From 142e495a9fa83b67f5f8c045e5cd254f5d68806d Mon Sep 17 00:00:00 2001 From: mkslofstra Date: Tue, 3 Dec 2019 14:09:03 +0100 Subject: [PATCH 1/4] fix(HistoryWriter): Make sure writer works with new export --- preprocessing/HistoryWriter.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/preprocessing/HistoryWriter.py b/preprocessing/HistoryWriter.py index ed28a28..2235ed7 100644 --- a/preprocessing/HistoryWriter.py +++ b/preprocessing/HistoryWriter.py @@ -15,23 +15,23 @@ def parse_comments_file(comments_file): headers = [] comments = {} for i, line in enumerate(opened_file): - line = line.strip('\n').split('\t') + line = line.strip('\n').replace('"', '').split('\t') if i == 0: headers = line else: - comments[line[headers.index('"id"')]] = line[headers.index('"comments"')] + comments[line[headers.index('id')]] = line[headers.index('comments')] opened_file.close() return comments @staticmethod def _remove_column(column): - return column.endswith('link"') or column == '"history"' + return column.endswith('link') or column == 'history' def _get_export_moment(self): yymm = str(self.yymm) - year = "20" + yymm[0:2] + year = '20' + yymm[0:2] month = datetime.date(1900, int(yymm[2:4]), 1).strftime('%B') - return '"{} {}"\n'.format(month, year) + return '{} {}\n'.format(month, year) def parse_consensus_file(self, consensus_file, history_file_name): history_file = open(history_file_name, 'w') @@ -40,19 +40,19 @@ def parse_consensus_file(self, consensus_file, history_file_name): remove_pos = [] comments_pos = 0 for i, line in enumerate(opened_file): - line = line.strip('\n').split('\t') + line = line.strip('\n').replace('"', '').split('\t') if i == 0: - id_pos = line.index('"id"') - comments_pos = line.index('"comments"') + id_pos = line.index('id') + comments_pos = line.index('comments') remove_pos = [line.index(link) for link in line if self._remove_column(link)] headers = [column for column in line if not self._remove_column(column)] - headers.append('"export"\n') + headers.append('export\n') history_file.write('\t'.join(headers)) else: # move comments value to comments column line[comments_pos] = self.comments[line[id_pos]] # rename id - line[id_pos] = '"{}_{}"'.format(self.yymm, eval(line[id_pos])) + line[id_pos] = '{}_{}'.format(self.yymm, line[id_pos]) # remove lab link + history columns for link_idx in remove_pos[::-1]: del line[link_idx] @@ -69,7 +69,7 @@ def main(): output_folder = config.output previous = config.previous[-1] HistoryWriter(previous, input_folder + 'vkgl_consensus20{}.tsv'.format(previous), - input_folder + 'vkgl_consensus_comments20{}}.tsv'.format(previous), + input_folder + 'vkgl_consensus_comments20{}.tsv'.format(previous), output_folder + '/vkgl_consensus_history.tsv') From fa674955963a4488800698edcf19d3b04c3acb5f Mon Sep 17 00:00:00 2001 From: mkslofstra Date: Tue, 3 Dec 2019 14:24:43 +0100 Subject: [PATCH 2/4] fix(mcmd): Fix bug in clean raw labs --- mcmd_scripts/vkgl_cleanup_raw_labs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mcmd_scripts/vkgl_cleanup_raw_labs b/mcmd_scripts/vkgl_cleanup_raw_labs index 6d83f3c..e4f4a5a 100644 --- a/mcmd_scripts/vkgl_cleanup_raw_labs +++ b/mcmd_scripts/vkgl_cleanup_raw_labs @@ -2,7 +2,7 @@ delete --data vkgl_raw_amc_v2 -f delete --data vkgl_raw_radboud_v2 -f delete --data vkgl_raw_lumc_v2 -f delete --data vkgl_raw_erasmus_v2 -f -delete --data vkgl_radboud_mumc -f +delete --data vkgl_raw_radboud_v2 -f delete --data vkgl_raw_nki_v2 -f delete --data vkgl_raw_umcg_v2 -f delete --data vkgl_raw_vumc_v2 -f \ No newline at end of file From 3fd37635bca70bb5486371de294e5cb1c65bde03 Mon Sep 17 00:00:00 2001 From: mkslofstra Date: Tue, 3 Dec 2019 15:50:54 +0100 Subject: [PATCH 3/4] fix(emx): Make transcript,cdna and protein text datatype --- emx/vkgl-model.xlsx | Bin 28712 -> 28696 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/emx/vkgl-model.xlsx 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zspCVx=de@I07IWFriHfJ*W$;&_@dck)KO=&w3I?I7scA-mPq=(%qrs#fa~)XmV*x; z%_4-i+xnuH%CYv_J~}B(`}|X?&BN$48L zbK>tNEl1q{zTm}K&NJaeI+n#9*spjnyY+EY?KH>Sx)UL%Y$?V Date: Tue, 3 Dec 2019 15:51:18 +0100 Subject: [PATCH 4/4] fix(setup): Make work with setup --- consensus/__main__.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/consensus/__main__.py b/consensus/__main__.py index 35d8d94..5be7576 100644 --- a/consensus/__main__.py +++ b/consensus/__main__.py @@ -9,7 +9,7 @@ def main(): # Get data from config - config = ConfigParser('../config/config.txt') + config = ConfigParser('config/config.txt') # To run by pressing play in pycharm, use ../config/config.txt consensus_table = config.prefix + config.consensus comments_table = config.prefix + config.comments molgenis_server = molgenis.Session(config.server) diff --git a/setup.py b/setup.py index 625b34d..e54c1a9 100644 --- a/setup.py +++ b/setup.py @@ -1,6 +1,6 @@ from setuptools import setup, find_packages setup( - name='ConsensusTableUploader', + name='consensus', version='1.0', packages=find_packages(), install_requires=['molgenis-py-client>=2.1.0', 'progressbar2==3.39.3', 'termcolor==1.1.0', 'yaspin==0.14.3', 'pandas'],