--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager.py	Fri Nov 08 18:47:32 2019 -0500
@@ -0,0 +1,133 @@
+import argparse
+import json
+import os
+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 = {
+    "silva_132": "Silva version 132",
+    "silva_128": "Silva version 128",
+    "rdp_16": "RDP trainset 16",
+    "rdp_14": "RDP trainset 14",
+    "greengenes_13.84": "GreenGenes version 13.84",
+    "unite_8.0_fungi": "UNITE: General Fasta release 8.0 for Fungi",
+    "unite_8.0_fungi_singletons": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons",
+    "RefSeq_RDP_2018_05": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)",
+    "gtdb_2018_11": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)",
+    "hitdb_1": "HitDB version 1 (Human InTestinal 16S rRNA)",
+    "silva_euk_18S_132": "Silva version 132 Eukaryotic 18S",
+    "PR2_4.11.1": "Protist Ribosomal Reference database (PR2) 4.11.1"
+}
+
+FILE2TAXURL = {
+    "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1",
+    "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",
+    "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
+    "rdp_14": "https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1",
+    "unite_8.0_fungi": "https://files.plutof.ut.ee/public/orig/EB/0C/EB0CCB3A871B77EA75E472D13926271076904A588D2E1C1EA5AFCF7397D48378.zip",
+    "unite_8.0_fungi_singletons": "https://files.plutof.ut.ee/doi/06/A2/06A2C86256EED64085670EB0C54B7115F6DAC8F311C656A9CB33E386CFABA0D0.zip",
+    "greengenes_13.84": "https://zenodo.org/record/158955/files/gg_13_8_train_set_97.fa.gz?download=1",
+    "RefSeq_RDP_2018_05": "https://zenodo.org/record/2541239/files/RefSeq-RDP16S_v2_May2018.fa.gz?download=1",
+    "gtdb_2018_11": "https://zenodo.org/record/2541239/files/GTDB_bac-arc_ssu_r86.fa.gz?download=1",
+    "hitdb_1": "https://zenodo.org/record/159205/files/hitdb_v1.00.fa.gz?download=1",
+    "silva_euk_18S_132": "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz?download=1",
+    "PR2_4.11.1": "https://github.com/pr2database/pr2database/releases/download/4.11.1/pr2_version_4.11.1_dada2.fasta.gz"
+}
+
+FILE2SPECIESURL = {
+    "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1",
+    "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1",
+    "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1",
+    "rdp_14": "https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1"
+}
+
+FILE2TAXLEVELS = {
+    "PR2_4.11.1": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species"
+}
+
+
+def url_download(url, fname, workdir):
+    """
+    download url to workdir/fname
+    """
+    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()
+
+#   special treatment of UNITE DBs: they are zip files containing two fasta (xyz.fasta and developer/xyz.fasta)
+    if fname.startswith("unite"):
+        import glob
+        import gzip
+        import shutil
+        import zipfile
+        # unzip download
+        zip_ref = zipfile.ZipFile(file_path, 'r')
+        zip_ref.extractall(workdir)
+        zip_ref.close()
+        # gzip top level fasta file
+        fastas = glob.glob("%s/*fasta" % workdir)
+        if len(fastas) != 1:
+            msg = "UNITE download %s contained %d fasta file(s): %s" % (url, len(fastas), " ".join(fastas))
+            raise Exception(msg)
+        with open(fastas[0], 'rb') as f_in:
+            with gzip.open(file_path, 'wb') as f_out:
+                shutil.copyfileobj(f_in, f_out)
+
+
+def remote_dataset(dataset, outjson):
+
+    with open(outjson) as jf:
+        params = json.loads(jf.read())
+
+    workdir = params['output_data'][0]['extra_files_path']
+    os.mkdir(workdir)
+    url_download( FILE2TAXURL[dataset], dataset + ".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'] = dataset + ".taxonomy"
+    data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS)
+    data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry
+
+    if FILE2SPECIESURL.get(dataset, False ):
+        url_download( FILE2SPECIESURL[dataset], dataset + ".species", workdir)
+        data_manager_entry = {}
+        data_manager_entry['value'] = dataset
+        data_manager_entry['name'] = FILE2NAME[dataset]
+        data_manager_entry['path'] = dataset + ".species"
+        data_manager_json["data_tables"]["dada2_species"] = data_manager_entry
+
+    with file(outjson, 'w') as jf:
+        jf.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()
+
+    remote_dataset(args.dataset, args.out)