Apply PEP8 in sources and setup loki command in poetry

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 # Distribution / packaging
 .Python
 build/
+data/
 develop-eggs/
 dist/
 downloads/

biofilter_modules/biofilter_class.py

@@ -104,7 +104,7 @@ class Biofilter(
     def getVersionTuple(cls):
         # tuple = (major,minor,revision,dev,build,date)
         # dev must be in ('a','b','rc','release') for lexicographic comparison
-        return (2, 4, 4, "release", "", "2024-12-01")
+        return (3, 0, 1, "release", "", "2025-01-01")
 
     @classmethod
     def getVersionString(cls):

loki_modules/__init__.py

@@ -3,7 +3,8 @@
 
 sys.path.insert(0, os.path.abspath(os.path.dirname(__file__)))
 
-from loki_modules.loki_db import Database
+from loki_modules.loki_db import Database  # noqa E402
+from loki_modules.loki_build import main  # noqa E402
 from loki_modules.loki_mixins import (  # noqa E402
     Schema,
     VersionMixin,
@@ -13,9 +14,17 @@
     DatabaseOperationsMixin,
     DatabaseLiftOverMixin,
     DatabaseQueryMixin,
+    SourceUtilityMethods,
+    SourceDbOperations,
+    UpdaterDownloadMixin,
+    UpdaterDatabaseMixin,
+    UpdaterLiftOverMixin,
+    UpdaterOperationsMixin,
 )
 
+
 __all__ = [
+    "main",
     "Database",
     "loki_db",
     "loki_source",
@@ -30,4 +39,10 @@
     "DatabaseOperationsMixin",
     "DatabaseLiftOverMixin",
     "DatabaseQueryMixin",
+    "SourceUtilityMethods",
+    "SourceDbOperations",
+    "UpdaterDownloadMixin",
+    "UpdaterDatabaseMixin",
+    "UpdaterLiftOverMixin",
+    "UpdaterOperationsMixin",
 ]

loki_modules/loaders/loki_source_biogrid.py

@@ -6,7 +6,7 @@ class Source_biogrid(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.1 (2022-04-13)"
+        return "3.0.0 (2025-01-01)"
 
     def download(self, options, path):
         # download the latest source files

loki_modules/loaders/loki_source_chainfiles.py

@@ -26,7 +26,7 @@ class Source_chainfiles(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.2 (2014-06-27)"
+        return "3.0.0 (2025-01-01)"
 
     def download(self, options, path):
         # define callback to search for all available hgX liftover chain files

loki_modules/loaders/loki_source_dbsnp.py

@@ -52,7 +52,7 @@ def _identifyLatestSNPContig(self, filenames):
 
     @classmethod
     def getVersionString(cls):
-        return "2.3 (2018-11-01)"
+        return "3.0.0 (2025-01-01)"
 
     @classmethod
     def getOptions(cls):
@@ -132,7 +132,7 @@ def remFilesCallback(ftp, path):
             string = urlpath.read().decode("utf-8")
             onlyfiles = list(
                 set(
-                    re.findall(r"b([0-9]+)_SNPContigLocusId_(.*)\.bcp\.gz", string)
+                    re.findall(r"b([0-9]+)_SNPContigLocusId_(.*)\.bcp\.gz", string)  # noqa E501
                 )  # noqa E501
             )
             bestfile = self._identifyLatestSNPContig(onlyfiles)
@@ -247,10 +247,10 @@ def update(self, options, path):
                 name = words[1]
                 desc = words[2]
                 coding = (
-                    int(words[5]) if (len(words) > 5 and words[5] != "") else None
+                    int(words[5]) if (len(words) > 5 and words[5] != "") else None  # noqa E501
                 )  # noqa E501
                 exon = (
-                    int(words[6]) if (len(words) > 6 and words[6] != "") else None
+                    int(words[6]) if (len(words) > 6 and words[6] != "") else None  # noqa E501
                 )  # noqa E501
 
                 roleID[code] = self.addRole(name, desc, coding, exon)
@@ -261,38 +261,38 @@ def update(self, options, path):
 
             # process SNP roles
             """ /* from human_9606_table.sql.gz */
-CREATE TABLE [b137_SNPContigLocusId]
-(
-[snp_id] [int] NULL ,
-[contig_acc] [varchar](32) NOT NULL ,
-[contig_ver] [tinyint] NULL ,
-[asn_from] [int] NULL ,
-[asn_to] [int] NULL ,
-[locus_id] [int] NULL ,
-[locus_symbol] [varchar](64) NULL ,
-[mrna_acc] [varchar](32) NOT NULL ,
-[mrna_ver] [smallint] NOT NULL ,
-[protein_acc] [varchar](32) NULL ,
-[protein_ver] [smallint] NULL ,
-[fxn_class] [int] NULL ,
-[reading_frame] [int] NULL ,
-[allele] [varchar](255) NULL ,
-[residue] [varchar](1000) NULL ,
-[aa_position] [int] NULL ,
-[build_id] [varchar](4) NOT NULL ,
-[ctg_id] [int] NULL ,
-[mrna_start] [int] NULL ,
-[mrna_stop] [int] NULL ,
-[codon] [varchar](1000) NULL ,
-[protRes] [char](3) NULL ,
-[contig_gi] [int] NULL ,
-[mrna_gi] [int] NULL ,
-[mrna_orien] [tinyint] NULL ,
-[cp_mrna_ver] [int] NULL ,
-[cp_mrna_gi] [int] NULL ,
-[verComp] [int] NULL
-)
-"""
+            CREATE TABLE [b137_SNPContigLocusId]
+            (
+            [snp_id] [int] NULL ,
+            [contig_acc] [varchar](32) NOT NULL ,
+            [contig_ver] [tinyint] NULL ,
+            [asn_from] [int] NULL ,
+            [asn_to] [int] NULL ,
+            [locus_id] [int] NULL ,
+            [locus_symbol] [varchar](64) NULL ,
+            [mrna_acc] [varchar](32) NOT NULL ,
+            [mrna_ver] [smallint] NOT NULL ,
+            [protein_acc] [varchar](32) NULL ,
+            [protein_ver] [smallint] NULL ,
+            [fxn_class] [int] NULL ,
+            [reading_frame] [int] NULL ,
+            [allele] [varchar](255) NULL ,
+            [residue] [varchar](1000) NULL ,
+            [aa_position] [int] NULL ,
+            [build_id] [varchar](4) NOT NULL ,
+            [ctg_id] [int] NULL ,
+            [mrna_start] [int] NULL ,
+            [mrna_stop] [int] NULL ,
+            [codon] [varchar](1000) NULL ,
+            [protRes] [char](3) NULL ,
+            [contig_gi] [int] NULL ,
+            [mrna_gi] [int] NULL ,
+            [mrna_orien] [tinyint] NULL ,
+            [cp_mrna_ver] [int] NULL ,
+            [cp_mrna_gi] [int] NULL ,
+            [verComp] [int] NULL
+            )
+            """
             self.log("processing SNP roles ...\n")
             setRole = set()
             numRole = numOrphan = numInc = 0
@@ -502,7 +502,7 @@ def processChmSNPs(
             for chm, listPos in listChrPos.items():
                 self.addChromosomeSNPLoci(self._loki.chr_num[chm], listPos)
             self.log(
-                "writing chromosome %s SNPs to the database completed\n" % fileChm
+                "writing chromosome %s SNPs to the database completed\n" % fileChm  # noqa E501
             )  # noqa E501
 
         # print results
@@ -527,6 +527,6 @@ def processChmSNPs(
             )
         if setBadChr:
             self.log(
-                "WARNING: %d SNPs on mismatching chromosome\n" % (len(setBadChr))
+                "WARNING: %d SNPs on mismatching chromosome\n" % (len(setBadChr))  # noqa E501
             )  # noqa E501
         listChrPos = setBadBuild = setBadVers = setBadFilter = setBadChr = None

loki_modules/loaders/loki_source_entrez.py

@@ -7,7 +7,7 @@ class Source_entrez(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.4 (2022-04-12)"
+        return "3.0.0 (2025-01-01)"
 
     @classmethod
     def getOptions(cls):
@@ -378,9 +378,9 @@ def update(self, options, path):
                     % (len(setBadChr))  # noqa E501
                 )
             self.logPop()
-            entrezChm = setOrphan = setBadNC = setBadBuild = setBadChr = setBadVers = (
+            entrezChm = setOrphan = setBadNC = setBadBuild = setBadChr = setBadVers = (  # noqa E501
                 buildGenes
-            ) = None  # noqa E501  # noqa E501
+            ) = None  # noqa E501
 
             # store gene regions
             self.log("writing gene regions to the database ...\n")

loki_modules/loaders/loki_source_go.py

@@ -7,7 +7,7 @@ class Source_go(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.1 (2022-04-14)"
+        return "3.0.0 (2025-01-01)"
 
     # getVersionString()
 

loki_modules/loaders/loki_source_gwas.py

@@ -10,7 +10,7 @@ class Source_gwas(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.5 (2016-09-19)"
+        return "3.0.0 (2025-01-01)"
 
     def download(self, options, path):
         # download the latest source files

loki_modules/loaders/loki_source_mint.py

@@ -34,7 +34,7 @@ def _identifyLatestFilename(self, filenames):
 
     @classmethod
     def getVersionString(cls):
-        return "2.2 (2018-02-20)"
+        return "3.0.0 (2025-01-01)"
 
     def download(self, options, path):
         self.downloadFilesFromHTTP(

loki_modules/loaders/loki_source_oreganno.py

@@ -15,7 +15,7 @@ class Source_oreganno(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.1 (2016-09-19)"
+        return "3.0.0 (2025-01-01)"
 
     def download(self, options):
         """

loki_modules/loaders/loki_source_pfam.py

@@ -6,7 +6,7 @@ class Source_pfam(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.2 (2016-02-08)"
+        return "3.0.0 (2025-01-01)"
 
     def download(self, options, path):
         self.downloadFilesFromHTTP(

loki_modules/loaders/loki_source_pharmgkb.py

@@ -6,7 +6,7 @@ class Source_pharmgkb(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.3 (2018-10-30)"
+        return "3.0.0 (2025-01-01)"
 
     def download(self, options, path):
         self.downloadFilesFromHTTPS(

loki_modules/loaders/loki_source_reactome.py

@@ -7,7 +7,7 @@ class Source_reactome(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.1 (2015-01-23)"
+        return "3.0.0 (2025-01-01)"
 
     def download(self, options):
         # download the latest source files

loki_modules/loaders/loki_source_ucsc_ecr.py

@@ -48,7 +48,7 @@ class Source_ucsc_ecr(loki_source.Source):
 
     @classmethod
     def getVersionString(cls):
-        return "2.0.1 (2013-03-01)"
+        return "3.0.0 (2025-01-01)"
 
     @classmethod
     def getOptions(cls):

loki_modules/loki-build.py → loki_modules/loki_build.py

@@ -81,7 +81,7 @@
 from loki_modules import loki_db
 
 
-if __name__ == "__main__":
+def main():
     version = "LOKI version %s" % (loki_db.Database.getVersionString())
 
     # define arguments
@@ -442,4 +442,7 @@ def rmtree_error(func, path, exc):
                 db.testDatabaseWriteable()
                 db.optimizeDatabase()
     # if knowledge
-# __main__
+
+
+if __name__ == "__main__":
+    main()

loki_modules/loki_mixins/source_utility_methods_mixin.py

@@ -8,7 +8,7 @@
 import urllib.request as urllib2
 import zlib
 import wget
-from datetime import datetime
+from datetime import datetime, timezone
 
 
 class SourceUtilityMethods:
@@ -211,7 +211,7 @@ def downloadFilesFromFTP(self, remHost, remFiles):
             if os.path.exists(locPath):
                 stat = os.stat(locPath)
                 locSize[locPath] = int(stat.st_size)
-                locTime[locPath] = datetime.datetime.fromtimestamp(
+                locTime[locPath] = datetime.fromtimestamp(
                     stat.st_mtime
                 )  # noqa E501
 
@@ -220,7 +220,7 @@ def downloadFilesFromFTP(self, remHost, remFiles):
         # format, but most servers return "ls -l"-ish space-delimited columns
         # (permissions) (?) (user) (group) (size) (month) (day) (year-or-time)
         # (filename)
-        now = datetime.datetime.utcnow()
+        now = datetime.now(timezone.utc)
 
         def ftpDirCB(rem_dir, line):
             words = line.split()
@@ -229,15 +229,15 @@ def ftpDirCB(rem_dir, line):
                 remSize[remFn] = int(words[4])
                 timestamp = " ".join(words[5:8])
                 try:
-                    time = datetime.datetime.strptime(timestamp, "%b %d %Y")
+                    time = datetime.strptime(timestamp, "%b %d %Y")
                 except ValueError:
                     try:
-                        time = datetime.datetime.strptime(
+                        time = datetime.strptime(
                             "%s %d" % (timestamp, now.year), "%b %d %H:%M %Y"
                         )
                     except ValueError:
                         try:
-                            time = datetime.datetime.strptime(
+                            time = datetime.strptime(
                                 "%s %d" % (timestamp, now.year - 1),
                                 "%b %d %H:%M %Y",  # noqa E501
                             )
@@ -342,7 +342,7 @@ def _downloadHTTP(
             if os.path.exists(locPath):
                 stat = os.stat(locPath)
                 locSize[locPath] = int(stat.st_size)
-                locTime[locPath] = datetime.datetime.fromtimestamp(
+                locTime[locPath] = datetime.fromtimestamp(
                     stat.st_mtime
                 )  # noqa E501
         # check remote file sizes and times
@@ -366,11 +366,11 @@ def _downloadHTTP(
                 last_modified = info.get("last-modified")
                 if last_modified:
                     try:
-                        remTime[locPath] = datetime.datetime.strptime(
+                        remTime[locPath] = datetime.strptime(
                             last_modified, "%a, %d %b %Y %H:%M:%S %Z"
                         )
                     except ValueError:
-                        remTime[locPath] = datetime.datetime.utcnow()
+                        remTime[locPath] = datetime.now(timezone.utc)
 
                 response.close()
             self.log(" OK\n")