diff data_manager/data_manager.py @ 0:1f839ba466da draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager.py	Thu Nov 01 12:25:53 2018 -0400
@@ -0,0 +1,103 @@
+import argparse
+import datetime
+import json
+import os
+import shutil
+import tarfile
+import zipfile
+try:
+    # For Python 3.0 and later
+    from urllib.request import Request, urlopen
+except ImportError:
+    # Fall back to Python 2 imports
+    from urllib2 import Request, urlopen
+
+FILE2NAME = {
+    "prot_acc2tax-June2018X1.abin.zip":"Protein accession to NCBI-taxonomy (June2018X1)",
+    "nucl_acc2tax-June2018.abin.zip":"Nucleotide accession to NCBI-taxonomy (June2018)",
+    "acc2interpro-June2018X.abin.zip":"Protein accession to InterPro (June2018X)",
+    "acc2eggnog-Oct2016X.abin.zip":"Protein accession to eggNOG (Oct2016X)",
+    "acc2seed-May2015XX.abin.zip":"Protein accession to SEED (May2015XX)",
+    "acc2kegg-Dec2017X1-ue.abin.zip":"Protein accession to KEGG (Dec2017X1). Only for use with the Ultimate Edition of MEGAN.",
+    "SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz":"SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz",
+    "SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz":"SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz",
+    "prot_gi2tax-Aug2016X.bin.zip":"Protein accession to NCBI-taxonomy (Aug2016X)",
+    "nucl_gi2tax-Aug2016.bin.zip":"Nucleotide accession to NCBI-taxonomy (Aug2016)",
+    "gi2eggnog-June2016X.bin.zip":"Protein accession to InterPro (June2016X)",
+    "gi2interpro-June2016X.bin.zip":"Protein accession to eggNOG (June2016X)",
+    "gi2seed-May2015X.bin.zip":"Protein accession to SEED (May2015X)",
+    "gi2kegg-Aug2016X-ue.bin.zip":"Protein accession to KEGG (Aug2016X). Only for use with the Ultimate Edition of MEGAN."
+}
+
+FILE2TYPE = {
+    "prot_acc2tax-June2018X1.abin.zip":"acc2tax",
+    "nucl_acc2tax-June2018.abin.zip":"acc2tax",
+    "acc2interpro-June2018X.abin.zip":"acc2interpro",
+    "acc2eggnog-Oct2016X.abin.zip":"acc2eggnog",
+    "acc2seed-May2015XX.abin.zip":"acc2seed",
+    "acc2kegg-Dec2017X1-ue.abin.zip":"acc2kegg",
+    "SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz":"syn2taxa",
+    "SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz":"syn2taxa",
+    "prot_gi2tax-Aug2016X.bin.zip":"gi2tax",
+    "nucl_gi2tax-Aug2016.bin.zip":"gi2tax",
+    "gi2eggnog-June2016X.bin.zip":"gi2eggnog",
+    "gi2interpro-June2016X.bin.zip":"gi2interpro",
+    "gi2seed-May2015X.bin.zip":"gi2seed-",
+    "gi2kegg-Aug2016X-ue.bin.zip":"gi2kegg"
+}
+
+def url_download(fname, workdir):
+    file_path = os.path.join(workdir, 'download.dat')
+    if not os.path.exists(workdir):
+        os.makedirs(workdir)
+    src = None
+    dst = None
+    try:
+        req = Request("http://ab.inf.uni-tuebingen.de/data/software/megan6/download/"+fname)
+        src = urlopen(req)
+        with open(file_path, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
+    finally:
+        if src:
+            src.close()
+    if zipfile.is_zipfile(file_path):
+        fh = zipfile.ZipFile(file_path, 'r')
+    else:
+        return
+    fh.extractall(workdir)
+    os.remove(file_path)
+
+
+def main(fname, outjson):
+    workdir = os.path.join(os.getcwd(), 'megan_tools')
+    url_download(fname, workdir)
+
+    data_manager_entry = {}
+    data_manager_entry['value'] = fname.split(".")[0]
+    data_manager_entry['name'] = FILE2NAME[fname]
+    data_manager_entry['type'] = FILE2TYPE[fname]
+    data_manager_entry['path'] = '.'
+
+    data_manager_json = dict(data_tables=dict(megan_tools=data_manager_entry))
+
+    params = json.loads(open(outjson).read())
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
+    output_path = os.path.abspath(os.path.join(os.getcwd(), 'megan_tools'))
+    for filename in os.listdir(workdir):
+        shutil.move(os.path.join(output_path, filename), target_directory)
+    file(outjson, 'w').write(json.dumps(data_manager_json))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Create data manager json.')
+    parser.add_argument('--out', action='store', help='JSON filename')
+    parser.add_argument('--file', action='store', help='Download filename')
+    args = parser.parse_args()
+
+    main(args.file, args.out)