diff eutils.py @ 0:68cd8d564e0a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eutils.py	Thu Jul 07 02:39:21 2016 -0400
@@ -0,0 +1,127 @@
+import os
+import json
+import StringIO
+from Bio import Entrez
+Entrez.tool = "GalaxyEutils_1_0"
+BATCH_SIZE = 200
+
+
+class Client(object):
+
+    def __init__(self, history_file=None, user_email=None, admin_email=None):
+        self.using_history = False
+
+        if user_email is not None and admin_email is not None:
+            Entrez.email = ';'.join((admin_email, user_email))
+        elif user_email is not None:
+            Entrez.email = user_email
+        elif admin_email is not None:
+            Entrez.email = admin_email
+        else:
+            Entrez.email = os.environ.get('NCBI_EUTILS_CONTACT', None)
+
+        if Entrez.email is None:
+            raise Exception("Cannot continue without an email; please set "
+                            "administrator email in NCBI_EUTILS_CONTACT")
+
+        if history_file is not None:
+            with open(history_file, 'r') as handle:
+                data = json.loads(handle.read())
+                self.query_key = data['QueryKey']
+                self.webenv = data['WebEnv']
+                self.using_history = True
+
+    def get_history(self):
+        if not self.using_history:
+            return {}
+        else:
+            return {
+                'query_key': self.query_key,
+                'WebEnv': self.webenv,
+            }
+
+    def post(self, database, **payload):
+        return json.dumps(Entrez.read(Entrez.epost(database, **payload)), indent=4)
+
+    def fetch(self, db, ftype=None, **payload):
+        os.makedirs("downloads")
+
+        if 'id' in payload:
+            summary = self.id_summary(db, payload['id'])
+        else:
+            summary = self.history_summary(db)
+
+        count = len(summary)
+        payload['retmax'] = BATCH_SIZE
+
+        # This may be bad. I'm not sure yet. I think it will be ... but UGH.
+        for i in range(0, count, BATCH_SIZE):
+            payload['retstart'] = i
+            file_path = os.path.join('downloads', 'EFetch Results Chunk %s.%s' % (i, ftype))
+            with open(file_path, 'w') as handle:
+                handle.write(Entrez.efetch(db, **payload).read())
+
+    def id_summary(self, db, id_list):
+        payload = {
+            'db': db,
+            'id': id_list,
+        }
+        return Entrez.read(Entrez.esummary(**payload))
+
+    def history_summary(self, db):
+        if not self.using_history:
+            raise Exception("History must be available for this method")
+
+        payload = {
+            'db': db,
+            'query_key': self.query_key,
+            'WebEnv': self.webenv,
+        }
+        return Entrez.read(Entrez.esummary(**payload))
+
+    def summary(self, **payload):
+        return Entrez.esummary(**payload).read()
+
+    def link(self, **payload):
+        return Entrez.elink(**payload).read()
+
+    def extract_history(self, xml_data):
+        parsed_data = Entrez.read(StringIO.StringIO(xml_data))
+        history = {}
+        for key in ('QueryKey', 'WebEnv'):
+            if key in parsed_data:
+                history[key] = parsed_data[key]
+
+        return history
+
+    def search(self, **payload):
+        return Entrez.esearch(**payload).read()
+
+    def info(self, **kwargs):
+        return Entrez.einfo(**kwargs).read()
+
+    def gquery(self, **kwargs):
+        return Entrez.egquery(**kwargs).read()
+
+    def citmatch(self, **kwargs):
+        return Entrez.ecitmatch(**kwargs).read()
+
+    @classmethod
+    def parse_ids(cls, id_list, id, history_file):
+        """Parse IDs passed on --cli or in a file passed to the cli
+        """
+        merged_ids = []
+        if id is not None:
+            for pid in id.replace('__cn__', ',').replace('\n', ',').split(','):
+                if pid is not None and len(pid) > 0:
+                    merged_ids.append(pid)
+
+        if id_list is not None:
+            with open(id_list, 'r') as handle:
+                merged_ids += [x.strip() for x in handle.readlines()]
+
+        # Exception hanlded here for uniformity
+        if len(merged_ids) == 0 and history_file is None:
+            raise Exception("Must provide history file or IDs")
+
+        return merged_ids