diff data_manager/data_manager.py @ 0:419037fe1150 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager.py	Thu Mar 07 09:33:43 2019 -0500
@@ -0,0 +1,106 @@
+import argparse
+import json
+import os
+import shutil
+import sys
+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
+
+DEFAULT_TAXLEVELS="Kingdom,Phylum,Class,Order,Family,Genus,Species"
+
+FILE2NAME = {
+    "silva132":"Silva version 132",
+    "silva128":"Silva version 128",
+    "rdp16":"RDP trainset 16",
+    "rdp14":"RDP trainset 14",
+    "gg13.84":"GreenGenes version 13.8",
+}
+
+FILE2TAXURL = {
+    "silva132":"https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1",
+    "silva128":"https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",
+    "rdp16":"https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
+    "rdp14":"https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
+    "gg13.84":"https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
+}
+
+FILE2SPECIESURL = {
+    "silva132":"https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1",
+    "silva128":"https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1",
+    "rdp16":"https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1",
+    "rdp14":"https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1"
+}
+
+FILE2TAXLEVELS = {
+}
+
+def url_download(url, fname, workdir):
+    """
+    download url to workdir/fname
+    
+    return the path to the resulting file 
+    """
+    file_path = os.path.join(workdir, fname)
+    if not os.path.exists(workdir):
+        os.makedirs(workdir)
+    src = None
+    dst = None
+    try:
+        req = Request(url)
+        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()
+    return os.path.join(workdir, fname)
+
+def main(dataset, outjson):
+
+    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(), 'dada2'))
+
+    workdir = os.path.join(os.getcwd(), 'dada2') 
+    path = url_download( FILE2TAXURL[dataset], taxdataset+".taxonomy", workdir)
+
+    data_manager_json = {"data_tables":{}}
+    data_manager_entry = {}
+    data_manager_entry['value'] = dataset
+    data_manager_entry['name'] = FILE2NAME[dataset]
+    data_manager_entry['path'] = path
+    data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS)
+    data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry
+
+
+    if FILE2SPECIES.get(dataset, False ):
+        path = url_download( FILE2SPECIES[dataset], taxdataset+".species", workdir)
+    
+        data_manager_entry = {}
+        data_manager_entry['value'] = dataset
+        data_manager_entry['name'] = FILE2NAME[dataset]
+        data_manager_entry['path'] = path
+        data_manager_json["data_tables"]["dada2_species"] = data_manager_entry
+    
+    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('--dataset', action='store', help='Download data set name')
+    args = parser.parse_args()
+
+    main(args.dataset, args.out)