Merge pull request #1 from AxelGiottonini/plugin_version

plugin version

Plugins/__caller__.py

@@ -0,0 +1,62 @@
+#__caller__.py
+
+"""
+"""
+from Plugins.__verify__ import FailedVerification
+
+
+class Caller:
+    """
+    """
+    def __init__(self, app):
+        self.app = app
+        self.status = True
+        self.last_result = None
+
+    """
+    """
+    def run(self, callback_function, *args):
+        if args[1] not in ["default", "verify", "bypass"]:
+            raise UnknownCallerModeError(f"{args[1]} mode is not defined.")
+
+        if self.status and args[1] in ["default"]:
+            self.last_result = callback_function(*args)
+            return self.last_result
+
+        elif self.status and args[1] in ["verify"]:
+            try:
+                callback_function(self.app, self.last_result)
+            except FailedVerification:
+                self.status = False
+                raise CallerFailedVerification()
+            return None
+
+        elif not self.status and args[1] in ["bypass"]:
+            self.last_result = callback_function(*args)
+            return self.last_result
+
+class UnknownCallerModeError(Exception):
+    def __init__(self, *args):
+        if args:
+            self.message = args[0]
+        else:
+            self.message = None
+
+    def __str__(self):
+        if self.message:
+            return f"UnknownCallerModeError: {self.message}"
+        else:
+            return "UnknownCallerModeError has been raised"
+
+class CallerFailedVerification(Exception):
+    def __init__(self, *args):
+        if args:
+            self.message = args[0]
+        else:
+            self.message = None
+
+    def __str__(self):
+        if self.message:
+            return f"CallerFailedVerification: {self.message}"
+        else:
+            return "CallerFailedVerification has been raised"

Plugins/__init__.py

@@ -0,0 +1,28 @@
+#__init.py__
+
+from Plugins.__caller__ import Caller, UnknownCallerModeError, CallerFailedVerification
+
+from Plugins.__plugin__ import __Plugin__, RequiredMetadataError, UndefinedMethodError
+from Plugins.__read__ import __Read__
+from Plugins.__read_gff_maker__ import __ReadGFFMaker__
+from Plugins.__read_tab_pannzer__ import __ReadTabPannzer__
+from Plugins.__verify__ import __Verify__, FailedVerification
+
+from Plugins.read_fasta import Plugin
+
+from Plugins.read_gff_maker_3UTR import Plugin
+from Plugins.read_gff_maker_5UTR import Plugin
+from Plugins.read_gff_maker_CDS import Plugin
+from Plugins.read_gff_maker_exon import Plugin
+from Plugins.read_gff_maker_gene import Plugin
+from Plugins.read_gff_maker_mRNA import Plugin
+from Plugins.read_gff_maker_source import Plugin
+
+from Plugins.read_tab_pannzer_CDS import Plugin
+from Plugins.read_tab_pannzer_gene import Plugin
+
+from Plugins.to_handle_fasta import Plugin
+from Plugins.to_handle_gff_maker import Plugin
+from Plugins.to_handle_tab_pannzer import Plugin
+
+from Plugins.verify_gff_maker_CDS import Plugin

Plugins/__plugin__.py

@@ -0,0 +1,38 @@
+#__plugin__.py
+
+class __Plugin__:
+    def process(*args):
+        raise UndefinedMethodError("process has not been defined")
+
+    def required_metadata_check(*args):
+        return True
+
+"""
+"""
+class RequiredMetadataError(Exception):
+    def __init__(self, *args):
+        if args:
+            self.message = args[0]
+        else:
+            self.message = None
+
+    def __str__(self):
+        if self.message:
+            return f"RequiredMetadataError: {self.message}"
+        else:
+            return "RequiredMetadataError has been raised"
+
+"""
+"""
+class UndefinedMethodError(Exception):
+    def __init__(self, *args):
+        if args:
+            self.message = args[0]
+        else:
+            self.message = None
+
+    def __str__(self):
+        if self.message:
+            return f"UndefinedMethodError: {self.message}"
+        else:
+            return "UndefinedMethodError has been raised"

Plugins/__read__.py

@@ -0,0 +1,60 @@
+# __read__.py
+
+from Plugins.__plugin__ import __Plugin__, RequiredMetadataError, UndefinedMethodError
+from Plugins.__caller__ import Caller, CallerFailedVerification
+
+class __Read__(__Plugin__):
+
+    """
+    """
+    def feature_initialize(self, pre_feature, metadata):
+        raise UndefinedMethodError("feature_initialize has not been defined.")
+
+    """
+    """
+    def callbacks(self, app, calls, target):
+        raise UndefinedMethodError("callbacks has not been defined.")
+
+    """
+    """
+    def callbacks_extend(self, app, calls, target):
+        caller = Caller(app)
+        sender = []
+        for app, key_plugin, *args in calls:
+            temp = None
+            try:
+                temp = caller.run(app.plugins[key_plugin].process, app, *args, target)
+            except CallerFailedVerification:
+                sender = []
+            if temp:
+                sender.extend(temp)
+        return sender
+
+    """
+    """
+    def callbacks_append(self, app, calls, target):
+        caller = Caller(app)
+        sender = []
+        for app, key_plugin, *args in calls:
+            temp = None
+            try:
+                temp = caller.run(app.plugins[key_plugin].process, app, *args, target)
+            except CallerFailedVerification:
+                sender = []
+            if temp:
+                sender.append(temp)
+        return sender
+
+    """
+    """
+    def merge(self, feature, receiver):
+        return feature
+
+    """
+    """
+    def required_metadata_check(self, app, keys:list=[]):
+        if keys:
+            for key in keys:
+                if not key in app.metadata:
+                    raise RequiredMetadataError(f"Required metadata attribute, {key}, not found.")
+        return True

Plugins/__read_gff_maker__.py

@@ -0,0 +1,21 @@
+#__read_gff_maker__.py
+
+from Plugins.__read__ import __Read__
+
+class __ReadGFFMaker__(__Read__):
+
+    """
+    """
+    def multi_feature_initialize(self, pre_multi_feature, metadata):
+        raise UndefinedMethodError("multi_feature_initialize has not been defined.")
+
+    """
+    """
+    def callbacks(self, app, calls, target):
+        return super().callbacks_append(app, calls, target)
+
+    """
+    """
+    def callbacks_with_iterator(self, app, calls, target, iterator):
+        raise UndefinedMethodError("callbacks_with_iterator has not been defined.")
+

Plugins/__read_tab_pannzer__.py

@@ -0,0 +1,10 @@
+#__read_tab_pannzer__.py
+
+from Plugins.__read__ import __Read__
+
+class __ReadTabPannzer__(__Read__):
+
+    """
+    """
+    def callbacks(self, app, calls, target):
+        return self.callbacks_extend(app, calls, target)