From 822320eb0d562da354faaa82b898bfb88aa685c7 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Wed, 4 Oct 2017 12:42:42 -0400 Subject: [PATCH 01/30] Auto-create sandbox for tests if it is not already there. --- tests/Makefile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/Makefile b/tests/Makefile index f1d93eb..2b044f2 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -83,6 +83,10 @@ test_invoke: @$(PYTHON) $(SRC)/gdc_mirror.py --help >/dev/null @$(PYTHON) $(SRC)/gdc_list.py --help >/dev/null @echo Test assorted features or API calls directly, instead of via tools + @if [ ! -d $(TEST_ROOT) ] ; then \ + echo creating $(TEST_ROOT) ;\ + mkdir -p "$(TEST_ROOT)" ;\ + fi @$(PYTHON) misctests.py > $(TEST_ROOT)/misctests.txt diff $(TEST_ROOT)/misctests.txt baselines/misctests.txt From 44ffe880f173b88b1b7ca9d8ee5f15091fd2e878 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Wed, 4 Oct 2017 14:44:13 -0400 Subject: [PATCH 02/30] back out changes for first time directory creation --- tests/Makefile | 4 ---- 1 file changed, 4 deletions(-) diff --git a/tests/Makefile b/tests/Makefile index 2b044f2..f1d93eb 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -83,10 +83,6 @@ test_invoke: @$(PYTHON) $(SRC)/gdc_mirror.py --help >/dev/null @$(PYTHON) $(SRC)/gdc_list.py --help >/dev/null @echo Test assorted features or API calls directly, instead of via tools - @if [ ! -d $(TEST_ROOT) ] ; then \ - echo creating $(TEST_ROOT) ;\ - mkdir -p "$(TEST_ROOT)" ;\ - fi @$(PYTHON) misctests.py > $(TEST_ROOT)/misctests.txt diff $(TEST_ROOT)/misctests.txt baselines/misctests.txt From cbaafd72c252210226f124a313dd4523f6e82e41 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Thu, 5 Oct 2017 14:00:52 -0400 Subject: [PATCH 03/30] updates for atomic mirror file saving --- gdctools/gdc_mirror.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index ea4c6b1..52c43ad 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -77,6 +77,9 @@ def config_customize(self): def mirror(self): + #TODO remove **gs** + print('hello world') + config = self.config if not os.path.isdir(config.mirror.dir): os.makedirs(config.mirror.dir) @@ -147,6 +150,7 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): ''' strict = not self.config.mirror.legacy savepath = meta.mirror_path(proj_root, file_d, strict=strict) + partialsavepath = savepath + '.partial' dirname, basename = os.path.split(savepath) logging.info("Mirroring file {0} | {1} of {2}".format(basename, n, total)) @@ -168,9 +172,9 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): #Download file uuid = file_d['file_id'] if self.has_cURL: - api.curl_download_file(uuid, savepath, max_time=time) + api.curl_download_file(uuid, partialsavepath, max_time=time) else: - api.py_download_file(uuid, savepath) + api.py_download_file(uuid, partialsavepath) break except Exception as e: logging.warning("Download failed: " + str(e) + '\nRetrying...') @@ -182,12 +186,18 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): if retry > retries: # A partially downloaded file will interfere with subsequent # mirrors - common.silent_rm(savepath) + common.silent_rm(partialsavepath) logging.error("Error downloading file {0}, too many retries ({1})".format(savepath, retries)) + #TODO set flag **gs** else: - #Save md5 checksum on success + #success! First remove old md5, then rename file, then write new md5 + #That way, if the process gets interrupted, future runs will be consider + # the file dirty unless each of these steps complete. md5sum = file_d['md5sum'] md5path = savepath + ".md5" + if os.path.exists(md5path): + os.remove(md5path) + os.rename(partialsavepath,savepath) with open(md5path, 'w') as mf: mf.write(md5sum + " " + basename) From 518409f7b4b29aec4aafbf8cebba2beb79a7388a Mon Sep 17 00:00:00 2001 From: gsaksena Date: Thu, 5 Oct 2017 14:23:19 -0400 Subject: [PATCH 04/30] removed metadata-based mirror caching, added initial status aggregation --- gdctools/gdc_mirror.py | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index 52c43ad..f6fd2f0 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -19,6 +19,7 @@ import logging import time import json +import collections from gdctools.GDCcore import * from gdctools.GDCtool import GDCtool @@ -159,7 +160,7 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): os.makedirs(dirname) md5path = savepath + ".md5" - + file_status = 'cached' # Download if force is enabled or if the file is not on disk if (self.force_download or not meta.md5_matches(file_d, md5path, strict) or not os.path.isfile(savepath)): @@ -167,6 +168,7 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): # New file, mirror to this folder time = 180 retry = 0 + file_status = 'error' while retry <= retries: try: #Download file @@ -200,6 +202,9 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): os.rename(partialsavepath,savepath) with open(md5path, 'w') as mf: mf.write(md5sum + " " + basename) + file_status = 'pass' + + return file_status def mirror_project(self, program, project): '''Mirror one project folder''' @@ -276,20 +281,18 @@ def mirror_category(self, program, project, category, [case for case in file_metadata[idx]["cases"] \ if case["submitter_id"] in cases] - new_metadata = file_metadata - # If we aren't forcing a full mirror, check the existing metadata - # to see what files are new - if not self.force_download: - new_metadata = meta.files_diff(proj_dir, file_metadata, - prev_metadata, strict) - num_files = len(new_metadata) + num_files = len(file_metadata) logging.info("{0} new {1} files".format(num_files, category)) - for n, file_d in enumerate(new_metadata): - self.__mirror_file(file_d, proj_dir, n+1, num_files) + status_tally = collections.Counter() + for n, file_d in enumerate(file_metadata): + file_status = self.__mirror_file(file_d, proj_dir, n+1, num_files) + status_tally[file_status] += 1 + #TODO remove **gs** + print (str(status_tally)) return file_metadata def execute(self): From 9ce8811766191983fcf07f4e258f63a0f3ef0256 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Thu, 5 Oct 2017 14:31:31 -0400 Subject: [PATCH 05/30] propagate mirror status to top --- gdctools/gdc_mirror.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index f6fd2f0..25d8d3f 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -132,16 +132,19 @@ def mirror(self): program_projects[prgm].append(project) # Now loop over each program, acquiring lock + prgm_status_tally = collections.Counter() for prgm in program_projects: projects = program_projects[prgm] prgm_root = os.path.abspath(os.path.join(config.mirror.dir, prgm)) with common.lock_context(prgm_root, "mirror"): for project in sorted(projects): - self.mirror_project(prgm, project) + proj_status_tally = self.mirror_project(prgm, project) + prgm_status_tally.update(proj_status_tally) # Update the datestamps file with this version of the mirror self.update_datestamps_file() + logging.info(str(prgm_status_tally)) logging.info("Mirror completed successfully.") def __mirror_file(self, file_d, proj_root, n, total, retries=3): @@ -233,11 +236,13 @@ def mirror_project(self, program, project): # Mirror each category separately, recording metadata (file dicts) file_metadata = [] + proj_status_tally = collections.Counter() for cat in sorted(categories): - cat_data = self.mirror_category(program, project, cat, + cat_data, cat_status_tally = self.mirror_category(program, project, cat, self.workflow, prev_metadata) file_metadata.extend(cat_data) + proj_status_tally.update(cat_status_tally) # Record project-level metadata # file dicts, counts, redactions, blacklist, etc. @@ -252,6 +257,8 @@ def mirror_project(self, program, project): with open(meta_json, 'w') as jf: json.dump(file_metadata, jf, indent=2) + return proj_status_tally + def mirror_category(self, program, project, category, workflow, prev_metadata): '''Mirror one category of data in a particular project. @@ -292,8 +299,8 @@ def mirror_category(self, program, project, category, status_tally[file_status] += 1 #TODO remove **gs** - print (str(status_tally)) - return file_metadata + #print (str(status_tally)) + return file_metadata, status_tally def execute(self): super(gdc_mirror, self).execute() From e2fb22b50fb137ea420f3c0d1a47809c3a43db05 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Mon, 9 Oct 2017 23:15:35 -0400 Subject: [PATCH 06/30] tweak top level error reporting for gdc_mirror --- gdctools/gdc_mirror.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index 25d8d3f..84ee391 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -78,8 +78,6 @@ def config_customize(self): def mirror(self): - #TODO remove **gs** - print('hello world') config = self.config if not os.path.isdir(config.mirror.dir): @@ -145,7 +143,11 @@ def mirror(self): # Update the datestamps file with this version of the mirror self.update_datestamps_file() logging.info(str(prgm_status_tally)) - logging.info("Mirror completed successfully.") + if prgm_status_tally['error'] == 0: + logging.info("Mirror completed successfully.") + else: + logging.error("Mirror FAILED downloading one or more files.") + def __mirror_file(self, file_d, proj_root, n, total, retries=3): '''Mirror a file into //. @@ -192,8 +194,7 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): # A partially downloaded file will interfere with subsequent # mirrors common.silent_rm(partialsavepath) - logging.error("Error downloading file {0}, too many retries ({1})".format(savepath, retries)) - #TODO set flag **gs** + logging.warning("Error downloading file {0}, too many retries ({1})".format(savepath, retries)) else: #success! First remove old md5, then rename file, then write new md5 #That way, if the process gets interrupted, future runs will be consider From 7da50d1ab63be7a3eebe77901821e979529e9b8d Mon Sep 17 00:00:00 2001 From: gsaksena Date: Tue, 10 Oct 2017 13:35:19 -0400 Subject: [PATCH 07/30] make dicer data file writes atomic, as a responsibility of the converter --- gdctools/lib/convert/copy.py | 5 ++++- gdctools/lib/convert/maf.py | 4 +++- gdctools/lib/convert/py_clinical.py | 5 ++++- gdctools/lib/convert/seg.py | 5 ++++- gdctools/lib/convert/tsv2idtsv.py | 5 ++++- gdctools/lib/convert/tsv2magetab.py | 5 ++++- 6 files changed, 23 insertions(+), 6 deletions(-) diff --git a/gdctools/lib/convert/copy.py b/gdctools/lib/convert/copy.py index 7111341..c333f2e 100644 --- a/gdctools/lib/convert/copy.py +++ b/gdctools/lib/convert/copy.py @@ -1,4 +1,5 @@ import shutil +import os from ..meta import tcga_id, diced_file_paths from ..common import safeMakeDirs @@ -7,7 +8,9 @@ def process(file_dict, mirror_path, dice_path): _tcga_id = tcga_id(file_dict) filepath = diced_file_paths(dice_path, file_dict)[0] + filepath_partial = filepath + '.partial' safeMakeDirs(dice_path) # copy to new name in - shutil.copy(mirror_path, filepath) + shutil.copy(mirror_path, filepath_partial) + os.rename(filepath_partial, filepath) diff --git a/gdctools/lib/convert/maf.py b/gdctools/lib/convert/maf.py index 7e7a59f..0f007f0 100644 --- a/gdctools/lib/convert/maf.py +++ b/gdctools/lib/convert/maf.py @@ -45,9 +45,11 @@ def process(file_dict, mafFile, outdir, is_compressed=True): sample_maf_filename = ".".join([sample_id, maf_uuid, "maf.txt"]) logging.info("Writing sample MAF: " + sample_maf_filename) sample_maf_filename = os.path.join(outdir, sample_maf_filename) - with safe_open(sample_maf_filename, 'w') as smf: + sample_maf_filename_partial = sample_maf_filename + '.partial' + with safe_open(sample_maf_filename_partial, 'w') as smf: outwriter = csv.writer(smf, delimiter='\t') outwriter.writerows(tcgaSampleIdToMafLinesMap[sample_id]) + os.rename(sample_maf_filename_partial,sample_maf_filename) #=============================================================================== diff --git a/gdctools/lib/convert/py_clinical.py b/gdctools/lib/convert/py_clinical.py index 84d1cfb..a1aaa87 100644 --- a/gdctools/lib/convert/py_clinical.py +++ b/gdctools/lib/convert/py_clinical.py @@ -1,10 +1,13 @@ from ..meta import diced_file_paths from ..clinxml import parse_clinical_xml from ..common import safeMakeDirs +import os def process(file_dict, infile, outdir): # should only produce one file filepath = diced_file_paths(outdir, file_dict)[0] + filepath_partial = filepath + '.partial' safeMakeDirs(outdir) - parse_clinical_xml(infile, filepath) + parse_clinical_xml(infile, filepath_partial) + os.rename(filepath_partial, filepath) return filepath diff --git a/gdctools/lib/convert/seg.py b/gdctools/lib/convert/seg.py index 8c9937b..4ec97fa 100644 --- a/gdctools/lib/convert/seg.py +++ b/gdctools/lib/convert/seg.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import csv +import os from ..common import safeMakeDirs, writeCsvFile from .. import meta @@ -9,6 +10,7 @@ def process(file_dict, infile, outdir, dialect='seg_broad'): # Should only produce one outfile outfile = meta.diced_file_paths(outdir, file_dict)[0] + outfile_partial = outfile + '.partial' hyb_id = file_dict['file_name'].split('.',1)[0] tcga_id = meta.aliquot_id(file_dict) @@ -19,7 +21,8 @@ def process(file_dict, infile, outdir, dialect='seg_broad'): seg_file_data = generate_seg_file(csvfile, converter, tcga_id, hyb_id) safeMakeDirs(outdir) - writeCsvFile(outfile, seg_file_data) + writeCsvFile(outfile_partial, seg_file_data) + os.rename(outfile_partial, outfile) rawfile.close() return outfile diff --git a/gdctools/lib/convert/tsv2idtsv.py b/gdctools/lib/convert/tsv2idtsv.py index 3c9aeda..a589de8 100644 --- a/gdctools/lib/convert/tsv2idtsv.py +++ b/gdctools/lib/convert/tsv2idtsv.py @@ -1,12 +1,14 @@ #!/usr/bin/env python import csv +import os from ..common import safeMakeDirs, map_blank_to_na, writeCsvFile from ..meta import tcga_id, diced_file_paths def process(file_dict, infile, outdir): # Should only produce one file filepath = diced_file_paths(outdir, file_dict)[0] + filepath_partial = filepath + '.partial' _tcga_id = tcga_id(file_dict) rawfile = open(infile, 'r') csvfile = csv.reader(rawfile, dialect='excel-tab') @@ -15,7 +17,8 @@ def process(file_dict, infile, outdir): csvfile_with_NAs = map_blank_to_na(csvfile_with_ids) safeMakeDirs(outdir) - writeCsvFile(filepath, csvfile_with_NAs) + writeCsvFile(filepath_partial, csvfile_with_NAs) + os.rename(filepath_partial, filepath) rawfile.close() diff --git a/gdctools/lib/convert/tsv2magetab.py b/gdctools/lib/convert/tsv2magetab.py index be65f32..b82c9ce 100644 --- a/gdctools/lib/convert/tsv2magetab.py +++ b/gdctools/lib/convert/tsv2magetab.py @@ -2,6 +2,7 @@ import csv from os.path import basename +import os from ..common import safeMakeDirs, getTabFileHeader, map_blank_to_na, writeCsvFile, rearrange_columns from ..meta import tcga_id, diced_file_paths @@ -20,6 +21,7 @@ def process(file_dict, infile, outdir, fpkm=False, col_order=None, data_cols=Non filepath = diced_file_paths(outdir, file_dict)[0] + filepath_partial = filepath + '.partial' safeMakeDirs(outdir) _tcga_id = tcga_id(file_dict) @@ -38,7 +40,8 @@ def process(file_dict, infile, outdir, fpkm=False, col_order=None, data_cols=Non csvfile_with_new_column_order = csvfile_with_NAs safeMakeDirs(outdir) - writeCsvFile(filepath, csvfile_with_new_column_order) + writeCsvFile(filepath_partial, csvfile_with_new_column_order) + os.rename(filepath_partial, filepath) rawfile.close() From 3ec8fa148a03d80b2493f86c0eb530ea6f217af4 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Tue, 10 Oct 2017 14:02:15 -0400 Subject: [PATCH 08/30] factor out file naming magic from dice converters --- gdctools/lib/convert/copy.py | 6 +++--- gdctools/lib/convert/py_clinical.py | 6 +++--- gdctools/lib/convert/seg.py | 4 ++-- gdctools/lib/convert/tsv2idtsv.py | 6 +++--- gdctools/lib/convert/tsv2magetab.py | 6 +++--- gdctools/lib/meta.py | 14 ++++++++++++++ 6 files changed, 28 insertions(+), 14 deletions(-) diff --git a/gdctools/lib/convert/copy.py b/gdctools/lib/convert/copy.py index c333f2e..5faa902 100644 --- a/gdctools/lib/convert/copy.py +++ b/gdctools/lib/convert/copy.py @@ -1,14 +1,14 @@ import shutil import os -from ..meta import tcga_id, diced_file_paths +from ..meta import tcga_id, diced_file_path, diced_file_path_partial from ..common import safeMakeDirs # Copy from mirror to dice dir def process(file_dict, mirror_path, dice_path): _tcga_id = tcga_id(file_dict) - filepath = diced_file_paths(dice_path, file_dict)[0] - filepath_partial = filepath + '.partial' + filepath = diced_file_path(dice_path, file_dict) + filepath_partial = diced_file_path_partial(dice_path, file_dict) safeMakeDirs(dice_path) # copy to new name in diff --git a/gdctools/lib/convert/py_clinical.py b/gdctools/lib/convert/py_clinical.py index a1aaa87..482bc2d 100644 --- a/gdctools/lib/convert/py_clinical.py +++ b/gdctools/lib/convert/py_clinical.py @@ -1,12 +1,12 @@ -from ..meta import diced_file_paths +from ..meta import diced_file_path, diced_file_path_partial from ..clinxml import parse_clinical_xml from ..common import safeMakeDirs import os def process(file_dict, infile, outdir): # should only produce one file - filepath = diced_file_paths(outdir, file_dict)[0] - filepath_partial = filepath + '.partial' + filepath = diced_file_path(outdir, file_dict) + filepath_partial = diced_file_path_partial(outdir, file_dict) safeMakeDirs(outdir) parse_clinical_xml(infile, filepath_partial) os.rename(filepath_partial, filepath) diff --git a/gdctools/lib/convert/seg.py b/gdctools/lib/convert/seg.py index 4ec97fa..c5757b2 100644 --- a/gdctools/lib/convert/seg.py +++ b/gdctools/lib/convert/seg.py @@ -9,8 +9,8 @@ def process(file_dict, infile, outdir, dialect='seg_broad'): # Should only produce one outfile - outfile = meta.diced_file_paths(outdir, file_dict)[0] - outfile_partial = outfile + '.partial' + outfile = meta.diced_file_path(outdir, file_dict) + outfile_partial = meta.diced_file_path_partial(outdir, file_dict) hyb_id = file_dict['file_name'].split('.',1)[0] tcga_id = meta.aliquot_id(file_dict) diff --git a/gdctools/lib/convert/tsv2idtsv.py b/gdctools/lib/convert/tsv2idtsv.py index a589de8..c848bf9 100644 --- a/gdctools/lib/convert/tsv2idtsv.py +++ b/gdctools/lib/convert/tsv2idtsv.py @@ -3,12 +3,12 @@ import csv import os from ..common import safeMakeDirs, map_blank_to_na, writeCsvFile -from ..meta import tcga_id, diced_file_paths +from ..meta import tcga_id, diced_file_path, diced_file_path_partial def process(file_dict, infile, outdir): # Should only produce one file - filepath = diced_file_paths(outdir, file_dict)[0] - filepath_partial = filepath + '.partial' + filepath = diced_file_path(outdir, file_dict) + filepath_partial = diced_file_path_partial(outdir, file_dict) _tcga_id = tcga_id(file_dict) rawfile = open(infile, 'r') csvfile = csv.reader(rawfile, dialect='excel-tab') diff --git a/gdctools/lib/convert/tsv2magetab.py b/gdctools/lib/convert/tsv2magetab.py index b82c9ce..60d36ff 100644 --- a/gdctools/lib/convert/tsv2magetab.py +++ b/gdctools/lib/convert/tsv2magetab.py @@ -5,7 +5,7 @@ import os from ..common import safeMakeDirs, getTabFileHeader, map_blank_to_na, writeCsvFile, rearrange_columns -from ..meta import tcga_id, diced_file_paths +from ..meta import tcga_id, diced_file_path, diced_file_path_partial def process(file_dict, infile, outdir, fpkm=False, col_order=None, data_cols=None): @@ -20,8 +20,8 @@ def process(file_dict, infile, outdir, fpkm=False, col_order=None, data_cols=Non ''' - filepath = diced_file_paths(outdir, file_dict)[0] - filepath_partial = filepath + '.partial' + filepath = diced_file_path(outdir, file_dict) + filepath_partial = diced_file_path_partial(outdir, file_dict) safeMakeDirs(outdir) _tcga_id = tcga_id(file_dict) diff --git a/gdctools/lib/meta.py b/gdctools/lib/meta.py index d2c622c..36b5664 100644 --- a/gdctools/lib/meta.py +++ b/gdctools/lib/meta.py @@ -220,6 +220,20 @@ def mirror_path(proj_root, file_dict, strict=True): name = file_basename(file_dict, strict) return os.path.join(proj_root, category, data_type, name).replace(' ', '_') + +def diced_file_path_partial(root, file_dict): + diced_path = diced_file_path(root, file_dict) + diced_path_partial = diced_path + '.partial' + return diced_file_path_partial + +def diced_file_path(root, file_dict): + diced_paths = diced_file_paths(root, file_dict) + if len(diced_paths) != 1: + raise ValueError("Expected one path, found %d for %s"% + (len(diced_paths), json.dumps(file_dict, indent=2))) + diced_path = diced_paths[0] + return diced_path + def diced_file_paths(root, file_dict): '''Return the name of the diced file to be created''' _ext = dice_extension(file_dict) From be4f31c489149648ddd010bc4fdc6ad44d92a5b2 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Tue, 10 Oct 2017 14:15:42 -0400 Subject: [PATCH 09/30] debug previous checkin --- gdctools/lib/meta.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gdctools/lib/meta.py b/gdctools/lib/meta.py index 36b5664..9cfa6c0 100644 --- a/gdctools/lib/meta.py +++ b/gdctools/lib/meta.py @@ -224,7 +224,7 @@ def mirror_path(proj_root, file_dict, strict=True): def diced_file_path_partial(root, file_dict): diced_path = diced_file_path(root, file_dict) diced_path_partial = diced_path + '.partial' - return diced_file_path_partial + return diced_path_partial def diced_file_path(root, file_dict): diced_paths = diced_file_paths(root, file_dict) From 855d01144cc6624cf844bfd6c6b2fed90c2c0965 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Tue, 10 Oct 2017 14:55:13 -0400 Subject: [PATCH 10/30] add error tolerance and aggregate reporting to gdc_dice --- gdctools/gdc_dice.py | 27 ++++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/gdctools/gdc_dice.py b/gdctools/gdc_dice.py index e663aeb..13db8bd 100644 --- a/gdctools/gdc_dice.py +++ b/gdctools/gdc_dice.py @@ -81,6 +81,7 @@ def dice(self): program = config.programs[0] diced_prog_root = os.path.join(config.dice.dir, program) mirror_prog_root = os.path.join(config.mirror.dir, program) + prog_status_tally = Counter() # Ensure no simultaneous mirroring/dicing with common.lock_context(diced_prog_root, "dice"), \ @@ -164,17 +165,20 @@ def dice(self): for tcga_id in tcga_lookup: # Dice single sample files first for file_d in viewvalues(tcga_lookup[tcga_id]): - dice_one(file_d, trans_dict, raw_project_root, + dice_one_status = dice_one(file_d, trans_dict, raw_project_root, diced_project_root, mfw, dry_run=self.options.dry_run, force=self.force) + prog_status_tally[dice_one_status] += 1 #Then dice the multi_sample_files for file_d in multi_sample_files: - dice_one(file_d, trans_dict, raw_project_root, + dice_one_status = dice_one(file_d, trans_dict, raw_project_root, diced_project_root, mfw, dry_run=self.options.dry_run, force=self.force) + prog_status_tally[dice_one_status] += 1 + # Bookkeeping code -- write some useful tables # and figures needed for downstream sample reports. @@ -217,7 +221,11 @@ def dice(self): _write_combined_counts(all_counts_file, all_counts, all_totals) _link_to_prog(all_counts_file, datestamp, diced_prog_root) - logging.info("Dicing completed successfuly") + logging.info(str(prog_status_tally)) + if prog_status_tally['error'] == 0: + logging.info("Dicing completed successfuly") + else: + logging.warn("One or more diced files FAILED") def execute(self): super(gdc_dice, self).execute() @@ -361,10 +369,11 @@ def dice_one(file_dict, translation_dict, mirror_proj_root, diced_root, true, a debug message will be displayed instead of performing the actual dicing operation. """ + dice_one_status = 'error' mirror_path = meta.mirror_path(mirror_proj_root, file_dict) if not os.path.isfile(mirror_path): # Bad, this means there are integrity issues - raise ValueError("Expected mirror file missing: " + mirror_path) + logging.warning("Expected mirror file missing: " + mirror_path) else: ## Get the right annotation and converter for this file annot, convert = get_annotation_converter(file_dict, translation_dict) @@ -380,12 +389,19 @@ def dice_one(file_dict, translation_dict, mirror_proj_root, diced_root, already_diced = all(os.path.isfile(p) for p in expected_paths) if force or not already_diced: logging.info("Dicing file " + mirror_path) - convert(file_dict, mirror_path, dice_path) + try: + convert(file_dict, mirror_path, dice_path) + dice_one_status = 'pass' + except Exception as e: + logging.warning('Dice converter failed: %s'%str(e)) else: logging.info("Skipping file " + mirror_path + " (already diced)") + dice_one_status = 'cached' append_diced_metadata(file_dict, expected_paths, annot, meta_file_writer) + else: + dice_one_status = 'dry_run' else: # To verbose to log the entire json, log just log data_type and file_id warning_info = { @@ -396,6 +412,7 @@ def dice_one(file_dict, translation_dict, mirror_proj_root, diced_root, } logging.warn('Unrecognized data:\n%s' % json.dumps(warning_info, indent=2)) + return dice_one_status def get_annotation_converter(file_dict, translation_dict): k = metadata_to_key(file_dict) From cf9b5f85c5408b0a009c7c8d01a179a6de33c816 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Wed, 11 Oct 2017 19:25:49 -0400 Subject: [PATCH 11/30] coded changes to set datestamp the new way --- gdctools/GDCtool.py | 61 +++++++++++++++++++++++++++++++++++++-------- 1 file changed, 50 insertions(+), 11 deletions(-) diff --git a/gdctools/GDCtool.py b/gdctools/GDCtool.py index fe9aa9c..91fec3d 100644 --- a/gdctools/GDCtool.py +++ b/gdctools/GDCtool.py @@ -57,23 +57,64 @@ def execute(self): self.config_customize() self.config_finalize() + #TODO perhaps refactor for better encapsulation, moving part to + # GDCtool.config_initialize() and part to gdc_mirror.config_customize(). + # Though it is nice to have all the logic for setting datestamp in one place. + #TODO variable renaming - datestamp_required and datestamp, to make them reflect current usage + datestamp = self.options.datestamp if self.datestamp_required: - datestamp = self.options.datestamp - if not datestamp: - datestamp = 'latest' + #non-gdc_mirror case existing_dates = self.datestamps() # ascending sort order if len(existing_dates) == 0: raise ValueError("No datestamps found, use upstream tool first") + if not datestamp: + #default value = 'latest' + datestamp = 'latest' + if datestamp == 'latest': - datestamp = existing_dates[-1] + # find last datestamp in existing_dates that is in date format + for d in reversed(existing_dates): + if common.DATESTAMP_REGEX.match(d) is not None: + datestamp = d + break + else: + #TODO make this error message more helpful + raise ValueError("Looking for latest datestamp, but no datestamps found in correct format") elif datestamp not in existing_dates: raise ValueError("Requested datestamp not present in " + self.config.datestamps + "\n" + "Existing datestamps: " + repr(existing_dates)) else: - datestamp = time.strftime('%Y_%m_%d', time.localtime()) + #gdc_mirror case + if not datestamp: + # default value = today's datestamp + datestamp = common.datestamp() + elif datestamp == 'pool': + pass + else: + #other strings such as , 'latest', valid variable names, and everything else are not allowed + raise ValueError("For gdc_mirror, date must be blank or 'pool'") + + # TODO remove this old code **gs** + # if self.datestamp_required: + # datestamp = self.options.datestamp + # if not datestamp: + # datestamp = 'latest' + + # existing_dates = self.datestamps() # ascending sort order + # if len(existing_dates) == 0: + # raise ValueError("No datestamps found, use upstream tool first") + + # if datestamp == 'latest': + # datestamp = existing_dates[-1] + # elif datestamp not in existing_dates: + # raise ValueError("Requested datestamp not present in " + # + self.config.datestamps + "\n" + # + "Existing datestamps: " + repr(existing_dates)) + # else: + # datestamp = time.strftime('%Y_%m_%d', time.localtime()) self.datestamp = datestamp self.init_logging() @@ -98,12 +139,10 @@ def config_add_args(self): cli = self.cli cli.add_argument('--config', nargs='+', type=argparse.FileType('r'), help='One or more configuration files') - - if self.datestamp_required: - cli.add_argument('--date', nargs='?', dest='datestamp', - help='Use data from a given dated version (snapshot) of ' - 'GDC data, specified in YYYY_MM_DD form. If omitted, ' - 'the latest available snapshot will be used.') + cli.add_argument('--date', nargs='?', dest='datestamp', + help='Use data from a given dated version (snapshot) of ' + 'GDC data, specified in YYYY_MM_DD form. If omitted, ' + 'the latest available snapshot will be used.') cli.add_argument('--cases', nargs='+', metavar='case_id', help='Process data only from these GDC cases') cli.add_argument('--categories',nargs='+',metavar='category', From f9e3e9dce22f2cdeda16b888ebb46f83d5fd2d24 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Wed, 11 Oct 2017 20:24:03 -0400 Subject: [PATCH 12/30] add code to optionally append mirror metadata --- gdctools/gdc_mirror.py | 45 +++++++++++++++++++++++++++++++----------- 1 file changed, 33 insertions(+), 12 deletions(-) diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index 84ee391..4a9af2a 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -46,6 +46,8 @@ def __init__(self): cli.add_argument('-f', '--force-download', action='store_true', help='Download files even if already mirrored locally.'+ ' (DO NOT use during incremental mirroring)') + cli.add_argument('--append', default=False, action='store_true', + help='') # Detect if we have curl installed self.has_cURL = api.curl_exists() @@ -76,6 +78,17 @@ def config_customize(self): # ONLY supports MIRRORING of legacy, nothing else api.set_legacy(config.mirror.legacy) + + # Check for append in config file, then allow commandline to override it + if config.mirror.append: + # Append mode has been requested in config file, coerce to boolean + # TODO also validate legal false values + value = config.mirror.append.lower() + config.mirror.append = (value in ["1", "true", "on", "yes"]) + if opts.append: + config.mirror.append = opts.append + + def mirror(self): @@ -228,12 +241,14 @@ def mirror_project(self, program, project): proj_dir = os.path.join(config.mirror.dir, program, project) logging.info("Mirroring data to " + proj_dir) - # Read the previous metadata, if present - prev_datestamp = meta.latest_datestamp(proj_dir, None) - prev_metadata = [] - if prev_datestamp is not None: - prev_stamp_dir = os.path.join(proj_dir, "metadata", prev_datestamp) - prev_metadata = meta.latest_metadata(prev_stamp_dir) + # TODO remove this old code **gs** along with the prev_metadata variable + # # Read the previous metadata, if present + # prev_datestamp = meta.latest_datestamp(proj_dir, None) + # prev_metadata = [] + # if prev_datestamp is not None: + # prev_stamp_dir = os.path.join(proj_dir, "metadata", prev_datestamp) + # prev_metadata = meta.latest_metadata(prev_stamp_dir) + prev_metadata = None # Mirror each category separately, recording metadata (file dicts) file_metadata = [] @@ -251,12 +266,20 @@ def mirror_project(self, program, project): stamp_folder = os.path.join(meta_folder, datestamp) if not os.path.isdir(stamp_folder): os.makedirs(stamp_folder) - - # Write file metadata meta_json = ".".join(["metadata", project, datestamp, "json" ]) meta_json = os.path.join(stamp_folder, meta_json) + + if config.mirror.append and os.path.exists(meta_json): + #merge current metadata with previous metadata with same datestamp + with open(meta_json) as jsonf: + output_metadata = json.load(jsonf) + output_metadata.update(file_metadata) + else: + output_metadata = file_metadata + + # Write file metadata with open(meta_json, 'w') as jf: - json.dump(file_metadata, jf, indent=2) + json.dump(output_metadata, jf, indent=2) return proj_status_tally @@ -299,8 +322,6 @@ def mirror_category(self, program, project, category, file_status = self.__mirror_file(file_d, proj_dir, n+1, num_files) status_tally[file_status] += 1 - #TODO remove **gs** - #print (str(status_tally)) return file_metadata, status_tally def execute(self): @@ -324,7 +345,7 @@ def update_datestamps_file(self): # Now read the file datestamps_file = open(datestamps_file, 'r+') stamps = datestamps_file.read().strip().split('\n') - if stamps[-1] != self.datestamp: + if self.datestamp not in stamps: datestamps_file.write(self.datestamp + '\n') def main(): From 2bf501bddb0b947689323632a801a39f54aaf571 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Wed, 18 Oct 2017 13:09:05 -0400 Subject: [PATCH 13/30] fix --append mode, properly interleave mirror metadata --- gdctools/gdc_mirror.py | 28 +++++++++++++++++++++++++--- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index 4a9af2a..49b1db2 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -223,6 +223,28 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): return file_status + @staticmethod + def __merge_mirror_metadata(old, new): + pass + file_item_dict = {} + for file_item in old: + key = file_item['file_id'] + file_item['md5sum'] + file_item_dict[key] = file_item + + if new is not None: + for file_item in new: + key = file_item['file_id'] + file_item['md5sum'] + # TODO should there be a check whether the rest of the metadata matches? + file_item_dict[key] = file_item + + file_item_list = [] + file_item_keys = list(file_item_dict.keys()) + file_item_keys.sort() + for key in file_item_keys: + file_item_list.append(file_item_dict[key]) + return file_item_list + + def mirror_project(self, program, project): '''Mirror one project folder''' @@ -272,10 +294,10 @@ def mirror_project(self, program, project): if config.mirror.append and os.path.exists(meta_json): #merge current metadata with previous metadata with same datestamp with open(meta_json) as jsonf: - output_metadata = json.load(jsonf) - output_metadata.update(file_metadata) + old_metadata = json.load(jsonf) + output_metadata = self.__merge_mirror_metadata(old_metadata, file_metadata) else: - output_metadata = file_metadata + output_metadata = self.__merge_mirror_metadata(file_metadata, None) # Write file metadata with open(meta_json, 'w') as jf: From 7b8e95c5290485b77862af808dbe212c5260a0d2 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sat, 28 Oct 2017 15:19:39 -0400 Subject: [PATCH 14/30] updated help docs --- gdctools/GDCtool.py | 6 ++++-- gdctools/gdc_mirror.py | 9 ++++++--- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/gdctools/GDCtool.py b/gdctools/GDCtool.py index 91fec3d..7b1f784 100644 --- a/gdctools/GDCtool.py +++ b/gdctools/GDCtool.py @@ -141,8 +141,10 @@ def config_add_args(self): help='One or more configuration files') cli.add_argument('--date', nargs='?', dest='datestamp', help='Use data from a given dated version (snapshot) of ' - 'GDC data, specified in YYYY_MM_DD form. If omitted, ' - 'the latest available snapshot will be used.') + 'GDC data, specified in YYYY_MM_DD form. The special ' + 'value "pool" can be used for date agnostic snapshots, typically' + 'along with "--append". ' + 'If omitted, the latest available snapshot will be used.') cli.add_argument('--cases', nargs='+', metavar='case_id', help='Process data only from these GDC cases') cli.add_argument('--categories',nargs='+',metavar='category', diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index 49b1db2..17357b6 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -40,14 +40,17 @@ def __init__(self): cli = self.cli cli.add_argument('-m', '--mirror-dir', help='Root of mirrored data folder tree') - cli.add_argument('-l', '--legacy', default=False, action='store_true', + cli.add_argument('-l', '--legacy', action='store_true', help='Retrieve legacy data (e.g. TCGA HG19), instead of ' 'data harmonized at the GDC (the default)') cli.add_argument('-f', '--force-download', action='store_true', help='Download files even if already mirrored locally.'+ ' (DO NOT use during incremental mirroring)') - cli.add_argument('--append', default=False, action='store_true', - help='') + cli.add_argument('--append', action='store_true', + help='Specify this if you want downstream tools like ' + 'gdc_dice and gdc_loadfile to also apply to data ' + 'downloaded in the previous mirrorring of the data ' + 'at this datestamp, in addition to the current mirroring. ') # Detect if we have curl installed self.has_cURL = api.curl_exists() From 2557ad51f1202dace81fcb11ecbc221b946dcef7 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sat, 28 Oct 2017 15:33:17 -0400 Subject: [PATCH 15/30] tweaked docs --- gdctools/GDCtool.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gdctools/GDCtool.py b/gdctools/GDCtool.py index 7b1f784..471cbaa 100644 --- a/gdctools/GDCtool.py +++ b/gdctools/GDCtool.py @@ -141,9 +141,9 @@ def config_add_args(self): help='One or more configuration files') cli.add_argument('--date', nargs='?', dest='datestamp', help='Use data from a given dated version (snapshot) of ' - 'GDC data, specified in YYYY_MM_DD form. The special ' - 'value "pool" can be used for date agnostic snapshots, typically' - 'along with "--append". ' + 'GDC data. The special value "pool" can be used for date ' + 'agnostic snapshots, typically along with "--append". ' + 'For tools other than gdc_mirror, you can give a date in YYYY_MM_DD form.' 'If omitted, the latest available snapshot will be used.') cli.add_argument('--cases', nargs='+', metavar='case_id', help='Process data only from these GDC cases') From 2155b016948f797f1eda77d77e755a1e3431bbd6 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sat, 28 Oct 2017 16:54:17 -0400 Subject: [PATCH 16/30] improve merge mirror metadata semantics --- gdctools/gdc_mirror.py | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index 17357b6..36aa1aa 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -228,17 +228,16 @@ def __mirror_file(self, file_d, proj_root, n, total, retries=3): @staticmethod def __merge_mirror_metadata(old, new): - pass file_item_dict = {} - for file_item in old: - key = file_item['file_id'] + file_item['md5sum'] - file_item_dict[key] = file_item - - if new is not None: - for file_item in new: + if old is not None: + for file_item in old: key = file_item['file_id'] + file_item['md5sum'] - # TODO should there be a check whether the rest of the metadata matches? - file_item_dict[key] = file_item + file_item_dict[key] = file_item + + for file_item in new: + key = file_item['file_id'] + file_item['md5sum'] + # TODO should there be a check whether the rest of the metadata matches? + file_item_dict[key] = file_item file_item_list = [] file_item_keys = list(file_item_dict.keys()) @@ -295,12 +294,14 @@ def mirror_project(self, program, project): meta_json = os.path.join(stamp_folder, meta_json) if config.mirror.append and os.path.exists(meta_json): - #merge current metadata with previous metadata with same datestamp + #fetch previous metadata with same datestamp with open(meta_json) as jsonf: old_metadata = json.load(jsonf) - output_metadata = self.__merge_mirror_metadata(old_metadata, file_metadata) else: - output_metadata = self.__merge_mirror_metadata(file_metadata, None) + old_metadata = None + + output_metadata = self.__merge_mirror_metadata(old_metadata, file_metadata) + # Write file metadata with open(meta_json, 'w') as jf: From 03fe15d85e8e1d7d5c33b48139bdfe984c436e5d Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sat, 28 Oct 2017 21:21:38 -0400 Subject: [PATCH 17/30] make unrecognized datatypes give more helpful error msg --- gdctools/gdc_dice.py | 41 +++++++++++++++++++++++++---------------- 1 file changed, 25 insertions(+), 16 deletions(-) diff --git a/gdctools/gdc_dice.py b/gdctools/gdc_dice.py index 13db8bd..9b6c78b 100644 --- a/gdctools/gdc_dice.py +++ b/gdctools/gdc_dice.py @@ -225,7 +225,9 @@ def dice(self): if prog_status_tally['error'] == 0: logging.info("Dicing completed successfuly") else: - logging.warn("One or more diced files FAILED") + logging.error("One or more diced files FAILED") + #raise Exception("One or more diced files FAILED") + def execute(self): super(gdc_dice, self).execute() @@ -402,27 +404,34 @@ def dice_one(file_dict, translation_dict, mirror_proj_root, diced_root, annot, meta_file_writer) else: dice_one_status = 'dry_run' - else: - # To verbose to log the entire json, log just log data_type and file_id - warning_info = { - 'data_type' : file_dict["data_type"], - 'data_category' : file_dict["data_category"], - 'file_id' : file_dict["file_id"], - 'file_name': file_dict['file_name'] - } - logging.warn('Unrecognized data:\n%s' % json.dumps(warning_info, - indent=2)) + return dice_one_status def get_annotation_converter(file_dict, translation_dict): - k = metadata_to_key(file_dict) + dictkey = metadata_to_dictkey(file_dict) + k = frozenset(dictkey.items()) if k in translation_dict: return translation_dict[k] else: - # FIXME: Gracefully handle this instead of creating a new annotation type + warning_info = \ +""" + file_id: {0} + file_name: {1} + + data_category: {data_category} + data_type: {data_type} + experimental_strategy: {experimental_strategy} + platform: {platform} + center_namespace: {center_namespace} + tags: {tags} + workflow_type: {workflow_type} +""".format(file_dict["file_id"], file_dict['file_name'], **dictkey) + + logging.warn('Unrecognized data:\n%s' % warning_info) + return "UNRECOGNIZED", None -def metadata_to_key(file_dict): +def metadata_to_dictkey(file_dict): """Converts the file metadata in file_dict into a key in the TRANSLATION_DICT""" # Required fields data_type = file_dict.get("data_type", '') @@ -433,7 +442,7 @@ def metadata_to_key(file_dict): center_namespace = file_dict['center']['namespace'] if 'center' in file_dict else '' workflow_type = file_dict['analysis']['workflow_type'] if 'analysis' in file_dict else '' - return frozenset({ + return { "data_type" : data_type, "data_category" : data_category, "experimental_strategy" : experimental_strategy, @@ -441,7 +450,7 @@ def metadata_to_key(file_dict): "tags" : tags, "center_namespace" : center_namespace, "workflow_type" : workflow_type - }.items()) + } def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): '''Write one or more rows for the given file_dict using meta_file_writer. From 613c77c311f9484eb0bc9d09b9d8b7d95e4c9f0c Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sat, 28 Oct 2017 21:58:53 -0400 Subject: [PATCH 18/30] add 3 new maf datatypes, update tests --- gdctools/lib/annotations_table.tsv | 3 + gdctools/lib/common.py | 5 +- tests/baselines/dice-files.txt | 27 ++++ tests/baselines/dice-md5sums.txt | 187 ++++++++++++++---------- tests/baselines/load-md5sums-google.txt | 2 +- tests/baselines/load-md5sums.txt | 2 +- 6 files changed, 143 insertions(+), 83 deletions(-) diff --git a/gdctools/lib/annotations_table.tsv b/gdctools/lib/annotations_table.tsv index 09401eb..d4bb295 100644 --- a/gdctools/lib/annotations_table.tsv +++ b/gdctools/lib/annotations_table.tsv @@ -11,3 +11,6 @@ mRNA__geneExp__FPKM unzip_fpkm2magetab Transcriptome Profiling Gene Expression Q mRNA__geneExpNormed__FPKM unzip_fpkm2magetab Transcriptome Profiling Gene Expression Quantification RNA-Seq HTSeq - FPKM-UQ mRNA__counts__FPKM unzip_fpkm2magetab Transcriptome Profiling Gene Expression Quantification RNA-Seq HTSeq - Counts SNV__mutect maf Simple Nucleotide Variation Masked Somatic Mutation WXS MuTect2 Variant Aggregation and Masking +SNV__somaticsniper maf Simple Nucleotide Variation Masked Somatic Mutation WXS SomaticSniper Variant Aggregation and Masking +SNV__muse maf Simple Nucleotide Variation Masked Somatic Mutation WXS MuSE Variant Aggregation and Masking +SNV__varscan maf Simple Nucleotide Variation Masked Somatic Mutation WXS VarScan2 Variant Aggregation and Masking diff --git a/gdctools/lib/common.py b/gdctools/lib/common.py index 7a2e08a..5f04f25 100644 --- a/gdctools/lib/common.py +++ b/gdctools/lib/common.py @@ -31,7 +31,10 @@ 'mRNA__geneExp__FPKM' : 'mRNA', 'mRNA__geneExpNormed__FPKM' : 'mRNA', 'mRNA__counts__FPKM' : 'mRNA', - 'SNV__mutect' : 'MAF' + 'SNV__mutect' : 'MAF', + 'SNV__somaticsniper' : 'MAF', + 'SNV__muse' : 'MAF', + 'SNV__varscan' : 'MAF' } __PY3__ = sys.version_info > (3,) diff --git a/tests/baselines/dice-files.txt b/tests/baselines/dice-files.txt index afcd710..0b2f33c 100644 --- a/tests/baselines/dice-files.txt +++ b/tests/baselines/dice-files.txt @@ -6,9 +6,18 @@ TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5K2-01A-11D-A29H-01.b0ef98ef-b83b-4f51-9 TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5K2-10B-01D-A29K-01.a774d500-8c68-4071-a3b1-328f346b417c.txt TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5L1-01A-11D-A309-01.477185ad-aafa-4da0-be72-780bd66fb6cd.txt TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5L1-10A-01D-A309-01.7c263070-5b38-4d8c-9a31-899e1ba9d91d.txt +TCGA-ACC/SNV__muse/TCGA-OR-A5K2-01A-11D-A29I-10.c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.maf.txt +TCGA-ACC/SNV__muse/TCGA-OR-A5L1-01A-11D-A30A-10.c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.maf.txt +TCGA-ACC/SNV__muse/c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.maf.txt TCGA-ACC/SNV__mutect/TCGA-OR-A5K2-01A-11D-A29I-10.ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.maf.txt TCGA-ACC/SNV__mutect/TCGA-OR-A5L1-01A-11D-A30A-10.ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.maf.txt TCGA-ACC/SNV__mutect/ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.maf.txt +TCGA-ACC/SNV__somaticsniper/TCGA-OR-A5K2-01A-11D-A29I-10.da92b810-c396-4963-b538-5454f13a297c.maf.txt +TCGA-ACC/SNV__somaticsniper/TCGA-OR-A5L1-01A-11D-A30A-10.da92b810-c396-4963-b538-5454f13a297c.maf.txt +TCGA-ACC/SNV__somaticsniper/da92b810-c396-4963-b538-5454f13a297c.maf.txt +TCGA-ACC/SNV__varscan/2ff3f6bd-6114-431d-ab3b-656d7ab13996.maf.txt +TCGA-ACC/SNV__varscan/TCGA-OR-A5K2-01A-11D-A29I-10.2ff3f6bd-6114-431d-ab3b-656d7ab13996.maf.txt +TCGA-ACC/SNV__varscan/TCGA-OR-A5L1-01A-11D-A30A-10.2ff3f6bd-6114-431d-ab3b-656d7ab13996.maf.txt TCGA-ACC/clinical__biospecimen/TCGA-OR-A5K2.2fde5970-89ee-46d3-ad62-8172804ca952.txt TCGA-ACC/clinical__biospecimen/TCGA-OR-A5L1.2c6c5c9b-2ac1-46aa-83ef-401cb9e20bfc.txt TCGA-ACC/clinical__primary/TCGA-OR-A5K2.e3e4a2d6-e5d6-46ec-8cef-d5b15ca4d9e4.txt @@ -27,9 +36,18 @@ TCGA-ESCA/CNV__unfiltered__snp6/TCGA-IG-A3YB-01A-11D-A246-01.7789cfd4-2eab-416b- TCGA-ESCA/CNV__unfiltered__snp6/TCGA-IG-A3YB-10A-01D-A246-01.a22ec975-483d-4a5d-92ba-5762f246d741.txt TCGA-ESCA/CNV__unfiltered__snp6/TCGA-L5-A4OI-01A-11D-A25X-01.92990d84-9f3c-46d6-89ab-fb631dd4139f.txt TCGA-ESCA/CNV__unfiltered__snp6/TCGA-L5-A4OI-11A-11D-A25X-01.57dd98d2-a674-4b94-8a51-60b3e32f0a14.txt +TCGA-ESCA/SNV__muse/71e290d0-170a-4e26-944f-91f9eeebc27a.maf.txt +TCGA-ESCA/SNV__muse/TCGA-IG-A3YB-01A-11D-A247-09.71e290d0-170a-4e26-944f-91f9eeebc27a.maf.txt +TCGA-ESCA/SNV__muse/TCGA-L5-A4OI-01A-11D-A27G-09.71e290d0-170a-4e26-944f-91f9eeebc27a.maf.txt TCGA-ESCA/SNV__mutect/TCGA-IG-A3YB-01A-11D-A247-09.c7fe427a-b447-4840-8cd1-fe33a236dfe7.maf.txt TCGA-ESCA/SNV__mutect/TCGA-L5-A4OI-01A-11D-A27G-09.c7fe427a-b447-4840-8cd1-fe33a236dfe7.maf.txt TCGA-ESCA/SNV__mutect/c7fe427a-b447-4840-8cd1-fe33a236dfe7.maf.txt +TCGA-ESCA/SNV__somaticsniper/8de9f66a-ca56-4d68-a7a1-dbc00f2601cc.maf.txt +TCGA-ESCA/SNV__somaticsniper/TCGA-IG-A3YB-01A-11D-A247-09.8de9f66a-ca56-4d68-a7a1-dbc00f2601cc.maf.txt +TCGA-ESCA/SNV__somaticsniper/TCGA-L5-A4OI-01A-11D-A27G-09.8de9f66a-ca56-4d68-a7a1-dbc00f2601cc.maf.txt +TCGA-ESCA/SNV__varscan/TCGA-IG-A3YB-01A-11D-A247-09.a007d8f1-2368-48cb-b3be-df712788eba7.maf.txt +TCGA-ESCA/SNV__varscan/TCGA-L5-A4OI-01A-11D-A27G-09.a007d8f1-2368-48cb-b3be-df712788eba7.maf.txt +TCGA-ESCA/SNV__varscan/a007d8f1-2368-48cb-b3be-df712788eba7.maf.txt TCGA-ESCA/clinical__biospecimen/TCGA-IG-A3YB.719ce235-bde8-4e97-af75-e0c679df992e.txt TCGA-ESCA/clinical__biospecimen/TCGA-L5-A4OI.0815e9e1-5e21-483b-adcc-dc1e6b6c66e9.txt TCGA-ESCA/clinical__primary/TCGA-IG-A3YB.c1aa26ce-a85d-4266-8758-90e56a7533ea.txt @@ -59,9 +77,18 @@ TCGA-SKCM/CNV__unfiltered__snp6/TCGA-D3-A3C7-06A-11D-A194-01.9dfcb350-d18e-4400- TCGA-SKCM/CNV__unfiltered__snp6/TCGA-D3-A3C7-10A-01D-A195-01.3d11f3d8-1fde-46ea-a962-187a56da4700.txt TCGA-SKCM/CNV__unfiltered__snp6/TCGA-EE-A3J8-06A-11D-A20B-01.bd0e36f9-88c5-4750-86d6-00ca853ce452.txt TCGA-SKCM/CNV__unfiltered__snp6/TCGA-EE-A3J8-10A-01D-A20B-01.0dd468b0-4e9f-47a7-8594-10e9dc675d50.txt +TCGA-SKCM/SNV__muse/TCGA-D3-A3C7-06A-11D-A196-08.a1fe3943-5377-4763-8494-5e4e61545820.maf.txt +TCGA-SKCM/SNV__muse/TCGA-EE-A3J8-06A-11D-A20D-08.a1fe3943-5377-4763-8494-5e4e61545820.maf.txt +TCGA-SKCM/SNV__muse/a1fe3943-5377-4763-8494-5e4e61545820.maf.txt TCGA-SKCM/SNV__mutect/7d62b913-4ae8-4c59-9819-71711f12b3b2.maf.txt TCGA-SKCM/SNV__mutect/TCGA-D3-A3C7-06A-11D-A196-08.7d62b913-4ae8-4c59-9819-71711f12b3b2.maf.txt TCGA-SKCM/SNV__mutect/TCGA-EE-A3J8-06A-11D-A20D-08.7d62b913-4ae8-4c59-9819-71711f12b3b2.maf.txt +TCGA-SKCM/SNV__somaticsniper/8cce7734-539b-4fba-bf9a-69735906d962.maf.txt +TCGA-SKCM/SNV__somaticsniper/TCGA-D3-A3C7-06A-11D-A196-08.8cce7734-539b-4fba-bf9a-69735906d962.maf.txt +TCGA-SKCM/SNV__somaticsniper/TCGA-EE-A3J8-06A-11D-A20D-08.8cce7734-539b-4fba-bf9a-69735906d962.maf.txt +TCGA-SKCM/SNV__varscan/TCGA-D3-A3C7-06A-11D-A196-08.e751c317-d661-4290-b755-2b5c4d9cd0a4.maf.txt +TCGA-SKCM/SNV__varscan/TCGA-EE-A3J8-06A-11D-A20D-08.e751c317-d661-4290-b755-2b5c4d9cd0a4.maf.txt +TCGA-SKCM/SNV__varscan/e751c317-d661-4290-b755-2b5c4d9cd0a4.maf.txt TCGA-SKCM/clinical__biospecimen/TCGA-D3-A3C7.192bbf1c-4f69-463c-b9ec-8d7827c8312a.txt TCGA-SKCM/clinical__biospecimen/TCGA-EE-A3J8.b6b16c1b-e0c3-4e43-83dd-3d450ed53c33.txt TCGA-SKCM/clinical__primary/TCGA-D3-A3C7.51c48680-6b80-4722-a06d-bdcc6e84c087.txt diff --git a/tests/baselines/dice-md5sums.txt b/tests/baselines/dice-md5sums.txt index d5c16f1..eb90891 100644 --- a/tests/baselines/dice-md5sums.txt +++ b/tests/baselines/dice-md5sums.txt @@ -1,80 +1,107 @@ -062d34020b3242dc793cb033cacd5bd4 TCGA-ESCA/methylation__HM450/TCGA-L5-A4OI-11A-11D-A265-05.20048f6e-2f05-4029-af70-a664411f0fe7.data.txt -0f7a6227b6a8487e560987080127aa36 TCGA-SKCM/CNV__snp6/TCGA-D3-A3C7-10A-01D-A195-01.0a4bab0b-00f6-4f13-a1e6-31c20b2c16d6.txt -102a70dbc7cf0fb3e82d2f67d4fc1930 TCGA-ACC/methylation__HM450/TCGA-OR-A5K2-01A-11D-A29J-05.c5a36e2a-33cd-484a-91db-4f030a5f5415.data.txt -112134bb595f54a643047375f480eec5 TCGA-ESCA/miR__isoformExp/TCGA-IG-A3YB-01A-11R-A24L-13.e80ec825-2da2-4fa3-a42e-afaf4a18d9bf.txt -12762a0ec28570817a695ed0f591ca87 TCGA-ACC/clinical__biospecimen/TCGA-OR-A5K2.2fde5970-89ee-46d3-ad62-8172804ca952.txt -128d550feab7b613334fad401b35c4d2 TCGA-SKCM/SNV__mutect/TCGA-D3-A3C7-06A-11D-A196-08.7d62b913-4ae8-4c59-9819-71711f12b3b2.maf.txt -14c1ffa80aa11a2f7fd1ae2907831cad TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5L1-01A-11D-A309-01.477185ad-aafa-4da0-be72-780bd66fb6cd.txt -196990803691564c5083d954ed611f85 TCGA-SKCM/miR__isoformExp/TCGA-D3-A3C7-06A-11R-A18X-13.65fb92ff-5b86-424c-8d3f-39444e2bf3e5.txt -19babe0242f4388422b23ccb196cc6d4 TCGA-ESCA/CNV__unfiltered__snp6/TCGA-L5-A4OI-01A-11D-A25X-01.92990d84-9f3c-46d6-89ab-fb631dd4139f.txt -1a1e2d8629af0f483c061c04dedb5952 TCGA-ESCA/methylation__HM450/TCGA-L5-A4OI-01A-11D-A265-05.09f09483-ca1b-4cc6-9d4f-784d22471df7.data.txt -22d0ae2785a2ad29ad4f3235a0425bcf TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5K2-10B-01D-A29K-01.a774d500-8c68-4071-a3b1-328f346b417c.txt -24e038ab5c968d7b68d97e824e3b0790 TCGA-SKCM/SNV__mutect/TCGA-EE-A3J8-06A-11D-A20D-08.7d62b913-4ae8-4c59-9819-71711f12b3b2.maf.txt -28d71455d82579a23875cb0e7711e2a9 TCGA-SKCM/CNV__snp6/TCGA-D3-A3C7-06A-11D-A194-01.6ee6e045-fe18-4e98-bd7f-9bf133605bc4.txt -2beebd9031b3b58e0018091ea5a27565 TCGA-ESCA/miR__geneExp/TCGA-IG-A3YB-01A-11R-A24L-13.7622ed32-0f43-425f-b4b2-4087c0bb64a7.txt -2db6f5d94dae082b9d7618f904f2e332 TCGA-ESCA/SNV__mutect/TCGA-IG-A3YB-01A-11D-A247-09.c7fe427a-b447-4840-8cd1-fe33a236dfe7.maf.txt -2f00a3baa579bfa1db4143daa8d77618 TCGA-SKCM/mRNA__counts__FPKM/TCGA-EE-A3J8-06A-11R-A20F-07.9c488510-a229-45e9-b708-0b666c257dbc.txt -338cd5adbdf7a6cd61e9cd8ce1eb5cfd 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e1ecc0e..981294c 100644 --- a/tests/baselines/load-md5sums-google.txt +++ b/tests/baselines/load-md5sums-google.txt @@ -1 +1 @@ -a1f90f9778db43a208ccfd7b754170bb load-munged.txt +a2cfdcc0f115fd8322c47fddb530ddbd load-munged.txt diff --git a/tests/baselines/load-md5sums.txt b/tests/baselines/load-md5sums.txt index 8d13be8..0e7a238 100644 --- a/tests/baselines/load-md5sums.txt +++ b/tests/baselines/load-md5sums.txt @@ -1 +1 @@ -e3b0b1a9be28513b473ad828d8aad1b5 load-munged.txt +c6091b4dcac8a27edf13a07d8c5a5fbe load-munged.txt From 4f4f39e1995b689603ed12c312123e990ac65c95 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sat, 28 Oct 2017 22:06:37 -0400 Subject: [PATCH 19/30] raise exception at end of failing mirror and dice --- gdctools/gdc_dice.py | 2 +- gdctools/gdc_mirror.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/gdctools/gdc_dice.py b/gdctools/gdc_dice.py index 9b6c78b..ac0ab44 100644 --- a/gdctools/gdc_dice.py +++ b/gdctools/gdc_dice.py @@ -226,7 +226,7 @@ def dice(self): logging.info("Dicing completed successfuly") else: logging.error("One or more diced files FAILED") - #raise Exception("One or more diced files FAILED") + raise Exception("One or more diced files FAILED") def execute(self): diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index 36aa1aa..3b94e2c 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -163,6 +163,7 @@ def mirror(self): logging.info("Mirror completed successfully.") else: logging.error("Mirror FAILED downloading one or more files.") + raise Exception("Mirror FAILED downloading one or more files.") def __mirror_file(self, file_d, proj_root, n, total, retries=3): From 57b3c7d6fccd1ba3e4be275c734a5ceb5632246b Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sat, 28 Oct 2017 22:48:25 -0400 Subject: [PATCH 20/30] add test that dicer actually returns an error --- tests/Makefile | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/tests/Makefile b/tests/Makefile index 02eb75d..1db769e 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -149,6 +149,18 @@ test_dice: $(FIND_DICE_FILES) -exec $(MD5) {} \; | $(SORT) > $(TEST_ROOT)/dice-md5sums.txt diff -b baselines/dice-md5sums.txt $(TEST_ROOT)/. +test_dice_error: + @echo + @echo Test that dicing throws error when mirror is corrupted + @$(PYTHON) ../gdctools/gdc_mirror.py --config corrupt_mirror.cfg + @rm -r ./corrupt_sandbox/mirror/TCGA/TCGA-ACC/Copy_Number_Variation + @$(PYTHON) ../gdctools/gdc_dice.py --config corrupt_mirror.cfg || Result=$$? ; \ + $(ENSURE_FAILURE_EXIT_CODE) + @echo Test that error goes away when mirror is fixed + @$(PYTHON) ../gdctools/gdc_mirror.py --config corrupt_mirror.cfg + @$(PYTHON) ../gdctools/gdc_dice.py --config corrupt_mirror.cfg + + test_loadfiles: # By default GDCtools generates firecloud-style loadfiles, so exercise other @$(EMAKE) test_loadfile From 47c5ff14424a36bb6585bd797ac71a962cc6f961 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sat, 28 Oct 2017 23:52:10 -0400 Subject: [PATCH 21/30] add test_pool --- tests/Makefile | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/tests/Makefile b/tests/Makefile index 1db769e..7919d1d 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -156,10 +156,37 @@ test_dice_error: @rm -r ./corrupt_sandbox/mirror/TCGA/TCGA-ACC/Copy_Number_Variation @$(PYTHON) ../gdctools/gdc_dice.py --config corrupt_mirror.cfg || Result=$$? ; \ $(ENSURE_FAILURE_EXIT_CODE) + @echo @echo Test that error goes away when mirror is fixed @$(PYTHON) ../gdctools/gdc_mirror.py --config corrupt_mirror.cfg @$(PYTHON) ../gdctools/gdc_dice.py --config corrupt_mirror.cfg +test_pool: + @echo + @echo Test that mirror metadata is appended only when --append flag present + @rm -r ./pool_sandbox + @$(PYTHON) ../gdctools/gdc_mirror.py --config pool1.cfg + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg 2>&1 | grep Counter | grep '10}' + + @$(PYTHON) ../gdctools/gdc_mirror.py --config pool2.cfg + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg 2>&1 | grep Counter | grep '16}' + + @$(PYTHON) ../gdctools/gdc_mirror.py --config pool2.cfg --append + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg 2>&1 | grep Counter | grep '16}' + + @$(PYTHON) ../gdctools/gdc_mirror.py --config pool1.cfg --append + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg 2>&1 | grep Counter | grep '22}' + + @$(PYTHON) ../gdctools/gdc_mirror.py --config pool1.cfg + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg 2>&1 | grep Counter | grep '10}' + + @$(PYTHON) ../gdctools/gdc_mirror.py --config pool2.cfg --date pool --append + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg 2>&1 | grep Counter | grep '10}' + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg --date pool 2>&1 | grep Counter | grep '16}' + + @$(PYTHON) ../gdctools/gdc_mirror.py --config pool1.cfg --date pool --append + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg 2>&1 | grep Counter | grep '10}' + @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg --date pool 2>&1 | grep Counter | grep '22}' test_loadfiles: # By default GDCtools generates firecloud-style loadfiles, so exercise other From 2949a395b6a4759db1a7079d154bfc4d5a6d4eb5 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sun, 29 Oct 2017 00:01:11 -0400 Subject: [PATCH 22/30] add new tests to top level target --- tests/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/Makefile b/tests/Makefile index 7919d1d..1bcd88c 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -71,7 +71,7 @@ help: @echo "4. publish Submit to PyPI" @echo -test: setup test_smoke test_dice test_loadfiles test_legacy test_report echo_success +test: setup test_smoke test_dice test_loadfiles test_legacy test_report echo_success test_dice_error test_pool test_smoke: setup echo_ver test_invoke test_mirror test_redo_mirror test_badcfg \ test_cases test_choose From ecf5ecf272448b0fd83d88b034070d3308b0663f Mon Sep 17 00:00:00 2001 From: gsaksena Date: Sun, 29 Oct 2017 00:01:48 -0400 Subject: [PATCH 23/30] delete commented out code --- gdctools/GDCtool.py | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/gdctools/GDCtool.py b/gdctools/GDCtool.py index 471cbaa..ff27fbb 100644 --- a/gdctools/GDCtool.py +++ b/gdctools/GDCtool.py @@ -97,24 +97,6 @@ def execute(self): #other strings such as , 'latest', valid variable names, and everything else are not allowed raise ValueError("For gdc_mirror, date must be blank or 'pool'") - # TODO remove this old code **gs** - # if self.datestamp_required: - # datestamp = self.options.datestamp - # if not datestamp: - # datestamp = 'latest' - - # existing_dates = self.datestamps() # ascending sort order - # if len(existing_dates) == 0: - # raise ValueError("No datestamps found, use upstream tool first") - - # if datestamp == 'latest': - # datestamp = existing_dates[-1] - # elif datestamp not in existing_dates: - # raise ValueError("Requested datestamp not present in " - # + self.config.datestamps + "\n" - # + "Existing datestamps: " + repr(existing_dates)) - # else: - # datestamp = time.strftime('%Y_%m_%d', time.localtime()) self.datestamp = datestamp self.init_logging() From b61aa36ec5767cedfa55ca9829ad46e7c0cf20b0 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Mon, 6 Nov 2017 11:26:33 -0500 Subject: [PATCH 24/30] add duplicate file detection, and first write metadata to .partial for dice and mirror --- gdctools/gdc_dice.py | 26 ++++++++++++++++++++++---- gdctools/gdc_mirror.py | 4 +++- 2 files changed, 25 insertions(+), 5 deletions(-) diff --git a/gdctools/gdc_dice.py b/gdctools/gdc_dice.py index ac0ab44..a16fe82 100644 --- a/gdctools/gdc_dice.py +++ b/gdctools/gdc_dice.py @@ -151,9 +151,10 @@ def dice(self): if not os.path.isdir(diced_meta_dir): os.makedirs(diced_meta_dir) diced_meta_file = os.path.join(diced_meta_dir, diced_meta_fname) + diced_meta_file_partial = diced_meta_file + '.partial' # Count project annotations - with open(diced_meta_file, 'w') as mf: + with open(diced_meta_file_partial, 'w') as mf: # Header META_HEADERS = ['case_id', 'tcga_barcode', 'sample_type', 'annotation', 'file_name', 'center', @@ -179,6 +180,9 @@ def dice(self): force=self.force) prog_status_tally[dice_one_status] += 1 + # move completed metadata file to final location + # note it may include diced files that had errors + os.rename(diced_meta_file_partial, diced_meta_file) # Bookkeeping code -- write some useful tables # and figures needed for downstream sample reports. @@ -400,8 +404,10 @@ def dice_one(file_dict, translation_dict, mirror_proj_root, diced_root, logging.info("Skipping file " + mirror_path + " (already diced)") dice_one_status = 'cached' - append_diced_metadata(file_dict, expected_paths, + duplicate_detected = append_diced_metadata(file_dict, expected_paths, annot, meta_file_writer) + if duplicate_detected: + dice_one_status = 'error' else: dice_one_status = 'dry_run' @@ -452,6 +458,9 @@ def metadata_to_dictkey(file_dict): "workflow_type" : workflow_type } +# globally scoped variable, for persistence +count_by_tcga_barcode_by_annot = defaultdict(Counter) + def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): '''Write one or more rows for the given file_dict using meta_file_writer. The number of rows will be equal to the length of diced_paths. @@ -459,7 +468,8 @@ def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): meta_file_writer must be a csv.DictWriter ''' - + + duplicate_detected = False # These fields will be shared regardless of the number of diced files rowdict = { 'annotation' : annot, @@ -474,11 +484,15 @@ def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): sample_type = None if meta.has_sample(file_dict): sample_type = meta.sample_type(file_dict) + tcga_barcode = meta.tcga_id(file_dict) + count_by_tcga_barcode_by_annot[tcga_barcode][annot] += 1 + if count_by_tcga_barcode_by_annot[tcga_barcode][annot] > 1: + duplicate_detected = True # Write row with csv.DictWriter.writerow() rowdict.update({ 'case_id' : meta.case_id(file_dict), - 'tcga_barcode' : meta.tcga_id(file_dict), + 'tcga_barcode' : tcga_barcode, 'sample_type' : sample_type, 'file_name' : diced_path, 'is_ffpe' : meta.is_ffpe(file_dict) @@ -500,6 +514,9 @@ def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): # case_id is the first twelve digits of the TCGA barcode case_id = tcga_barcode[:12] sample_type, is_ffpe = barcode_to_sample_dict[tcga_barcode] + count_by_tcga_barcode_by_annot[tcga_barcode][annot] += 1 + if count_by_tcga_barcode_by_annot[tcga_barcode][annot] > 1: + duplicate_detected = True rowdict.update({ 'case_id' : case_id, @@ -509,6 +526,7 @@ def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): 'is_ffpe' : is_ffpe }) meta_file_writer.writerow(rowdict) + return duplicate_detected def constrain(metadata, config): cases_chosen = set(config.cases) diff --git a/gdctools/gdc_mirror.py b/gdctools/gdc_mirror.py index 3b94e2c..6fee8d8 100644 --- a/gdctools/gdc_mirror.py +++ b/gdctools/gdc_mirror.py @@ -293,6 +293,7 @@ def mirror_project(self, program, project): os.makedirs(stamp_folder) meta_json = ".".join(["metadata", project, datestamp, "json" ]) meta_json = os.path.join(stamp_folder, meta_json) + meta_json_partial = meta_json + '.partial' if config.mirror.append and os.path.exists(meta_json): #fetch previous metadata with same datestamp @@ -305,8 +306,9 @@ def mirror_project(self, program, project): # Write file metadata - with open(meta_json, 'w') as jf: + with open(meta_json_partial, 'w') as jf: json.dump(output_metadata, jf, indent=2) + os.rename(meta_json_partial, meta_json) return proj_status_tally From 6566b1609b1ebc2a81eba89975d88d0037b020e2 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Mon, 6 Nov 2017 11:41:07 -0500 Subject: [PATCH 25/30] fix test_pool for case where pool_sandbox dir wasn't left over from last time --- tests/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/Makefile b/tests/Makefile index 1bcd88c..dcc4637 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -164,7 +164,7 @@ test_dice_error: test_pool: @echo @echo Test that mirror metadata is appended only when --append flag present - @rm -r ./pool_sandbox + @rm -rf ./pool_sandbox @$(PYTHON) ../gdctools/gdc_mirror.py --config pool1.cfg @$(PYTHON) ../gdctools/gdc_dice.py --config pool.cfg 2>&1 | grep Counter | grep '10}' From 97886daaa7d8a5c1b2fceb3f3dd2efb953117ae2 Mon Sep 17 00:00:00 2001 From: gsaksena Date: Mon, 6 Nov 2017 12:02:31 -0500 Subject: [PATCH 26/30] add error message when duplicate input files detected --- gdctools/gdc_dice.py | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/gdctools/gdc_dice.py b/gdctools/gdc_dice.py index a16fe82..6899795 100644 --- a/gdctools/gdc_dice.py +++ b/gdctools/gdc_dice.py @@ -485,9 +485,7 @@ def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): if meta.has_sample(file_dict): sample_type = meta.sample_type(file_dict) tcga_barcode = meta.tcga_id(file_dict) - count_by_tcga_barcode_by_annot[tcga_barcode][annot] += 1 - if count_by_tcga_barcode_by_annot[tcga_barcode][annot] > 1: - duplicate_detected = True + # Write row with csv.DictWriter.writerow() rowdict.update({ @@ -497,8 +495,13 @@ def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): 'file_name' : diced_path, 'is_ffpe' : meta.is_ffpe(file_dict) }) - meta_file_writer.writerow(rowdict) + + count_by_tcga_barcode_by_annot[tcga_barcode][annot] += 1 + if count_by_tcga_barcode_by_annot[tcga_barcode][annot] > 1: + duplicate_detected = True + logging.error('Multiple files contain data for the same sample: %s'%str(rowdict) ) + else: # Harder case, have to write a line for each unique file # We need to match the diced filenames back to the original samples @@ -514,9 +517,6 @@ def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): # case_id is the first twelve digits of the TCGA barcode case_id = tcga_barcode[:12] sample_type, is_ffpe = barcode_to_sample_dict[tcga_barcode] - count_by_tcga_barcode_by_annot[tcga_barcode][annot] += 1 - if count_by_tcga_barcode_by_annot[tcga_barcode][annot] > 1: - duplicate_detected = True rowdict.update({ 'case_id' : case_id, @@ -526,6 +526,13 @@ def append_diced_metadata(file_dict, diced_paths, annot, meta_file_writer): 'is_ffpe' : is_ffpe }) meta_file_writer.writerow(rowdict) + + count_by_tcga_barcode_by_annot[tcga_barcode][annot] += 1 + if count_by_tcga_barcode_by_annot[tcga_barcode][annot] > 1: + duplicate_detected = True + logging.error('Multiple files contain data for the same sample: %s'%str(rowdict) ) + + return duplicate_detected def constrain(metadata, config): From 46531286d5146c3890849b10a2eb99a269f8ca66 Mon Sep 17 00:00:00 2001 From: "Michael S. Noble" Date: Tue, 16 Jan 2018 20:37:18 -0500 Subject: [PATCH 27/30] gsaksena_mmd2 branch: update test baselines for latest GDC data release --- tests/baselines/dice-files.txt | 143 +++++++++++++----------- tests/baselines/dice-md5sums.txt | 143 +++++++++++++----------- tests/baselines/load-md5sums-google.txt | 2 +- tests/baselines/load-md5sums.txt | 2 +- tests/baselines/mirror-files.txt | 24 +++- 5 files changed, 174 insertions(+), 140 deletions(-) diff --git a/tests/baselines/dice-files.txt b/tests/baselines/dice-files.txt index 9c3aa39..82504d9 100644 --- a/tests/baselines/dice-files.txt +++ b/tests/baselines/dice-files.txt @@ -6,18 +6,21 @@ TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5K2-01A-11D-A29H-01.b0ef98ef-b83b-4f51-9 TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5K2-10B-01D-A29K-01.a774d500-8c68-4071-a3b1-328f346b417c.txt TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5L1-01A-11D-A309-01.477185ad-aafa-4da0-be72-780bd66fb6cd.txt TCGA-ACC/CNV__unfiltered__snp6/TCGA-OR-A5L1-10A-01D-A309-01.7c263070-5b38-4d8c-9a31-899e1ba9d91d.txt -TCGA-ACC/SNV__muse/TCGA-OR-A5K2-01A-11D-A29I-10.c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.maf.txt -TCGA-ACC/SNV__muse/TCGA-OR-A5L1-01A-11D-A30A-10.c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.maf.txt -TCGA-ACC/SNV__muse/c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.maf.txt +TCGA-ACC/SNV__muse/9d298cc7-71d2-43f5-835d-d7ef7a43bb11.maf.txt +TCGA-ACC/SNV__muse/TCGA-OR-A5K2-01A-11D-A29I-10.9d298cc7-71d2-43f5-835d-d7ef7a43bb11.maf.txt +TCGA-ACC/SNV__muse/TCGA-OR-A5L1-01A-11D-A30A-10.9d298cc7-71d2-43f5-835d-d7ef7a43bb11.maf.txt +TCGA-ACC/SNV__mutect/81ac2c46-37db-4dcd-923a-061a7ae626a3.maf.txt +TCGA-ACC/SNV__mutect/TCGA-OR-A5K2-01A-11D-A29I-10.81ac2c46-37db-4dcd-923a-061a7ae626a3.maf.txt TCGA-ACC/SNV__mutect/TCGA-OR-A5K2-01A-11D-A29I-10.ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.maf.txt +TCGA-ACC/SNV__mutect/TCGA-OR-A5L1-01A-11D-A30A-10.81ac2c46-37db-4dcd-923a-061a7ae626a3.maf.txt TCGA-ACC/SNV__mutect/TCGA-OR-A5L1-01A-11D-A30A-10.ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.maf.txt TCGA-ACC/SNV__mutect/ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.maf.txt -TCGA-ACC/SNV__somaticsniper/TCGA-OR-A5K2-01A-11D-A29I-10.da92b810-c396-4963-b538-5454f13a297c.maf.txt -TCGA-ACC/SNV__somaticsniper/TCGA-OR-A5L1-01A-11D-A30A-10.da92b810-c396-4963-b538-5454f13a297c.maf.txt -TCGA-ACC/SNV__somaticsniper/da92b810-c396-4963-b538-5454f13a297c.maf.txt -TCGA-ACC/SNV__varscan/2ff3f6bd-6114-431d-ab3b-656d7ab13996.maf.txt -TCGA-ACC/SNV__varscan/TCGA-OR-A5K2-01A-11D-A29I-10.2ff3f6bd-6114-431d-ab3b-656d7ab13996.maf.txt -TCGA-ACC/SNV__varscan/TCGA-OR-A5L1-01A-11D-A30A-10.2ff3f6bd-6114-431d-ab3b-656d7ab13996.maf.txt +TCGA-ACC/SNV__somaticsniper/422bff06-f1b2-4768-be4a-8bcb82644ce2.maf.txt +TCGA-ACC/SNV__somaticsniper/TCGA-OR-A5K2-01A-11D-A29I-10.422bff06-f1b2-4768-be4a-8bcb82644ce2.maf.txt +TCGA-ACC/SNV__somaticsniper/TCGA-OR-A5L1-01A-11D-A30A-10.422bff06-f1b2-4768-be4a-8bcb82644ce2.maf.txt +TCGA-ACC/SNV__varscan/747f92d2-3208-49cc-a564-3c5d0a2697ef.maf.txt +TCGA-ACC/SNV__varscan/TCGA-OR-A5K2-01A-11D-A29I-10.747f92d2-3208-49cc-a564-3c5d0a2697ef.maf.txt +TCGA-ACC/SNV__varscan/TCGA-OR-A5L1-01A-11D-A30A-10.747f92d2-3208-49cc-a564-3c5d0a2697ef.maf.txt TCGA-ACC/clinical__biospecimen/TCGA-OR-A5K2.2fde5970-89ee-46d3-ad62-8172804ca952.txt TCGA-ACC/clinical__biospecimen/TCGA-OR-A5L1.2c6c5c9b-2ac1-46aa-83ef-401cb9e20bfc.txt TCGA-ACC/clinical__primary/TCGA-OR-A5K2.e3e4a2d6-e5d6-46ec-8cef-d5b15ca4d9e4.txt @@ -52,46 +55,46 @@ TCGA-BLCA/CNV__unfiltered__snp6/TCGA-BL-A13J-01A-11D-A273-01.ae7bda94-c86a-4008- TCGA-BLCA/CNV__unfiltered__snp6/TCGA-BL-A13J-01B-04D-A273-01.4922dd35-5ab8-4117-9f6f-2fba7ebc86b2.txt TCGA-BLCA/CNV__unfiltered__snp6/TCGA-BL-A13J-10A-01D-A10T-01.0dee3246-0f12-4ee8-888e-75658bbb4a90.txt TCGA-BLCA/CNV__unfiltered__snp6/TCGA-BL-A13J-10A-01D-A273-01.045dae18-56ff-460f-9180-2fe17896044a.txt -TCGA-BLCA/SNV__muse/92f0f6c7-9f82-44e5-b7b2-66dbbfd30e70.maf.txt 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TCGA-ESCA/clinical__biospecimen/TCGA-IG-A3YB.719ce235-bde8-4e97-af75-e0c679df992e.txt TCGA-ESCA/clinical__biospecimen/TCGA-L5-A4OI.0815e9e1-5e21-483b-adcc-dc1e6b6c66e9.txt TCGA-ESCA/clinical__primary/TCGA-IG-A3YB.c1aa26ce-a85d-4266-8758-90e56a7533ea.txt @@ -207,18 +213,21 @@ TCGA-SKCM/CNV__unfiltered__snp6/TCGA-D3-A3C7-06A-11D-A194-01.9dfcb350-d18e-4400- TCGA-SKCM/CNV__unfiltered__snp6/TCGA-D3-A3C7-10A-01D-A195-01.3d11f3d8-1fde-46ea-a962-187a56da4700.txt TCGA-SKCM/CNV__unfiltered__snp6/TCGA-EE-A3J8-06A-11D-A20B-01.bd0e36f9-88c5-4750-86d6-00ca853ce452.txt TCGA-SKCM/CNV__unfiltered__snp6/TCGA-EE-A3J8-10A-01D-A20B-01.0dd468b0-4e9f-47a7-8594-10e9dc675d50.txt -TCGA-SKCM/SNV__muse/TCGA-D3-A3C7-06A-11D-A196-08.a1fe3943-5377-4763-8494-5e4e61545820.maf.txt -TCGA-SKCM/SNV__muse/TCGA-EE-A3J8-06A-11D-A20D-08.a1fe3943-5377-4763-8494-5e4e61545820.maf.txt -TCGA-SKCM/SNV__muse/a1fe3943-5377-4763-8494-5e4e61545820.maf.txt 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a/tests/baselines/load-md5sums-google.txt +++ b/tests/baselines/load-md5sums-google.txt @@ -1 +1 @@ -3a6a81fb97baa05d19f851dbef409cd6 load-munged.txt +2376270ba8546620fc7bb13b6a575762 load-munged.txt diff --git a/tests/baselines/load-md5sums.txt b/tests/baselines/load-md5sums.txt index 985575e..5b37530 100644 --- a/tests/baselines/load-md5sums.txt +++ b/tests/baselines/load-md5sums.txt @@ -1 +1 @@ -5385b54a5482afa1559cb55abeb0bf6b load-munged.txt +9227d7a702a984e46b15db9c9b8bbc83 load-munged.txt diff --git a/tests/baselines/mirror-files.txt b/tests/baselines/mirror-files.txt index c7243cb..624928f 100644 --- a/tests/baselines/mirror-files.txt +++ b/tests/baselines/mirror-files.txt @@ -11,10 +11,14 @@ TCGA-ACC/Copy_Number_Variation/Masked_Copy_Number_Segment/BLAIN_p_TCGA_282_304_b TCGA-ACC/Copy_Number_Variation/Masked_Copy_Number_Segment/GAMED_p_TCGA_B_312_313_314_NSP_GenomeWideSNP_6_E06_1361784.nocnv_grch38.seg.05a4633f-f012-43c0-90fd-268ad47f85b0.txt TCGA-ACC/Copy_Number_Variation/Masked_Copy_Number_Segment/GAMED_p_TCGA_B_312_313_314_NSP_GenomeWideSNP_6_E07_1361714.nocnv_grch38.seg.818e8b0a-04a7-42e5-929c-b9d11c64d1a9.txt TCGA-ACC/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_ACC.HumanMethylation450.1.lvl-3.TCGA-OR-A5K2-01A-11D-A29J-05.gdc_hg38.c5a36e2a-33cd-484a-91db-4f030a5f5415.txt +TCGA-ACC/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ACC.muse.9d298cc7-71d2-43f5-835d-d7ef7a43bb11.DR-10.0.somatic.maf.9d298cc7-71d2-43f5-835d-d7ef7a43bb11.gz TCGA-ACC/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ACC.muse.c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.DR-7.0.somatic.maf.c9d7ed14-11a0-49b3-a17f-e843c2a5cd88.gz +TCGA-ACC/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ACC.mutect.81ac2c46-37db-4dcd-923a-061a7ae626a3.DR-10.0.somatic.maf.81ac2c46-37db-4dcd-923a-061a7ae626a3.gz TCGA-ACC/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ACC.mutect.ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.DR-7.0.somatic.maf.ac3a9f5a-d78e-4b13-acb8-1001b215ffb6.gz +TCGA-ACC/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ACC.somaticsniper.422bff06-f1b2-4768-be4a-8bcb82644ce2.DR-10.0.somatic.maf.422bff06-f1b2-4768-be4a-8bcb82644ce2.gz TCGA-ACC/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ACC.somaticsniper.da92b810-c396-4963-b538-5454f13a297c.DR-7.0.somatic.maf.da92b810-c396-4963-b538-5454f13a297c.gz TCGA-ACC/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ACC.varscan.2ff3f6bd-6114-431d-ab3b-656d7ab13996.DR-7.0.somatic.maf.2ff3f6bd-6114-431d-ab3b-656d7ab13996.gz +TCGA-ACC/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ACC.varscan.747f92d2-3208-49cc-a564-3c5d0a2697ef.DR-10.0.somatic.maf.747f92d2-3208-49cc-a564-3c5d0a2697ef.gz TCGA-ACC/Transcriptome_Profiling/Gene_Expression_Quantification/26ac18a6-1e88-4a29-a514-05c2e0078aec.FPKM-UQ.1cf80958-0f98-445b-b91c-eae101b8fb38.txt.gz TCGA-ACC/Transcriptome_Profiling/Gene_Expression_Quantification/26ac18a6-1e88-4a29-a514-05c2e0078aec.FPKM.cc530ddb-02c2-47aa-9f3e-a5c39af69c5c.txt.gz TCGA-ACC/Transcriptome_Profiling/Gene_Expression_Quantification/26ac18a6-1e88-4a29-a514-05c2e0078aec.htseq.counts.76bfb639-1e16-4cf0-b280-a17305da2e13.gz @@ -60,10 +64,10 @@ TCGA-BLCA/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_BLCA.HumanMethylati TCGA-BLCA/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_BLCA.HumanMethylation450.2.lvl-3.TCGA-BL-A13I-01A-11D-A13Z-05.gdc_hg38.47c9b2e8-50fe-4433-8c04-fb0461db2509.txt TCGA-BLCA/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_BLCA.HumanMethylation450.2.lvl-3.TCGA-BL-A13I-01A-11D-A276-05.gdc_hg38.2e6821ed-8e54-4b8f-8a3e-581bb8eae81a.txt TCGA-BLCA/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_BLCA.HumanMethylation450.2.lvl-3.TCGA-BL-A13I-01B-04D-A276-05.gdc_hg38.79e66bef-80a0-42c8-8e35-00687018b4b0.txt -TCGA-BLCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.BLCA.muse.92f0f6c7-9f82-44e5-b7b2-66dbbfd30e70.DR-7.0.somatic.maf.92f0f6c7-9f82-44e5-b7b2-66dbbfd30e70.gz -TCGA-BLCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.BLCA.mutect.60fafc48-e348-411e-ac9d-869043bad259.DR-7.0.somatic.maf.60fafc48-e348-411e-ac9d-869043bad259.gz -TCGA-BLCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.BLCA.somaticsniper.a7cf5819-8b19-461c-aa4a-9f9513e60fa6.DR-7.0.somatic.maf.a7cf5819-8b19-461c-aa4a-9f9513e60fa6.gz -TCGA-BLCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.BLCA.varscan.fa676543-18a1-49ac-9523-54d6dd0d16d0.DR-7.0.somatic.maf.fa676543-18a1-49ac-9523-54d6dd0d16d0.gz +TCGA-BLCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.BLCA.muse.7ed5eb26-d52c-45c5-bfa1-e39f963007a8.DR-10.0.somatic.maf.7ed5eb26-d52c-45c5-bfa1-e39f963007a8.gz +TCGA-BLCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.BLCA.mutect.0e239d8f-47b0-4e47-9716-e9ecc87605b9.DR-10.0.somatic.maf.0e239d8f-47b0-4e47-9716-e9ecc87605b9.gz +TCGA-BLCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.BLCA.somaticsniper.17350cc9-f9ae-48c2-8663-25d794e873d1.DR-10.0.somatic.maf.17350cc9-f9ae-48c2-8663-25d794e873d1.gz +TCGA-BLCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.BLCA.varscan.4a755399-e5b5-4d0e-b1e3-dae24b81590e.DR-10.0.somatic.maf.4a755399-e5b5-4d0e-b1e3-dae24b81590e.gz TCGA-BLCA/Transcriptome_Profiling/Gene_Expression_Quantification/32841ed1-16e3-4a88-8f5c-7aaf24c84e70.FPKM-UQ.3a460d44-54ce-49dc-8cb7-39071f42e696.txt.gz TCGA-BLCA/Transcriptome_Profiling/Gene_Expression_Quantification/32841ed1-16e3-4a88-8f5c-7aaf24c84e70.FPKM.277e49dd-ae87-4b6a-91f2-121d47c6f330.txt.gz TCGA-BLCA/Transcriptome_Profiling/Gene_Expression_Quantification/32841ed1-16e3-4a88-8f5c-7aaf24c84e70.htseq.counts.48566693-0845-44b2-8612-4f713fee1bd7.gz @@ -130,8 +134,12 @@ TCGA-ESCA/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_ESCA.HumanMethylati TCGA-ESCA/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_ESCA.HumanMethylation450.2.lvl-3.TCGA-L5-A4OI-01A-11D-A265-05.gdc_hg38.09f09483-ca1b-4cc6-9d4f-784d22471df7.txt TCGA-ESCA/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_ESCA.HumanMethylation450.2.lvl-3.TCGA-L5-A4OI-11A-11D-A265-05.gdc_hg38.20048f6e-2f05-4029-af70-a664411f0fe7.txt TCGA-ESCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ESCA.muse.71e290d0-170a-4e26-944f-91f9eeebc27a.DR-7.0.somatic.maf.71e290d0-170a-4e26-944f-91f9eeebc27a.gz +TCGA-ESCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ESCA.muse.b267fee6-e9a0-4d50-88fb-79eb8da1e8dd.DR-10.0.somatic.maf.b267fee6-e9a0-4d50-88fb-79eb8da1e8dd.gz +TCGA-ESCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ESCA.mutect.7f8e1e7c-621c-4dfd-8fad-af07c739dbfc.DR-10.0.somatic.maf.7f8e1e7c-621c-4dfd-8fad-af07c739dbfc.gz TCGA-ESCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ESCA.mutect.c7fe427a-b447-4840-8cd1-fe33a236dfe7.DR-7.0.somatic.maf.c7fe427a-b447-4840-8cd1-fe33a236dfe7.gz +TCGA-ESCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ESCA.somaticsniper.56890408-24a5-4b5a-b822-aaf872c057b8.DR-10.0.somatic.maf.56890408-24a5-4b5a-b822-aaf872c057b8.gz TCGA-ESCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ESCA.somaticsniper.8de9f66a-ca56-4d68-a7a1-dbc00f2601cc.DR-7.0.somatic.maf.8de9f66a-ca56-4d68-a7a1-dbc00f2601cc.gz +TCGA-ESCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ESCA.varscan.9dab6855-ba5e-4afb-b3a0-f034a6f82eb2.DR-10.0.somatic.maf.9dab6855-ba5e-4afb-b3a0-f034a6f82eb2.gz TCGA-ESCA/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.ESCA.varscan.a007d8f1-2368-48cb-b3be-df712788eba7.DR-7.0.somatic.maf.a007d8f1-2368-48cb-b3be-df712788eba7.gz TCGA-ESCA/Transcriptome_Profiling/Gene_Expression_Quantification/43f1cfcf-5c61-4dcf-9168-9cce41f8673c.FPKM-UQ.3cf7418d-39a9-4e53-9136-1dbe8df9f1a6.txt.gz TCGA-ESCA/Transcriptome_Profiling/Gene_Expression_Quantification/43f1cfcf-5c61-4dcf-9168-9cce41f8673c.FPKM.e0ed1b91-be78-4e80-9a2a-8faf99ffd78c.txt.gz @@ -157,10 +165,14 @@ TCGA-LAML/Copy_Number_Variation/Masked_Copy_Number_Segment/TCGA_AB_2959_03A_01D_ TCGA-LAML/Copy_Number_Variation/Masked_Copy_Number_Segment/TCGA_AB_2959_11A_01D_0756_21.nocnv_grch38.seg.243db832-02fc-450d-855e-f4b94f209ab1.txt TCGA-LAML/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_LAML.HumanMethylation27.1.lvl-3.TCGA-AB-2959-03A-01D-0741-05.gdc_hg38.2a642684-5255-44d1-a840-93ad39a93eb9.txt TCGA-LAML/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_LAML.HumanMethylation450.2.lvl-3.TCGA-AB-2959-03A-01D-0741-05.gdc_hg38.1eddc899-c6f3-43c4-904e-2be625e162ea.txt +TCGA-LAML/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.LAML.muse.0cdf3c70-ad58-462d-b6ba-5004b26c618e.DR-10.0.somatic.maf.0cdf3c70-ad58-462d-b6ba-5004b26c618e.gz TCGA-LAML/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.LAML.muse.8f865e42-fff9-4646-81b9-a184218104e2.DR-7.0.somatic.maf.8f865e42-fff9-4646-81b9-a184218104e2.gz +TCGA-LAML/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.LAML.mutect.27f42413-6d8f-401f-9d07-d019def8939e.DR-10.0.somatic.maf.27f42413-6d8f-401f-9d07-d019def8939e.gz TCGA-LAML/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.LAML.mutect.bc63d2f8-da4e-4dba-8738-a92ea33ea338.DR-7.0.somatic.maf.bc63d2f8-da4e-4dba-8738-a92ea33ea338.gz +TCGA-LAML/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.LAML.somaticsniper.99c2a8ba-1930-4dc7-ad71-7883eb7e29a9.DR-10.0.somatic.maf.99c2a8ba-1930-4dc7-ad71-7883eb7e29a9.gz TCGA-LAML/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.LAML.somaticsniper.b4260581-e5b2-4871-8128-52f502ffca87.DR-7.0.somatic.maf.b4260581-e5b2-4871-8128-52f502ffca87.gz TCGA-LAML/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.LAML.varscan.be016fba-ce36-419c-8028-4cf5049c9468.DR-7.0.somatic.maf.be016fba-ce36-419c-8028-4cf5049c9468.gz +TCGA-LAML/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.LAML.varscan.e595f93d-41ac-435e-8c90-06df7e9d6742.DR-10.0.somatic.maf.e595f93d-41ac-435e-8c90-06df7e9d6742.gz TCGA-LAML/Transcriptome_Profiling/Gene_Expression_Quantification/ee84e537-c13b-403a-8cd9-a8ab39012c53.FPKM-UQ.d76ee50c-fde5-4719-ae88-0fe90931170c.txt.gz TCGA-LAML/Transcriptome_Profiling/Gene_Expression_Quantification/ee84e537-c13b-403a-8cd9-a8ab39012c53.FPKM.099fa9f6-096b-408d-8f2f-6b8aebcdc708.txt.gz TCGA-LAML/Transcriptome_Profiling/Gene_Expression_Quantification/ee84e537-c13b-403a-8cd9-a8ab39012c53.htseq.counts.b3e9baff-615a-49d3-b58c-607cf3a091de.gz @@ -181,8 +193,12 @@ TCGA-SKCM/Copy_Number_Variation/Masked_Copy_Number_Segment/COMMY_p_TCGA_194_198_ TCGA-SKCM/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_SKCM.HumanMethylation450.1.lvl-3.TCGA-D3-A3C7-06A-11D-A19B-05.gdc_hg38.2db5c7cc-25f8-4d93-991f-173b8704cb14.txt TCGA-SKCM/DNA_Methylation/Methylation_Beta_Value/jhu-usc.edu_SKCM.HumanMethylation450.2.lvl-3.TCGA-EE-A3J8-06A-11D-A211-05.gdc_hg38.342836f4-b506-4bf8-a1f6-949ce9cb17dc.txt TCGA-SKCM/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.SKCM.muse.a1fe3943-5377-4763-8494-5e4e61545820.DR-7.0.somatic.maf.a1fe3943-5377-4763-8494-5e4e61545820.gz +TCGA-SKCM/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.SKCM.muse.e433a47f-7281-42aa-8bba-0affd1eb6df0.DR-10.0.somatic.maf.e433a47f-7281-42aa-8bba-0affd1eb6df0.gz +TCGA-SKCM/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.SKCM.mutect.4b7a5729-b83e-4837-9b61-a6002dce1c0a.DR-10.0.somatic.maf.4b7a5729-b83e-4837-9b61-a6002dce1c0a.gz TCGA-SKCM/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.SKCM.mutect.7d62b913-4ae8-4c59-9819-71711f12b3b2.DR-7.0.somatic.maf.7d62b913-4ae8-4c59-9819-71711f12b3b2.gz TCGA-SKCM/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.SKCM.somaticsniper.8cce7734-539b-4fba-bf9a-69735906d962.DR-7.0.somatic.maf.8cce7734-539b-4fba-bf9a-69735906d962.gz +TCGA-SKCM/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.SKCM.somaticsniper.b8ef7b54-adb8-4751-93bd-c26349be4252.DR-10.0.somatic.maf.b8ef7b54-adb8-4751-93bd-c26349be4252.gz +TCGA-SKCM/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.SKCM.varscan.6c961926-7792-42fa-9a16-c62f60e2557b.DR-10.0.somatic.maf.6c961926-7792-42fa-9a16-c62f60e2557b.gz TCGA-SKCM/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/TCGA.SKCM.varscan.e751c317-d661-4290-b755-2b5c4d9cd0a4.DR-7.0.somatic.maf.e751c317-d661-4290-b755-2b5c4d9cd0a4.gz TCGA-SKCM/Transcriptome_Profiling/Gene_Expression_Quantification/2b485559-2b76-4729-83c8-82b788a9c5f7.FPKM-UQ.abc1a5a6-cd0b-450c-a650-dfe14fdb356b.txt.gz TCGA-SKCM/Transcriptome_Profiling/Gene_Expression_Quantification/2b485559-2b76-4729-83c8-82b788a9c5f7.FPKM.662e5a74-9217-413e-8321-07951d802b8a.txt.gz From 003518be1daee9321d8973589465175e3f012a6d Mon Sep 17 00:00:00 2001 From: gsaksena Date: Wed, 17 Jan 2018 16:18:02 -0500 Subject: [PATCH 28/30] adding additional .cfg files for tests --- tests/corrupt_mirror.cfg | 33 +++++++++++++++++++++++++++++++++ tests/pool.cfg | 33 +++++++++++++++++++++++++++++++++ tests/pool1.cfg | 33 +++++++++++++++++++++++++++++++++ tests/pool2.cfg | 33 +++++++++++++++++++++++++++++++++ 4 files changed, 132 insertions(+) create mode 100644 tests/corrupt_mirror.cfg create mode 100644 tests/pool.cfg create mode 100644 tests/pool1.cfg create mode 100644 tests/pool2.cfg diff --git a/tests/corrupt_mirror.cfg b/tests/corrupt_mirror.cfg new file mode 100644 index 0000000..138f164 --- /dev/null +++ b/tests/corrupt_mirror.cfg @@ -0,0 +1,33 @@ +# NOTE: this .cfg is intended for use as a local smoke test, and is NOT intended +# for production use. See config/tcga.cfg for a production config file (and +# more description of each config file section). Finally, note that to simplify +# simplify and hasten the tests, we choose 2 cases from each of ACC, LAML, OV, +# and SKCM cohorts: 1 blood tumor (TB), 1 MET (TM) and 2 primaries (TP). The +# case ids are in sorted order below, according to their cohort abbreviation. + +[DEFAULT] +ROOT_DIR: ./corrupt_sandbox +LOG_DIR: %(ROOT_DIR)s/logs +REFERENCE_DIR: ./reference +PROGRAMS: TCGA +DATESTAMPS: %(ROOT_DIR)s/datestamps.txt +PROJECTS: TCGA-ACC +CASES: TCGA-OR-A5L1 + +[mirror] +DIR: %(ROOT_DIR)s/mirror + +[dice] +DIR: %(ROOT_DIR)s/dice + +[loadfile] +DIR: %(ROOT_DIR)s/loadfiles +FILTERED_SAMPLES: %(ROOT_DIR)s/loadfiles/filtered_samples.txt + +[report] +DIR: %(ROOT_DIR)s/reports +HEATMAPS_DIR: %(ROOT_DIR)s/heatmaps +REDACTIONS_DIR: %(ROOT_DIR)s/redactions +BLACKLIST: %(ROOT_DIR)s/config/blacklist.tsv + + diff --git a/tests/pool.cfg b/tests/pool.cfg new file mode 100644 index 0000000..df026c7 --- /dev/null +++ b/tests/pool.cfg @@ -0,0 +1,33 @@ +# NOTE: this .cfg is intended for use as a local smoke test, and is NOT intended +# for production use. See config/tcga.cfg for a production config file (and +# more description of each config file section). Finally, note that to simplify +# simplify and hasten the tests, we choose 2 cases from each of ACC, LAML, OV, +# and SKCM cohorts: 1 blood tumor (TB), 1 MET (TM) and 2 primaries (TP). The +# case ids are in sorted order below, according to their cohort abbreviation. + +[DEFAULT] +ROOT_DIR: ./pool_sandbox +LOG_DIR: %(ROOT_DIR)s/logs +REFERENCE_DIR: ./reference +PROGRAMS: TCGA +DATESTAMPS: %(ROOT_DIR)s/datestamps.txt +PROJECTS: TCGA-ACC + + +[mirror] +DIR: %(ROOT_DIR)s/mirror + +[dice] +DIR: %(ROOT_DIR)s/dice + +[loadfile] +DIR: %(ROOT_DIR)s/loadfiles +FILTERED_SAMPLES: %(ROOT_DIR)s/loadfiles/filtered_samples.txt + +[report] +DIR: %(ROOT_DIR)s/reports +HEATMAPS_DIR: %(ROOT_DIR)s/heatmaps +REDACTIONS_DIR: %(ROOT_DIR)s/redactions +BLACKLIST: %(ROOT_DIR)s/config/blacklist.tsv + + diff --git a/tests/pool1.cfg b/tests/pool1.cfg new file mode 100644 index 0000000..d427c5f --- /dev/null +++ b/tests/pool1.cfg @@ -0,0 +1,33 @@ +# NOTE: this .cfg is intended for use as a local smoke test, and is NOT intended +# for production use. See config/tcga.cfg for a production config file (and +# more description of each config file section). Finally, note that to simplify +# simplify and hasten the tests, we choose 2 cases from each of ACC, LAML, OV, +# and SKCM cohorts: 1 blood tumor (TB), 1 MET (TM) and 2 primaries (TP). The +# case ids are in sorted order below, according to their cohort abbreviation. + +[DEFAULT] +ROOT_DIR: ./pool_sandbox +LOG_DIR: %(ROOT_DIR)s/logs +REFERENCE_DIR: ./reference +PROGRAMS: TCGA +DATESTAMPS: %(ROOT_DIR)s/datestamps.txt +PROJECTS: TCGA-ACC +CASES: TCGA-OR-A5L1 + +[mirror] +DIR: %(ROOT_DIR)s/mirror + +[dice] +DIR: %(ROOT_DIR)s/dice + +[loadfile] +DIR: %(ROOT_DIR)s/loadfiles +FILTERED_SAMPLES: %(ROOT_DIR)s/loadfiles/filtered_samples.txt + +[report] +DIR: %(ROOT_DIR)s/reports +HEATMAPS_DIR: %(ROOT_DIR)s/heatmaps +REDACTIONS_DIR: %(ROOT_DIR)s/redactions +BLACKLIST: %(ROOT_DIR)s/config/blacklist.tsv + + diff --git a/tests/pool2.cfg b/tests/pool2.cfg new file mode 100644 index 0000000..8500748 --- /dev/null +++ b/tests/pool2.cfg @@ -0,0 +1,33 @@ +# NOTE: this .cfg is intended for use as a local smoke test, and is NOT intended +# for production use. See config/tcga.cfg for a production config file (and +# more description of each config file section). Finally, note that to simplify +# simplify and hasten the tests, we choose 2 cases from each of ACC, LAML, OV, +# and SKCM cohorts: 1 blood tumor (TB), 1 MET (TM) and 2 primaries (TP). The +# case ids are in sorted order below, according to their cohort abbreviation. + +[DEFAULT] +ROOT_DIR: ./pool_sandbox +LOG_DIR: %(ROOT_DIR)s/logs +REFERENCE_DIR: ./reference +PROGRAMS: TCGA +DATESTAMPS: %(ROOT_DIR)s/datestamps.txt +PROJECTS: TCGA-ACC +CASES: TCGA-OR-A5K2 + +[mirror] +DIR: %(ROOT_DIR)s/mirror + +[dice] +DIR: %(ROOT_DIR)s/dice + +[loadfile] +DIR: %(ROOT_DIR)s/loadfiles +FILTERED_SAMPLES: %(ROOT_DIR)s/loadfiles/filtered_samples.txt + +[report] +DIR: %(ROOT_DIR)s/reports +HEATMAPS_DIR: %(ROOT_DIR)s/heatmaps +REDACTIONS_DIR: %(ROOT_DIR)s/redactions +BLACKLIST: %(ROOT_DIR)s/config/blacklist.tsv + + From 40a55246c15183facba018b4804d814e79bfdcfa Mon Sep 17 00:00:00 2001 From: "Michael S. Noble" Date: Wed, 17 Jan 2018 16:36:49 -0500 Subject: [PATCH 29/30] remove leftover header comments that do not apply here, to avoid misleading --- tests/corrupt_mirror.cfg | 5 +---- tests/pool.cfg | 5 +---- tests/pool1.cfg | 5 +---- tests/pool2.cfg | 5 +---- 4 files changed, 4 insertions(+), 16 deletions(-) diff --git a/tests/corrupt_mirror.cfg b/tests/corrupt_mirror.cfg index 138f164..b803894 100644 --- a/tests/corrupt_mirror.cfg +++ b/tests/corrupt_mirror.cfg @@ -1,9 +1,6 @@ # NOTE: this .cfg is intended for use as a local smoke test, and is NOT intended # for production use. See config/tcga.cfg for a production config file (and -# more description of each config file section). Finally, note that to simplify -# simplify and hasten the tests, we choose 2 cases from each of ACC, LAML, OV, -# and SKCM cohorts: 1 blood tumor (TB), 1 MET (TM) and 2 primaries (TP). The -# case ids are in sorted order below, according to their cohort abbreviation. +# more description of each config file section). [DEFAULT] ROOT_DIR: ./corrupt_sandbox diff --git a/tests/pool.cfg b/tests/pool.cfg index df026c7..27707cd 100644 --- a/tests/pool.cfg +++ b/tests/pool.cfg @@ -1,9 +1,6 @@ # NOTE: this .cfg is intended for use as a local smoke test, and is NOT intended # for production use. See config/tcga.cfg for a production config file (and -# more description of each config file section). Finally, note that to simplify -# simplify and hasten the tests, we choose 2 cases from each of ACC, LAML, OV, -# and SKCM cohorts: 1 blood tumor (TB), 1 MET (TM) and 2 primaries (TP). The -# case ids are in sorted order below, according to their cohort abbreviation. +# more description of each config file section). [DEFAULT] ROOT_DIR: ./pool_sandbox diff --git a/tests/pool1.cfg b/tests/pool1.cfg index d427c5f..c9c89db 100644 --- a/tests/pool1.cfg +++ b/tests/pool1.cfg @@ -1,9 +1,6 @@ # NOTE: this .cfg is intended for use as a local smoke test, and is NOT intended # for production use. See config/tcga.cfg for a production config file (and -# more description of each config file section). Finally, note that to simplify -# simplify and hasten the tests, we choose 2 cases from each of ACC, LAML, OV, -# and SKCM cohorts: 1 blood tumor (TB), 1 MET (TM) and 2 primaries (TP). The -# case ids are in sorted order below, according to their cohort abbreviation. +# more description of each config file section). [DEFAULT] ROOT_DIR: ./pool_sandbox diff --git a/tests/pool2.cfg b/tests/pool2.cfg index 8500748..da6d3a2 100644 --- a/tests/pool2.cfg +++ b/tests/pool2.cfg @@ -1,9 +1,6 @@ # NOTE: this .cfg is intended for use as a local smoke test, and is NOT intended # for production use. See config/tcga.cfg for a production config file (and -# more description of each config file section). Finally, note that to simplify -# simplify and hasten the tests, we choose 2 cases from each of ACC, LAML, OV, -# and SKCM cohorts: 1 blood tumor (TB), 1 MET (TM) and 2 primaries (TP). The -# case ids are in sorted order below, according to their cohort abbreviation. +# more description of each config file section). [DEFAULT] ROOT_DIR: ./pool_sandbox From 96f9b32b97aacd1f7a26c95da1d44c0d705f2951 Mon Sep 17 00:00:00 2001 From: "Michael S. Noble" Date: Wed, 17 Jan 2018 16:43:46 -0500 Subject: [PATCH 30/30] ensure that pool and corrupted dicing sandbox areas are also cleaned up --- tests/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/Makefile b/tests/Makefile index 928bf16..c6981ed 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -278,4 +278,4 @@ clean: rm -rf build dist *.egg-info *~ test_*.log bad.cfg rclean: clean - \rm -rf sandbox GDCtool gdctools_tmp onlycases legacy + \rm -rf *sandbox GDCtool gdctools_tmp onlycases legacy