0.11.37: resolved py3.6 import loops; moved pubmed related methods to…

… inputs.pubmed; fixes #157

src/pypath/__version__

@@ -1 +1 @@
-0.11.36
+0.11.37

src/pypath/core/entity.py

@@ -30,10 +30,8 @@
 import collections
 
 import pypath.share.common as common
-from pypath.internals import intera
 import pypath.share.session as session_mod
 import pypath.utils.mapping as mapping
-import pypath.utils.uniprot as uniprot
 import pypath.share.settings as settings
 
 
@@ -263,7 +261,7 @@ def _is_mirna(key):
     @staticmethod
     def _is_complex(key):
 
-        return isinstance(key, intera.Complex) or (
+        return key.__class__.__name__ == 'Complex' or (
             isinstance(key, common.basestring) and
             key.startswith('COMPLEX')
         )
@@ -468,6 +466,7 @@ def info(cls, identifier):
 
         if cls._is_protein(identifier):
 
+            import pypath.utils.uniprot as uniprot
             return utils_uniprot.info(identifier)
 
 

src/pypath/core/network.py

@@ -45,6 +45,7 @@
 import pypath.share.cache as cache_mod
 import pypath.utils.mapping as mapping
 import pypath.inputs.main as dataio
+import pypath.inputs.pubmed as pubmed_input
 import pypath.share.curl as curl
 import pypath.internals.refs as refs_mod
 import pypath.utils.reflists as reflists
@@ -1104,7 +1105,7 @@ def _read_resource(
 
                     refs = common.del_empty(list(set(refs)))
 
-                refs = dataio.only_pmids([str(r).strip() for r in refs])
+                refs = pubmed_input.only_pmids([str(r).strip() for r in refs])
 
                 if len(refs) == 0 and must_have_references:
                     ref_filtered += 1

src/pypath/inputs/main.py

@@ -3921,50 +3921,6 @@ def get_goslim(url = None):
     return result
 
 
-def get_pubmeds(pmids):
-    pmids = [str(pmid) for pmid in pmids]
-    url = urls.urls['pubmed-eutils']['url']
-    cache = len(pmids) < 10
-    data = {}
-    prg = progress.Progress(
-        len(pmids) / 100 + 1,
-        'Retrieving data from NCBI e-utils',
-        1,
-        percent = False)
-
-    for offset in xrange(0, len(pmids), 100):
-        prg.step()
-        post = {
-            'id': ','.join(pmids[offset:offset + 100]),
-            'retmode': 'json',
-            'db': 'pubmed'
-        }
-
-        for i in xrange(3):
-            try:
-                c = curl.Curl(
-                    url,
-                    silent = False,
-                    cache = cache,
-                    post = post,
-                    override_post = True,
-                )
-                res = c.result
-                data = dict([(k, v)
-                             for k, v in iteritems(json.loads(res)['result'])]
-                            + [(k, v) for k, v in iteritems(data)])
-
-                break
-
-            except ValueError:
-                sys.stdout.write('\t:: Error in JSON, retry %u\n' % i)
-                sys.stdout.flush()
-
-    prg.terminate()
-
-    return data
-
-
 def get_lincs_compounds():
     sys.stdout.write(
         '\n\tReturned dict has names, brand names or company specific\n'
@@ -4764,102 +4720,6 @@ def guide2pharma_complexes(**kwargs):
     return complexes
 
 
-def open_pubmed(pmid):
-    """
-    Opens PubMed record in web browser.
-
-    @pmid : str or int
-        PubMed ID
-    """
-
-    pmid = str(pmid)
-    url = urls.urls['pubmed']['url'] % pmid
-    webbrowser.open(url)
-
-
-def only_pmids(idList, strict = True):
-    """
-    Return elements unchanged which comply with the PubMed ID format,
-    and attempts to translate the DOIs and PMC IDs using NCBI
-    E-utils.
-    Returns list containing only PMIDs.
-
-    @idList : list, str
-        List of IDs or one single ID.
-    @strict : bool
-        Whether keep in the list those IDs which are not PMIDs,
-        neither DOIs or PMC IDs or NIH manuscript IDs.
-    """
-    if type(idList) in common.simple_types:
-        idList = [idList]
-
-    pmids = {i for i in idList if isinstance(i, int) or i.isdigit()}
-    pmcids = [i for i in idList if i.startswith('PMC')]
-    dois = [i for i in idList if '/' in i]
-    manuscids = [i for i in idList if i.startswith('NIHMS')]
-
-    if not strict:
-        pmids = set(pmids) | set(dois) | set(pmcids) | set(manuscids)
-
-    if len(pmcids) > 0:
-        pmids = pmids | set(pmids_list(pmcids))
-
-    if len(dois) > 0:
-        pmids = pmids | set(pmids_list(dois))
-
-    return list(pmids)
-
-
-def get_pmid(idList):
-    """
-    For a list of doi or PMC IDs
-    fetches the corresponding PMIDs.
-    """
-
-    if type(idList) in common.simple_types:
-        idList = [idList]
-
-    url = urls.urls['pubmed-eutils']['conv'] % ','.join(str(i) for i in idList)
-    c = curl.Curl(url, silent = True)
-    data = c.result
-
-    try:
-        js = json.loads(data)
-
-    except:
-        js = {}
-
-    return js
-
-
-def pmids_dict(idList):
-    jsn = get_pmid(idList)
-    result = {'doi': {}, 'pmc': {}}
-
-    if 'records' in jsn:
-        for r in jsn['records']:
-            if 'pmid' in r:
-                if 'doi' in r:
-                    result['doi'][r['pmid']] = r['doi']
-
-                if 'pmcid' in r:
-                    result['pmc'][r['pmid']] = r['pmcid']
-
-    return result
-
-
-def pmids_list(idList):
-    jsn = get_pmid(idList)
-    result = []
-
-    if 'records' in jsn:
-        for r in jsn['records']:
-            if 'pmid' in r:
-                result.append(r['pmid'])
-
-    return result
-
-
 def load_lmpid(organism = 9606):
     """
     Reads and processes LMPID data from local file

src/pypath/inputs/pubmed.py

@@ -0,0 +1,174 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+#
+#  This file is part of the `pypath` python module
+#
+#  Copyright
+#  2014-2020
+#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
+#
+#  File author(s): Dénes Türei ([email protected])
+#                  Nicolàs Palacio
+#                  Olga Ivanova
+#
+#  Distributed under the GPLv3 License.
+#  See accompanying file LICENSE.txt or copy at
+#      http://www.gnu.org/licenses/gpl-3.0.html
+#
+#  Website: http://pypath.omnipathdb.org/
+#
+
+from future.utils import iteritems
+
+import sys
+import json
+import webbrowser
+
+import pypath.resources.urls as urls
+import pypath.share.curl as curl
+import pypath.share.common as common
+import pypath.share.progress as progress
+
+
+def open_pubmed(pmid):
+    """
+    Opens PubMed record in web browser.
+
+    @pmid : str or int
+        PubMed ID
+    """
+
+    pmid = str(pmid)
+    url = urls.urls['pubmed']['url'] % pmid
+    webbrowser.open(url)
+
+
+def only_pmids(idList, strict = True):
+    """
+    Return elements unchanged which comply with the PubMed ID format,
+    and attempts to translate the DOIs and PMC IDs using NCBI
+    E-utils.
+    Returns list containing only PMIDs.
+
+    @idList : list, str
+        List of IDs or one single ID.
+    @strict : bool
+        Whether keep in the list those IDs which are not PMIDs,
+        neither DOIs or PMC IDs or NIH manuscript IDs.
+    """
+    if type(idList) in common.simple_types:
+        idList = [idList]
+
+    pmids = {i for i in idList if isinstance(i, int) or i.isdigit()}
+    pmcids = [i for i in idList if i.startswith('PMC')]
+    dois = [i for i in idList if '/' in i]
+    manuscids = [i for i in idList if i.startswith('NIHMS')]
+
+    if not strict:
+        pmids = set(pmids) | set(dois) | set(pmcids) | set(manuscids)
+
+    if len(pmcids) > 0:
+        pmids = pmids | set(pmids_list(pmcids))
+
+    if len(dois) > 0:
+        pmids = pmids | set(pmids_list(dois))
+
+    return list(pmids)
+
+
+def get_pmid(idList):
+    """
+    For a list of doi or PMC IDs
+    fetches the corresponding PMIDs.
+    """
+
+    if type(idList) in common.simple_types:
+        idList = [idList]
+
+    url = urls.urls['pubmed-eutils']['conv'] % ','.join(str(i) for i in idList)
+    c = curl.Curl(url, silent = True)
+    data = c.result
+
+    try:
+        js = json.loads(data)
+
+    except:
+        js = {}
+
+    return js
+
+
+def pmids_dict(idList):
+
+    jsn = get_pmid(idList)
+    result = {'doi': {}, 'pmc': {}}
+
+    if 'records' in jsn:
+        for r in jsn['records']:
+            if 'pmid' in r:
+                if 'doi' in r:
+                    result['doi'][r['pmid']] = r['doi']
+
+                if 'pmcid' in r:
+                    result['pmc'][r['pmid']] = r['pmcid']
+
+    return result
+
+
+def pmids_list(idList):
+
+    jsn = get_pmid(idList)
+    result = []
+
+    if 'records' in jsn:
+        for r in jsn['records']:
+            if 'pmid' in r:
+                result.append(r['pmid'])
+
+    return result
+
+
+def get_pubmeds(pmids):
+
+    pmids = [str(pmid) for pmid in pmids]
+    url = urls.urls['pubmed-eutils']['url']
+    cache = len(pmids) < 10
+    data = {}
+    prg = progress.Progress(
+        len(pmids) / 100 + 1,
+        'Retrieving data from NCBI e-utils',
+        1,
+        percent = False)
+
+    for offset in xrange(0, len(pmids), 100):
+        prg.step()
+        post = {
+            'id': ','.join(pmids[offset:offset + 100]),
+            'retmode': 'json',
+            'db': 'pubmed'
+        }
+
+        for i in xrange(3):
+            try:
+                c = curl.Curl(
+                    url,
+                    silent = False,
+                    cache = cache,
+                    post = post,
+                    override_post = True,
+                )
+                res = c.result
+                data = dict([(k, v)
+                             for k, v in iteritems(json.loads(res)['result'])]
+                            + [(k, v) for k, v in iteritems(data)])
+
+                break
+
+            except ValueError:
+                sys.stdout.write('\t:: Error in JSON, retry %u\n' % i)
+                sys.stdout.flush()
+
+    prg.terminate()
+
+    return data