- Can now take profit of env var 'TAXADB_CONFIG' or a config path at …

…object construction to set db parameters connection.

- Updated docuemntation.

Force port number to be int when connecting with peewee

Upated README.md to reflect use of configuration

Test codecov

Cover taxadb only, not test

Added codecov.yml

Remove some pieces of code not used or not reached. Remove some exception not thorwn by method used.

Added .dmp test files

Updated tests and added codeclimate configuration

- Introduced use of config file or environment variable.
- Increased test coverage up to 99%.
- Reviewed some method according to tests. Updated README

Fixed codeclimate warnings. Refactored method to load taxa table data into memory

do not test coverage for taxadb.app.py

Added configuration file <.landscape.yml> for code health checking

Increased test coverage and cleaned code reagarding landascape.io

Adjusted small stuff

Use of configuration file and/or environment variable TAXADB_CONFIG

.codeclimate.yml

@@ -0,0 +1,24 @@
+engines:
+  pep8:
+    enabled: true
+  duplication:
+    enabled: true
+    checks:
+      Similar Code:
+        enabled: true
+    config:
+      languages:
+        python:
+          python_version: 3
+  fixme:
+    enabled: true
+  radon:
+    enabled: true
+    config:
+      python_version: 3
+
+exclude_paths:
+  - "taxadb/test/*"
+ratings:
+  paths:
+    - "taxadb/*.py"

.codecov.yml

@@ -0,0 +1,3 @@
+ignore:
+  - "**/test/*.py" # ignore test scripts
+  - "**/app.py"    # ignore main application script

.gitignore

@@ -1,7 +1,7 @@
 # taxa_db specific stuff
 *accession2taxid*
 taxdump*
-*.dmp
+n*.dmp
 gc.prt
 readme.txt
 

.landscape.yml

@@ -0,0 +1,11 @@
+doc-warnings: yes
+test-warnings: no
+strictness: medium
+max-line-length: 80
+pep8:
+    full: true
+python-targets:
+    - 3
+ignore-paths:
+    - taxadb/test
+    - doc

.travis.yml

@@ -3,12 +3,16 @@ python:
 - '3.5'
 install:
 - pip install -r requirements.txt
+- pip install codecov
 - pip install -e .
-script: nosetests --tc-file taxadb.ini
+script: nosetests --tc-file taxadb.ini --with-coverage --cover-package=taxadb
 notifications:
   email: false
   slack:
     matrix:
     - sgbcgroup:LQx8YcBhBqAUTON9eMivOuFr
     rooms:
       secure: 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
+
+after_success:
+  - codecov

README.md

@@ -82,6 +82,34 @@ Get the taxonomic information for accession number(s).
     ('Z12029', 9915)
 ```
 
+You can also use a configuration file in order to automatically set database
+connection parameters at object build. Either set `config` parameter to `__init__`
+ object method:
+ ```python
+    >>> from taxadb.accessionid import AccessionID
+
+    >>> my_accessions = ['X17276', 'Z12029']
+    >>> accession = AccessionID(config='/path/to/taxadb.cfg')
+    >>> taxids = accession.taxid(my_accessions)
+    >>> ...
+ ```
+
+ or set environment variable `TAXADB_CONFIG` which point to configuration file:
+ ```bash
+    $ export TAXADB_CONFIG='/path/to/taxadb.cfg'
+ ```
+ then
+ ```python
+    >>> from taxadb.accessionid import AccessionID
+
+    >>> my_accessions = ['X17276', 'Z12029']
+    >>> accession = AccessionID()
+    >>> taxids = accession.taxid(my_accessions)
+    >>> ...
+ ```
+
+Check documentation for more information.
+
 ### Creating the Database
 
 #### Download data

doc/index.rst

@@ -23,7 +23,7 @@ In brief Taxadb:
   `PostgreSQL <https://www.postgresql.org>`_.
 * has available pre-built SQLite databases (:ref:`Download build databases <download>`).
 * has a comprehensive :ref:`API documentation <api>`.
-* is actively being developped on `GitHub <https://github.com/HadrienG/taxadb.git>`_ and available under the MIT license. Please see the `README <https://github.com/HadrienG/taxadb>`_ for more information on development, support, and contributing.
+* is actively being developed on `GitHub <https://github.com/HadrienG/taxadb.git>`_ and available under the MIT license. Please see the `README <https://github.com/HadrienG/taxadb>`_ for more information on development, support, and contributing.
 
 Quickstart
 ----------

doc/taxadb/api.rst

@@ -1,7 +1,7 @@
 .. _api:
 
 API Documentation
-==========================
+=================
 
 Contents:
 

doc/taxadb/query.rst

@@ -8,6 +8,76 @@ Firstly make sure you have :ref:`downloaded <download>` or :ref:`built <build_ow
 
 Below you can find basic examples. For more complex examples, please refer to the complete :ref:`documentation <api>`.
 
+.. _useconfig:
+
+Using configuration file or environment variable
+------------------------------------------------
+
+Taxadb can now take profit of configuration file or environment variable to
+set database connection parameters.
+
+* Using configuration file
+
+You can pass a configuration file when building your object:
+
+.. code-block:: python
+
+   >>> from taxadb.taxid import TaxID
+
+   >>> taxid = TaxID(config='/path/to/taxadb.cfg')
+   >>> name = taxid.sci_name(33208)
+   >>> ...
+
+* Configuration file format
+
+The configuration file must use syntax supported by `configparser object
+<https://docs.python.org/3.5/library/configparser.html>`_.
+You must set database connection parameters in a section called
+:code:`DBSETTINGS` as below:
+
+.. code-block:: bash
+
+   [DBSETTINGS]
+   dbtype=<sqlite|postgres|mysql>
+   dbname=taxadb
+   hostname=taxadb.domain.org
+   username=admin
+   password=s3cr3T
+   port=
+
+Some value will default it they are not set.
+
+**hostname** will be set to value :code:`localhost` and **port** is set to
+:code:`5432` for :code:`dbtype=postgres` and :code:`3306` for
+:code:`dbtype=mysql`.
+
+* Using environment variable
+
+Taxadb can as well use an environment variable to automatically point the
+application to a configuration file. To take profit of it, just set
+:code:`TAXADB_CONFIG` to the path of your configuration file:
+
+.. code-block:: bash
+
+   (bash) export TAXADB_CONFIG='/path/to/taxadb.cfg'
+   (csh) set TAXADB_CONFIG='/path/to/taxadb.cfg'
+
+Then, just create your object as follow:
+
+.. code-block:: python
+
+   >>> from taxadb.taxid import TaxID
+
+   >>> taxid = Taxid()
+   >>> name = taxid.sci_name(33208)
+   >>> ...
+
+.. note::
+
+   Arguments passed to object initiation will always overwrite default values
+   as well as values that might have been set by configuration file or
+   environment variable :code:`TAXADB_CONFIG`.
+
 .. _taxids:
 
 taxids

taxadb/accessionid.py

@@ -3,17 +3,15 @@
 
 
 class AccessionID(TaxaDB):
+
     """Main accession class
 
     Provide methods to request accession table and get associated taxonomy for
         accession ids.
 
     Args:
-        dbtype (:obj:`str`): Database to connect to
-        dbtype (:obj:`str`): Database type to connect to (`sqlite`, `postgre`,
-            `mysql`). Default `sqlite`
         **kwargs: Arbitrary arguments. Supported (username, password, port,
-            hostname)
+            hostname, config, dbtype, dbname)
 
     Raises:
         SystemExit: If table `accession` does not exist
@@ -41,16 +39,16 @@ def taxid(self, acc_number_list):
             query = Accession.select().where(
                 Accession.accession << acc_number_list)
             for i in query:
-                try:
-                    yield (i.accession, i.taxid.ncbi_taxid)
-                except Taxa.DoesNotExist:
-                    self._unmapped_taxid(i.accession)
+                yield (i.accession, i.taxid.ncbi_taxid)
+            # TODO: List accession ID not found?
+            # for noid in notfound:
+            #     self._unmapped_taxid(noid)
 
     def sci_name(self, acc_number_list):
         """Get taxonomic scientific name for accession ids
 
-        Given a list of acession numbers, yield the accession number and their
-            associated scientific name as tuples
+        Given a list of accession numbers, yield the accession number and their
+        associated scientific name as tuples
 
         Args:
             acc_number_list (:obj:`list`): a list of accession numbers
@@ -64,10 +62,10 @@ def sci_name(self, acc_number_list):
             query = Accession.select().where(
                 Accession.accession << acc_number_list)
             for i in query:
-                try:
-                    yield (i.accession, i.taxid.tax_name)
-                except Taxa.DoesNotExist:
-                    self._unmapped_taxid(i.accession)
+                yield (i.accession, i.taxid.tax_name)
+            # TODO: List accession ID not found?
+            # for noid in notfound:
+            #     self._unmapped_taxid(noid)
 
     def lineage_id(self, acc_number_list):
         """Get taxonomic lineage name for accession ids
@@ -87,20 +85,20 @@ def lineage_id(self, acc_number_list):
             query = Accession.select().where(
                 Accession.accession << acc_number_list)
             for i in query:
-                try:
-                    lineage_list = []
-                    current_lineage = i.taxid.tax_name
-                    current_lineage_id = i.taxid.ncbi_taxid
-                    parent = i.taxid.parent_taxid
-                    while current_lineage != 'root':
-                        lineage_list.append(current_lineage_id)
-                        new_query = Taxa.get(Taxa.ncbi_taxid == parent)
-                        current_lineage = new_query.tax_name
-                        current_lineage_id = new_query.ncbi_taxid
-                        parent = new_query.parent_taxid
-                    yield (i.accession, lineage_list)
-                except Taxa.DoesNotExist:
-                    self._unmapped_taxid(i.accession)
+                lineage_list = []
+                current_lineage = i.taxid.tax_name
+                current_lineage_id = i.taxid.ncbi_taxid
+                parent = i.taxid.parent_taxid
+                while current_lineage != 'root':
+                    lineage_list.append(current_lineage_id)
+                    new_query = Taxa.get(Taxa.ncbi_taxid == parent)
+                    current_lineage = new_query.tax_name
+                    current_lineage_id = new_query.ncbi_taxid
+                    parent = new_query.parent_taxid
+                yield (i.accession, lineage_list)
+            # TODO: List accession ID not found?
+            # for noid in notfound:
+            #     self._unmapped_taxid(noid)
 
     def lineage_name(self, acc_number_list):
         """Get a lineage name for accession ids
@@ -120,15 +118,15 @@ def lineage_name(self, acc_number_list):
             query = Accession.select().where(
                 Accession.accession << acc_number_list)
             for i in query:
-                try:
-                    lineage_list = []
-                    current_lineage = i.taxid.tax_name
-                    parent = i.taxid.parent_taxid
-                    while current_lineage != 'root':
-                        lineage_list.append(current_lineage)
-                        new_query = Taxa.get(Taxa.ncbi_taxid == parent)
-                        current_lineage = new_query.tax_name
-                        parent = new_query.parent_taxid
-                    yield (i.accession, lineage_list)
-                except Taxa.DoesNotExist:
-                    self._unmapped_taxid(i.accession)
+                lineage_list = []
+                current_lineage = i.taxid.tax_name
+                parent = i.taxid.parent_taxid
+                while current_lineage != 'root':
+                    lineage_list.append(current_lineage)
+                    new_query = Taxa.get(Taxa.ncbi_taxid == parent)
+                    current_lineage = new_query.tax_name
+                    parent = new_query.parent_taxid
+                yield (i.accession, lineage_list)
+            # TODO: List accession ID not found?
+            # for noid in notfound:
+            #     self._unmapped_taxid(noid)

taxadb/app.py

@@ -8,13 +8,13 @@
 
 from taxadb import util
 from taxadb.parser import TaxaDumpParser, Accession2TaxidParser
-from taxadb.schema import *
+from taxadb.schema import DatabaseFactory, db, Taxa, Accession
 
 
 def download(args):
     """Main function for the 'taxadb download' sub-command.
 
-    This function downloads taxump.tar.gz and the content of the accession2taxid
+    This function downloads taxump.tar.gz and the content of accession2taxid
     directory from the ncbi ftp.
 
     Arguments:
@@ -37,20 +37,20 @@ def download(args):
     os.chdir(os.path.abspath(out))
 
     for file in acc_dl_list:
-        print('Started Downloading %s' % (file))
+        print('Started Downloading %s' % file)
         with ftputil.FTPHost(ncbi_ftp, 'anonymous', 'password') as ncbi:
             ncbi.chdir('pub/taxonomy/accession2taxid/')
             ncbi.download_if_newer(file, file)
             ncbi.download_if_newer(file + '.md5', file + '.md5')
             util.md5_check(file)
 
-    print('Started Downloading %s' % (taxdump))
+    print('Started Downloading %s' % taxdump)
     with ftputil.FTPHost(ncbi_ftp, 'anonymous', 'password') as ncbi:
         ncbi.chdir('pub/taxonomy/')
         ncbi.download_if_newer(taxdump, taxdump)
         ncbi.download_if_newer(taxdump + '.md5', taxdump + '.md5')
         util.md5_check(taxdump)
-    print('Unpacking %s' % (taxdump))
+    print('Unpacking %s' % taxdump)
     with tarfile.open(taxdump, "r:gz") as tar:
         tar.extractall()
         tar.close()
@@ -90,7 +90,7 @@ def create_db(args):
     # If taxa table already exists, do not recreate and fill it
     # safe=True prevent not to create the table if it already exists
     if not Taxa.table_exists():
-        parser.verbose("Creating table %s" % str(Taxa._meta.db_table))
+        parser.verbose("Creating table %s" % str(Taxa.get_table_name()))
     db.create_table(Taxa, safe=True)
     parser = TaxaDumpParser(nodes_file=os.path.join(args.input, 'nodes.dmp'),
                             names_file=os.path.join(args.input, 'names.dmp'))
@@ -127,7 +127,7 @@ def create_db(args):
                 Accession.insert_many(data_dict[0:args.chunk]).execute()
                 inserted_rows += len(data_dict)
             print('%s: %s added to database (%d rows inserted)' % (
-                Accession._meta.db_table, acc_file, inserted_rows))
+                Accession.get_table_name(), acc_file, inserted_rows))
     print('Sequence: completed')
     db.close()