Merge pull request #36 from vinisalazar/dev

Merge v0.1.19

.gitignore

@@ -1,6 +1,7 @@
 # BioProv
 bioprov/db.json
 bioprov/provstore_api.txt
+**/*.log
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

CHANGELOG.md

@@ -7,6 +7,21 @@
     * .describe []
     * .write_paths_to_file, .copy_files_to_dir(), .link_files_to_dir()
 
+### v0.1.19
+* Debug API endpoint (#23) [x]
+* Implement logging [x]
+    * Implement Workflow logging [x]
+* Debug Workflow Steps [x]
+* Remove workflow main methods [x]
+    * Workflows must now be called only from the CLI [x]
+* Implement post-workflow actions [x]
+    * Update db [x]
+    * Upload to ProvStore [x]
+    * Write PROVN [x]
+    * Write PDF [x]
+* Add Sample.auto_update_db() methods [x]
+* Remove logger call when updating Project in database [x]
+
 ### v0.1.18a
 * Patch file deserializer bug [x]
 

bioprov/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 
 """

bioprov/bioprov

@@ -3,7 +3,7 @@ __author__ = "Vini Salazar"
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 """
 Executable that goes in $PATH. Code for the command-line is on the bioprov.py module.

bioprov/bioprov.py

@@ -2,24 +2,25 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 """
 BioProv command-line application. This module holds the main executable.
 """
 
 import argparse
 import sys
+from pathlib import Path
+
 import bioprov.src.config as bp_config_module
 from bioprov.src.config import config
+from bioprov.utils import parser_help, dict_to_string
 from bioprov.workflows import (
     WorkflowOptionsParser,
     genome_annotation,
     blastn_alignment,
     KaijuWorkflow,
 )
-from bioprov.utils import parser_help, dict_to_string
-from pathlib import Path
 
 
 def main(args=None):
@@ -90,7 +91,7 @@ def main(args=None):
     try:
         parser.parse_options(args)  # no cover
     except KeyError:
-        parser_help(bioprov_parser)
+        raise
 
 
 class CommandOptionsParser:

bioprov/data/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 
 """

bioprov/data/datasets/genome_annotation_input.tsv

@@ -1,2 +1,3 @@
 sample-id	assembly
 GCF_000010065.1_ASM1006v1_genomic.fna	bioprov/data/genomes/GCF_000010065.1_ASM1006v1_genomic.fna
+GCF_000007925.1_ASM792v1_genomic.fna	bioprov/data/genomes/GCF_000007925.1_ASM792v1_genomic.fna

bioprov/programs/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 
 from .programs import prodigal, diamond, blastn, blastp, prokka, kaiju, kaiju2table

bioprov/programs/programs.py

@@ -2,13 +2,15 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 
 """
 Module for holding preset instances of the Program class.
+Module for holding preset instances of the Program class.
 """
 
+import logging
 from os import path
 from pathlib import Path
 
@@ -117,8 +119,8 @@ def blastp(sample, db, query_tag="query", outformat=6):
     :param Sample sample: Instance of BioProv.Sample.
     :param str db: A string pointing to the reference database directory and title.
     :param str query_tag: A tag for the query file.
-    :param int outformat: The output format to gather from blastn.
-    :return: Instance of PresetProgram for BLASTN.
+    :param int outformat: The output format to gather from blastp.
+    :return: Instance of PresetProgram for BLASTP.
     :rtype: BioProv.PresetProgram.
     :raises AssertionError: Path to the reference database does not exist.
     """
@@ -192,10 +194,12 @@ def prokka(
     )
 
     for param in params:
-        _prokka.add_parameter(param, _print=False)
+        _prokka.add_parameter(param)
 
     if path.isdir(output_path):
-        print(f"Warning: {output_path} directory exists. Will overwrite.")  # no cover
+        config.logger.warning(
+            f"Warning: {output_path} directory exists. Will overwrite."
+        )  # no cover
         _prokka.add_parameter(
             Parameter(key="--force", value="", kind="misc")
         )  # no cover
@@ -223,8 +227,7 @@ def prokka(
 
     # Input goes here, must be last positionally.
     _prokka.add_parameter(
-        Parameter(key="", value=str(_sample.files[assembly]), kind="input"),
-        _print=False,
+        Parameter(key="", value=str(_sample.files[assembly]), kind="input")
     )
 
     return _prokka
@@ -274,7 +277,7 @@ def kaiju(
         Parameter(key="-o", value=output_path, kind="output"),
     )
     for p in params:
-        kaiju_.add_parameter(p, _print=False)
+        kaiju_.add_parameter(p)
 
     if add_param_str:
         kaiju_.cmd += f" {add_param_str}"  # no cover
@@ -324,7 +327,7 @@ def kaiju2table(
     )
 
     for p in params:
-        kaiju2table_.add_parameter(p, _print=False)
+        kaiju2table_.add_parameter(p)
 
     # Add final parameter:
     kaiju2table_.cmd += f" {str(_sample.files[kaiju_output])}"

bioprov/src/__init__.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 
 """

bioprov/src/config.py

@@ -2,7 +2,7 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 
 """
@@ -12,13 +12,15 @@
 """
 
 import os
-import bioprov
-from bioprov.data import data_dir, genomes_dir
+from pathlib import Path
+
 from prov.model import Namespace
 from provstore.api import Api
-from bioprov.utils import serializer, dict_to_sha1, serializer_filter
 from tinydb import TinyDB
-from pathlib import Path
+
+from bioprov import __file__ as bp_file
+from bioprov.data import data_dir, genomes_dir
+from bioprov.utils import serializer, dict_to_sha1, serializer_filter, create_logger
 
 
 class Config:
@@ -40,7 +42,7 @@ def __init__(self, db_path=None, threads=0):
         self.db = None
         self.db_path = None
         self.threads = threads
-        self.bioprov_dir = Path(bioprov.__file__).parent
+        self.bioprov_dir = Path(bp_file).parent
         self.data = data_dir
         self.genomes = genomes_dir
         if db_path is None:
@@ -52,6 +54,7 @@ def __init__(self, db_path=None, threads=0):
         self._provstore_token = None
         self._provstore_api = None
         self._provstore_endpoint = "https://openprovenance.org/store/api/v0/"
+        self._logger = None
 
     def __repr__(self):
         return f"BioProv Config class set in {__file__}"
@@ -76,7 +79,7 @@ def provstore_api(self):
             self._provstore_api = Api(
                 username=self.provstore_user, api_key=self.provstore_token
             )
-            Api.base_url = self._provstore_endpoint
+            self._provstore_api.base_url = self._provstore_endpoint
         return self._provstore_api
 
     @provstore_api.setter
@@ -113,12 +116,22 @@ def provstore_token(self):  # no cover
     def provstore_token(self, value):
         self._provstore_token = value
 
-    def create_provstore_file(self, user=None, token=None):
+    @property
+    def logger(self):
+        if self._logger is None:
+            self._logger = create_logger()
+        return self._logger
+
+    @logger.setter
+    def logger(self, value):
+        self._logger = value
+
+    def create_provstore_file(self, user=None, token=None):  # no cover
         with open(self.provstore_file, "w") as f:
             if user is None:
-                user = input("Please paste your ProvStore user: ")  # no cover
+                user = input("Please paste your ProvStore user: ")
             if token is None:
-                token = input("Please paste your ProvStore API token: ")  # no cover
+                token = input("Please paste your ProvStore API token: ")
             f.write(user + "\n")
             f.write(token + "\n")
 

bioprov/src/files.py

@@ -2,17 +2,20 @@
 __license__ = "MIT"
 __maintainer__ = "Vini Salazar"
 __url__ = "https://github.com/vinisalazar/bioprov"
-__version__ = "0.1.18a"
+__version__ = "0.1.19"
 
 
 """
 Contains the File and SeqFile classes and related functions.
 """
 
-import numpy as np
+import logging
 from dataclasses import dataclass
 from pathlib import Path
+
+import numpy as np
 from Bio import SeqIO, AlignIO
+
 from bioprov.utils import (
     get_size,
     Warnings,
@@ -113,12 +116,12 @@ def replace_path(self, old_terms, new, warnings=False):
         # TODO: replace these print statements for logger warning/debug level
         if warnings:
             if not self.exists and old_exists:
-                print(
-                    f"Warning: file {self.path} was marked as existing but was not found."
+                logging.warning(
+                    f"File {self.path} was marked as existing but was not found."
                 )
             if old_hash and self.sha1 != old_hash and self.exists:  # no cover
-                print(
-                    f"Warning: file {self.path} previous sha1 checksum differs from the current."
+                logging.warning(
+                    f"File {self.path} previous sha1 checksum differs from the current."
                 )
 
     def serializer(self):
@@ -159,7 +162,7 @@ def replace_path(self, old_terms, new, warnings=False):
         # TODO: replace these print statements for logger warning/debug level
         if warnings:
             if not self.exists and old_exists:
-                print(
+                logging.warning(
                     f"Warning: file {self.path} was marked as existing but was not found."
                 )
 
@@ -448,8 +451,8 @@ def seqrecordgenerator(path, format, parser="seq", warnings=False):
         return records
     except FileNotFoundError:
         if warnings:
-            print(Warnings()["not_exist"](path))
-            print(
+            logging.warning(Warnings()["not_exist"](path))
+            logging.warning(
                 "The file was loaded as a BioProv object, but it does not exist on the specified path."
             )
         return None