Fix uniprot limit of 25 items per page.

Fixing #244

Also big cleanup (black), refactoring of REST parent class into
attribute.

README.rst

@@ -191,6 +191,11 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.11.0    * Fix uniprot limitation of 25 results only (
+          * For developers: all services are now refactorised to use services
+            as an attribute rather than a parent class.
+          * Remove ReactomeOld and ReactomeAnalysis (deprecated)
+          * move rnaseq_ebi (deprecated) to attic for book_keeping
 1.10.4    * Fix v1.10.3 adding missing requirements.txt
 1.10.3    * Update pdb service to use v2 API
           * remove biocarta (website not accesible anymore)

setup.py

@@ -4,8 +4,8 @@
 
 
 _MAJOR               = 1
-_MINOR               = 10
-_MICRO               = 4
+_MINOR               = 11
+_MICRO               = 0
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)
 

src/bioservices/__init__.py

@@ -99,9 +99,6 @@
 from . import unichem
 from .unichem import *
 
-from . import rnaseq_ebi
-from .rnaseq_ebi import RNASEQ_EBI
-
 from . import reactome
 from .reactome import *
 

src/bioservices/attic/README.txt

@@ -6,4 +6,4 @@ no __init__.py on purpose to prevent tests to be run
 - geneprof.py  web site does not work anymore
 - miriam web site does not work anymore
 - biocarta not accesible anymore and could not find alternative website (sept 2022)
-
+- rnaseq_Ebi not accessible anymore 

src/bioservices/bigg.py

@@ -27,8 +27,6 @@
         -- BiGG Models Home Page, March 10, 2020.
 """
 
-import os.path as osp
-
 from bioservices.services import REST
 from bioservices.util import sequencify, squash
 

src/bioservices/biodbnet.py

@@ -35,7 +35,6 @@
     .. sectionauthor:: Thomas Cokelaer, Feb 2014
 
 """
-import io
 from bioservices.services import REST
 from bioservices import logger
 
@@ -90,7 +89,7 @@ def _interpret_output_db(self, input_db, output_db):
         # remove spaces so as to compare the input/output databases with the
         # list of databases returned by getInputs
         outputs = self._list_to_string(output_db)
-        inputResult = self.getInputs()
+        #inputResult = self.getInputs()
         # getOutputsForInput method
         outputResult = self.getOutputsForInput(input_db)
         outputResult = [this.lower().replace(" ", "") for this in outputResult]
@@ -259,8 +258,6 @@ def dbReport(self, input_db, input_values, taxon=9606):
             return request
         inputValues = self._interpret_input_db(inputValues)
 
-        # df = pd.readcsv(io.StringIO(res.strip()), sep="\t")
-
     def dbWalk(self, db_path, input_values, taxon=9606):
         """Walk through biological database network
 

src/bioservices/biomodels.py

@@ -32,25 +32,19 @@
 
 """
 import os
-import copy
-import webbrowser
-from functools import wraps
+from urllib.request import urlopen
+
 from bioservices import logger
+from bioservices.services import REST
 
 logger.name = __name__
 
-from bioservices.services import REST
 
-try:
-    # python 3
-    from urllib.request import urlopen
-except:
-    from urllib2 import urlopen
 
 __all__ = ["BioModels"]
 
 
-class BioModels(REST):
+class BioModels:
     """Interface to the `BioModels <http://www.ebi.ac.uk/biomodels>`_ service
 
     ::
@@ -91,7 +85,8 @@ def __init__(self, verbose=True):
 
 
         """
-        super(BioModels, self).__init__(name="BioModels", url=BioModels._url, verbose=verbose)
+        self.services = REST(name="BioModels", url=BioModels._url, verbose=verbose)
+
 
     def _check_format(self, frmt, supported=["json", "xml", "html"]):
         if frmt not in supported:
@@ -111,7 +106,7 @@ def get_all_models(self, chunk=100):
     def get_model(self, model_id, frmt="json"):
         """Fetch information about a given model at a particular revision."""
         self._check_format(frmt)
-        res = self.http_get(model_id, frmt=frmt, params={"format": frmt})
+        res = self.services.http_get(model_id, frmt=frmt, params={"format": frmt})
         return res
 
     def get_model_files(self, model_id, frmt="json"):
@@ -121,7 +116,7 @@ def get_model_files(self, model_id, frmt="json"):
         :param frmt: format of the output (json, xml)
         """
         self._check_format(frmt, ["xml", "json"])
-        res = self.http_get("model/files/{}".format(model_id), frmt=frmt, params={"format": frmt})
+        res = self.services.http_get("model/files/{}".format(model_id), frmt=frmt, params={"format": frmt})
         return res
 
     def get_model_download(self, model_id, filename=None, output_filename=None):
@@ -166,16 +161,16 @@ def get_model_download(self, model_id, filename=None, output_filename=None):
         if filename:
             params["filename"] = filename
 
-        res = self.http_get("model/download/{}".format(model_id), params=params)
+        res = self.services.http_get("model/download/{}".format(model_id), params=params)
 
         if filename:
-            self.logging.info("Saving {}".format(filename))
+            self.services.logging.info("Saving {}".format(filename))
             if output_filename is None:
                 output_filename = filename
             with open(output_filename, "wb") as fout:
                 fout.write(res.content)
         else:
-            self.logging.info("Saving file {}.zip".format(model_id))
+            self.services.logging.info("Saving file {}.zip".format(model_id))
             if output_filename is None:
                 output_filename = "{}.zip".format(model_id)
             with open(output_filename, "wb") as fout:
@@ -219,7 +214,7 @@ def search(self, query, offset=None, numResults=None, sort=None, frmt="json"):
         ]
         if sort and sort not in sort_options:
             raise ValueError("sort must be in {}. You provided {}".format(sort_options, sort))
-        res = self.http_get("search", params=params)
+        res = self.services.http_get("search", params=params)
         return res
 
     def search_download(self, models, output_filename="models.zip", force=False):
@@ -238,13 +233,13 @@ def search_download(self, models, output_filename="models.zip", force=False):
         """
         if isinstance(models, list):
             models = ",".join(models)
-        res = self.http_get("search/download", params={"models": models})
+        res = self.services.http_get("search/download", params={"models": models})
 
         if res == 404:
-            self.logging.error("One of your model ID was probably incorrect")
+            self.services.logging.error("One of your model ID was probably incorrect")
             return
 
-        self.logging.info(output_filename)
+        self.services.logging.info(output_filename)
         if os.path.exists(output_filename) and force is False:
             raise IOError(
                 "{} exists already. Set force to True or change the output_filename argument".format(output_filename)
@@ -287,7 +282,7 @@ def search_parameter(self, query, start=0, size=10, sort=None, frmt="json"):
         if sort:
             params["sort"] = sort
 
-        res = self.http_get("parameterSearch/search", params=params)
+        res = self.services.http_get("parameterSearch/search", params=params)
 
         return res
 
@@ -300,9 +295,9 @@ def get_p2m_missing(self, frmt="json"):
 
         """
         self._check_format(frmt)
-        res = self.http_get("p2m/missing", params={"format": frmt})
+        res = self.services.http_get("p2m/missing", params={"format": frmt})
         res = res["missing"]
-        self.logging.info("Found {} missing model".format(len(res)))
+        self.services.logging.info("Found {} missing model".format(len(res)))
         return res
 
     def get_p2m_representative(self, model, frmt="json"):
@@ -317,7 +312,7 @@ def get_p2m_representative(self, model, frmt="json"):
 
         """
         self._check_format(frmt)
-        res = self.http_get("p2m/representative", params={"format": frmt, "model": model})
+        res = self.services.http_get("p2m/representative", params={"format": frmt, "model": model})
         return res
 
     def get_p2m_representatives(self, models, frmt="json"):
@@ -347,7 +342,7 @@ def get_p2m_representatives(self, models, frmt="json"):
             models = ",".join([x.strip() for x in models.split(",")])
 
         self._check_format(frmt)
-        res = self.http_get("p2m/representatives", params={"format": frmt, "modelIds": models})
+        res = self.services.http_get("p2m/representatives", params={"format": frmt, "modelIds": models})
         return res
 
     def get_pdgsmm_missing(self, frmt="json"):
@@ -357,9 +352,9 @@ def get_pdgsmm_missing(self, frmt="json"):
         :return: list of model identifiers
         """
         self._check_format(frmt)
-        res = self.http_get("pdgsmm/missing", params={"format": frmt})
+        res = self.services.http_get("pdgsmm/missing", params={"format": frmt})
         res = res["missing"]
-        self.logging.info("Found {} missing model".format(len(res)))
+        self.services.logging.info("Found {} missing model".format(len(res)))
         return res
 
     def get_pdgsmm_representative(self, model, frmt="json"):
@@ -374,7 +369,7 @@ def get_pdgsmm_representative(self, model, frmt="json"):
 
         """
         self._check_format(frmt)
-        res = self.http_get("pdgsmm/representative", params={"format": frmt, "model": model})
+        res = self.services.http_get("pdgsmm/representative", params={"format": frmt, "model": model})
         return res
 
     def get_pdgsmm_representatives(self, models, frmt="json"):
@@ -397,5 +392,5 @@ def get_pdgsmm_representatives(self, models, frmt="json"):
             models = ",".join([x.strip() for x in models.split(",")])
 
         self._check_format(frmt)
-        res = self.http_get("pdgsmm/representatives", params={"format": frmt, "modelIds": models})
+        res = self.services.http_get("pdgsmm/representatives", params={"format": frmt, "modelIds": models})
         return res

src/bioservices/chembl.py

@@ -355,8 +355,7 @@ class ChEMBL:
     _url = "https://www.ebi.ac.uk/chembl/api/data"
 
     def __init__(self, verbose=False, cache=False):
-        self.services = REST(name="ChEMBL", url=ChEMBL._url, verbose=verbose, cache=cache, 
-            url_defined_later=True)
+        self.services = REST(name="ChEMBL", url=ChEMBL._url, verbose=verbose, cache=cache, url_defined_later=True)
         self.format = "json"
 
     def _get_data(self, name, params):
@@ -403,7 +402,7 @@ def _get_data(self, name, params):
 
         count = 1
 
-        with tqdm(total=N, desc='TEST') as pb:
+        with tqdm(total=N, desc="TEST") as pb:
             while res["page_meta"]["next"] and len(data) < max_data:
                 params["limit"] = limit
                 params["offset"] = limit * count + offset
@@ -881,7 +880,7 @@ def get_xref_source(self, query=None, limit=20, offset=0, filters=None):
         return self._get_this_service("xref_source", query, params=params)
 
     def get_image(self, query, dimensions=500, format="png", save=True, view=True, engine="indigo"):
-        """Get the image of a given compound in PNG png format.
+        r"""Get the image of a given compound in PNG png format.
 
         :param str query: a valid compound ChEMBLId or a list/tuple
             of valid compound ChEMBLIds.

src/bioservices/dbfetch.py

@@ -38,7 +38,7 @@
 __all__ = ["DBFetch"]
 
 
-class DBFetch(REST):
+class DBFetch:
     """Interface to `DBFetch <http://www.ebi.ac.uk/Tools/webservices/services/dbfetch_rest>`_ service
 
     ::
@@ -59,7 +59,8 @@ def __init__(self, verbose=False):
 
         :param bool verbose: print informative messages
         """
-        super(DBFetch, self).__init__(name="DBfetch", url=DBFetch._url, verbose=verbose)
+
+        self.services = REST(name="DBfetch", url=DBFetch._url, verbose=verbose)
         self._supportedDBs = None
         self._supportedFormats = None
         self._supportedStyles = None
@@ -93,7 +94,7 @@ def fetch(self, query, db="ena_sequence", format="default", style="raw", pageHtm
 
         """
         self._check_db(db)
-        res = self.http_get(
+        res = self.services.http_get(
             "dbfetch",
             params={
                 "db": db,
@@ -122,7 +123,7 @@ def get_database_info(self, db=None):
             'The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-references. Search UniProtKB to retrieve everything that is known about a particular sequence.'
 
         """
-        res = self.http_get("dbfetch/dbfetch.databases?style=json")
+        res = self.services.http_get("dbfetch/dbfetch.databases?style=json")
         if db:
             self._check_db(db)
             res = res[db]
@@ -158,7 +159,7 @@ def get_database_formats(self, db):
 
         """
         self._check_db(db)
-        res = self.http_get("dbfetch?info=formats&db={}".format(db)).content
+        res = self.services.http_get("dbfetch?info=formats&db={}".format(db)).content
         res = res.decode().split()
         return res
 
@@ -177,7 +178,7 @@ def get_database_format_styles(self, db, format):
 
         """
         self._check_db(db)
-        res = self.http_get("dbfetch?info=styles&format={}&db={}".format(format, db)).content
+        res = self.services.http_get("dbfetch?info=styles&format={}&db={}".format(format, db)).content
         res = res.decode().split()
         return res
 
@@ -189,7 +190,7 @@ def _getSupportedDBs(self):
         if self._supportedDBs:
             return self._supportedDBs
         else:
-            res = self.http_get("dbfetch?info=dbs").content
+            res = self.services.http_get("dbfetch?info=dbs").content
             self._supportedDBs = res.decode().split() + ["default"]
         return self._supportedDBs
 

src/bioservices/ensembl.py

@@ -1636,7 +1636,7 @@ def post_vep_by_id(self, species, identifiers):
         raise NotImplementedError
         # POST vep/:species/id/   Fetch variant consequences for multiple ids
         self._check_frmt(frmt, ["xml"])
-        res = self.services.http_get(
+        _ = self.services.http_get(
             "variation/{0}/{1}".format(species, identifier),
             frmt=frmt,
             headers=self.services.get_headers(content=frmt),