: self.unshare_with(item, user, flush=False), user))
|
||||
return [self.unshare_with(item, _, flush=False) for _ in user]
|
||||
# Look for and delete sharing relation for user.
|
||||
user_share_assoc = self.get_share_assocs(item, user=user)[0]
|
||||
self.session().delete(user_share_assoc)
|
||||
|
||||
@@ -1088,7 +1088,7 @@ class ToolTestDescription(object):
|
||||
return {
|
||||
"inputs": inputs_dict,
|
||||
"outputs": self.outputs,
|
||||
"output_collections": list(map(lambda o: o.to_dict(), self.output_collections)),
|
||||
"output_collections": [_.to_dict() for _ in self.output_collections],
|
||||
"num_outputs": self.num_outputs,
|
||||
"command_line": self.command_line,
|
||||
"command_version": self.command_version,
|
||||
|
||||
@@ -2637,7 +2637,8 @@ class DatabaseOperationTool(Tool):
|
||||
if not input_dataset_collection.collection.populated:
|
||||
raise ToolInputsNotReadyException("An input collection is not populated.")
|
||||
|
||||
list(map(check_dataset_instance, input_dataset_collection.dataset_instances))
|
||||
for dataset_instance in input_dataset_collection.dataset_instances:
|
||||
check_dataset_instance(dataset_instance)
|
||||
|
||||
def _add_datasets_to_history(self, history, elements, datasets_visible=False):
|
||||
datasets = []
|
||||
|
||||
@@ -26,6 +26,7 @@ import xml.dom.minidom
|
||||
from datetime import datetime
|
||||
from email.mime.multipart import MIMEMultipart
|
||||
from email.mime.text import MIMEText
|
||||
from functools import partial
|
||||
from hashlib import md5
|
||||
from os.path import relpath
|
||||
from xml.etree import ElementInclude, ElementTree
|
||||
@@ -188,6 +189,14 @@ def synchronized(func):
|
||||
return caller
|
||||
|
||||
|
||||
def iter_start_of_line(fh, chunk_size=None):
|
||||
"""
|
||||
Iterate over fh and call readline(chunk_size)
|
||||
"""
|
||||
for line in iter(partial(fh.readline, chunk_size), ""):
|
||||
yield line
|
||||
|
||||
|
||||
def file_iter(fname, sep=None):
|
||||
"""
|
||||
This generator iterates over a file and yields its lines
|
||||
@@ -198,9 +207,10 @@ def file_iter(fname, sep=None):
|
||||
>>> len(lines) != 0
|
||||
True
|
||||
"""
|
||||
for line in open(fname):
|
||||
if line and line[0] != '#':
|
||||
yield line.split(sep)
|
||||
with open(fname) as fh:
|
||||
for line in fh:
|
||||
if line and line[0] != '#':
|
||||
yield line.split(sep)
|
||||
|
||||
|
||||
def file_reader(fp, chunk_size=CHUNK_SIZE):
|
||||
|
||||
@@ -164,11 +164,11 @@ class SpecifiedDateListGrid(grids.Grid):
|
||||
# We are either filtering on a date like YYYY-MM-DD or on a month like YYYY-MM,
|
||||
# so we need to figure out which type of date we have
|
||||
if column_filter.count('-') == 2: # We are filtering on a date like YYYY-MM-DD
|
||||
year, month, day = list(map(int, column_filter.split("-")))
|
||||
year, month, day = map(int, column_filter.split("-"))
|
||||
start_date = date(year, month, day)
|
||||
end_date = start_date + timedelta(days=1)
|
||||
if column_filter.count('-') == 1: # We are filtering on a month like YYYY-MM
|
||||
year, month = list(map(int, column_filter.split("-")))
|
||||
year, month = map(int, column_filter.split("-"))
|
||||
start_date = date(year, month, 1)
|
||||
end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
|
||||
|
||||
@@ -371,7 +371,7 @@ class Jobs(BaseUIController, ReportQueryBuilder):
|
||||
specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
|
||||
specified_month = specified_date[:7]
|
||||
|
||||
year, month = list(map(int, specified_month.split("-")))
|
||||
year, month = map(int, specified_month.split("-"))
|
||||
start_date = date(year, month, 1)
|
||||
end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
|
||||
month_label = start_date.strftime("%B")
|
||||
@@ -472,7 +472,7 @@ class Jobs(BaseUIController, ReportQueryBuilder):
|
||||
# If specified_date is not received, we'll default to the current month
|
||||
specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
|
||||
specified_month = specified_date[:7]
|
||||
year, month = list(map(int, specified_month.split("-")))
|
||||
year, month = map(int, specified_month.split("-"))
|
||||
start_date = date(year, month, 1)
|
||||
end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
|
||||
month_label = start_date.strftime("%B")
|
||||
|
||||
@@ -61,7 +61,7 @@ class Users(BaseUIController, ReportQueryBuilder):
|
||||
# If specified_date is not received, we'll default to the current month
|
||||
specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
|
||||
specified_month = specified_date[:7]
|
||||
year, month = list(map(int, specified_month.split("-")))
|
||||
year, month = map(int, specified_month.split("-"))
|
||||
start_date = date(year, month, 1)
|
||||
end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
|
||||
month_label = start_date.strftime("%B")
|
||||
@@ -91,7 +91,7 @@ class Users(BaseUIController, ReportQueryBuilder):
|
||||
message = escape(util.restore_text(kwd.get('message', '')))
|
||||
# If specified_date is not received, we'll default to the current month
|
||||
specified_date = kwd.get('specified_date', datetime.utcnow().strftime("%Y-%m-%d"))
|
||||
year, month, day = list(map(int, specified_date.split("-")))
|
||||
year, month, day = map(int, specified_date.split("-"))
|
||||
start_date = date(year, month, day)
|
||||
end_date = start_date + timedelta(days=1)
|
||||
day_of_month = start_date.strftime("%d")
|
||||
|
||||
@@ -64,14 +64,14 @@ class SpecifiedDateListGrid(grids.Grid):
|
||||
# so we need to figure out which type of date we have
|
||||
if column_filter.count('-') == 2:
|
||||
# We are filtering on a date like YYYY-MM-DD
|
||||
year, month, day = list(map(int, column_filter.split("-")))
|
||||
year, month, day = map(int, column_filter.split("-"))
|
||||
start_date = date(year, month, day)
|
||||
end_date = start_date + timedelta(days=1)
|
||||
return query.filter(and_(self.model_class.table.c.create_time >= start_date,
|
||||
self.model_class.table.c.create_time < end_date))
|
||||
if column_filter.count('-') == 1:
|
||||
# We are filtering on a month like YYYY-MM
|
||||
year, month = list(map(int, column_filter.split("-")))
|
||||
year, month = map(int, column_filter.split("-"))
|
||||
start_date = date(year, month, 1)
|
||||
end_date = start_date + timedelta(days=calendar.monthrange(year, month)[1])
|
||||
return query.filter(and_(self.model_class.table.c.create_time >= start_date,
|
||||
|
||||
Reference in New Issue
Block a user