Mercurial > repos > iuc > query_tabular
changeset 15:cf4397560712 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
| author | iuc |
|---|---|
| date | Thu, 27 Jun 2024 17:23:34 +0000 |
| parents | 3a6b78c39dca |
| children | |
| files | filters.py load_db.py macros.xml query_tabular.xml |
| diffstat | 4 files changed, 36 insertions(+), 35 deletions(-) [+] |
line wrap: on
line diff
--- a/filters.py Wed Sep 13 12:15:42 2023 +0000 +++ b/filters.py Thu Jun 27 17:23:34 2024 +0000 @@ -11,7 +11,7 @@ def __init__(self, source, filter_dict): self.source = source self.filter_dict = filter_dict - self.func = lambda i, l: l.rstrip('\r\n') if l else None + self.func = lambda i, line: line.rstrip('\r\n') if line else None self.src_lines = [] self.src_line_cnt = 0 @@ -28,23 +28,23 @@ if filter_dict['filter'] == 'regex': rgx = re.compile(filter_dict['pattern']) if filter_dict['action'] == 'exclude_match': - self.func = lambda i, l: l if not rgx.match(l) else None + self.func = lambda i, line: line if not rgx.match(line) else None elif filter_dict['action'] == 'include_match': - self.func = lambda i, l: l if rgx.match(l) else None + self.func = lambda i, line: line if rgx.match(line) else None elif filter_dict['action'] == 'exclude_find': - self.func = lambda i, l: l if not rgx.search(l) else None + self.func = lambda i, line: line if not rgx.search(line) else None elif filter_dict['action'] == 'include_find': - self.func = lambda i, l: l if rgx.search(l) else None + self.func = lambda i, line: line if rgx.search(line) else None elif filter_dict['filter'] == 'select_columns': cols = [int(c) - 1 for c in filter_dict['columns']] - self.func = lambda i, l: self.select_columns(l, cols) + self.func = lambda i, line: self.select_columns(line, cols) elif filter_dict['filter'] == 'select_column_slices': cols = [x if isinstance(x, int) else [y if y is not None else None for y in [xint(k) for k in x.split(':')]] for x in [xint(c) for c in filter_dict['columns']]] if all([isinstance(x, int) for x in cols]): - self.func = lambda i, l: self.select_columns(l, cols) + self.func = lambda i, line: self.select_columns(line, cols) else: cols = [slice(x[0], x[1], x[2] if len(x) > 2 else None) if isinstance(x, list) else x for x in cols] - self.func = lambda i, l: self.select_slices(l, cols) + self.func = lambda i, line: self.select_slices(line, cols) elif filter_dict['filter'] == 'replace': p = filter_dict['pattern'] r = filter_dict['replace'] @@ -54,32 +54,32 @@ 'append', 'before', 'after']: - self.func = lambda i, l: '\t'.join( + self.func = lambda i, line: '\t'.join( [x if j != c else re.sub(p, r, x) - for j, x in enumerate(l.split('\t'))]) + for j, x in enumerate(line.split('\t'))]) else: a = 0 if filter_dict['add'] == 'prepend'\ else min(0, c - 1) if filter_dict['add'] == 'before'\ else c + 1 if filter_dict['add'] == 'after'\ else None - self.func = lambda i, l: self.replace_add(l, p, r, c, a) + self.func = lambda i, line: self.replace_add(line, p, r, c, a) elif filter_dict['filter'] == 'prepend_line_num': - self.func = lambda i, l: '%d\t%s' % (i, l) + self.func = lambda i, line: '%d\t%s' % (i, line) elif filter_dict['filter'] == 'append_line_num': - self.func = lambda i, l: '%s\t%d' % (l.rstrip('\r\n'), i) + self.func = lambda i, line: '%s\t%d' % (line.rstrip('\r\n'), i) elif filter_dict['filter'] == 'prepend_text': s = filter_dict['column_text'] - self.func = lambda i, l: '%s\t%s' % (s, l) + self.func = lambda i, line: '%s\t%s' % (s, line) elif filter_dict['filter'] == 'append_text': s = filter_dict['column_text'] - self.func = lambda i, l: '%s\t%s' % (l.rstrip('\r\n'), s) + self.func = lambda i, line: '%s\t%s' % (line.rstrip('\r\n'), s) elif filter_dict['filter'] == 'skip': cnt = filter_dict['count'] - self.func = lambda i, l: l if i > cnt else None + self.func = lambda i, line: line if i > cnt else None elif filter_dict['filter'] == 'normalize': cols = [int(c) - 1 for c in filter_dict['columns']] sep = filter_dict['separator'] - self.func = lambda i, l: self.normalize(l, cols, sep) + self.func = lambda i, line: self.normalize(line, cols, sep) def __iter__(self): return self
--- a/load_db.py Wed Sep 13 12:15:42 2023 +0000 +++ b/load_db.py Thu Jun 27 17:23:34 2024 +0000 @@ -328,4 +328,4 @@ c.close() except Exception as e: print('Failed: %s err: %s' % (index_def, e), file=sys.stderr) - raise(e) + raise e
--- a/macros.xml Wed Sep 13 12:15:42 2023 +0000 +++ b/macros.xml Thu Jun 27 17:23:34 2024 +0000 @@ -8,8 +8,8 @@ #set $skip_lines = None #if str($fi.filter.skip_lines) != '': #set $skip_lines = int($fi.filter.skip_lines) - #elif $tbl.table.metadata.comment_lines and $tbl.table.metadata.comment_lines > 0: - #set $skip_lines = int($tbl.table.metadata.comment_lines) + #elif $table.metadata.comment_lines and int($table.metadata.comment_lines) > 0: + #set $skip_lines = int($table.metadata.comment_lines) #end if #if $skip_lines is not None: #set $filter_dict = dict()
--- a/query_tabular.xml Wed Sep 13 12:15:42 2023 +0000 +++ b/query_tabular.xml Thu Jun 27 17:23:34 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="query_tabular" name="Query Tabular" version="3.3.1"> +<tool id="query_tabular" name="Query Tabular" version="3.3.2"> <description>using sqlite sql</description> <macros> @@ -37,6 +37,7 @@ #set $jtbls = [] #set $jtbldef['tables'] = $jtbls #for $i,$tbl in enumerate($tables): + #set $table = $tbl.table #set $jtbl = dict() #set $jtbl['file_path'] = str($tbl.table) #if $tbl.tbl_opts.table_name: @@ -137,7 +138,7 @@ You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns. </help> <sanitizer sanitize="False"/> - <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator> + <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|\[\S+[^,"]*\])?(,([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|\[\S+[^,"]*\])?)*$</validator> </param> <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/> <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name" @@ -148,7 +149,7 @@ <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/> <param name="index_columns" type="text" value="" label="Index on Columns"> <help>Create an index on the column names: e.g. for default column names: c1 or c2,c4 ( use the names you gave for columns)</help> - <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator> + <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|\[\S+[^,"]*\])(,([A-Za-z]\w*|"\S+[^,"]"|`\S+[^,`]*`|\[\S+[^,"]*\])?)*$</validator> <sanitizer sanitize="False"/> </param> </repeat> @@ -192,7 +193,7 @@ </outputs> <tests> <!-- Test 1 --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="customers.tsv"/> <section name="input_opts"> @@ -228,7 +229,7 @@ </test> <!-- Test 2 --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="customers.tsv"/> <section name="input_opts"> @@ -259,7 +260,7 @@ </test> <!-- Test 3 --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="customers.tsv"/> <section name="input_opts"> @@ -279,7 +280,7 @@ </test> <!-- Test 4 --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="IEDB.tsv"/> <section name="input_opts"> @@ -315,7 +316,7 @@ </test> <!-- Test 5 --> - <test> + <test expect_num_outputs="1"> <section name="add_to_database"> <param name="withdb" ftype="sqlite" value="testdb.sqlite"/> </section> @@ -365,7 +366,7 @@ </test> <!-- Test 6 --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="pets.tsv"/> <section name="input_opts"> @@ -446,7 +447,7 @@ </test> <!-- Test 7 --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="psm_report.tsv"/> <section name="input_opts"> @@ -472,7 +473,7 @@ </test> <!-- Test 8 column_names_from_first_line --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="psm_report.tsv"/> <section name="input_opts"> @@ -498,7 +499,7 @@ </test> <!-- Test 9 modify database --> - <test> + <test expect_num_outputs="2"> <repeat name="tables"> <param name="table" ftype="tabular" value="psm_report.tsv"/> <section name="input_opts"> @@ -539,7 +540,7 @@ </test> <!-- Test 10 column_names_from_first_line --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> <section name="input_opts"> @@ -565,7 +566,7 @@ </test> <!-- Test 11 --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> <section name="input_opts"> @@ -592,7 +593,7 @@ </test> <!-- Test 12 math functions --> - <test> + <test expect_num_outputs="1"> <repeat name="tables"> <param name="table" ftype="tabular" value="math_input.tsv"/> </repeat>