Formatting

Author: mikecormier

ggd/check_recipe.py

@@ -6,8 +6,8 @@
 import os
 import sys
 
+from .list_installed_pkgs import GGD_INFO, METADATA, get_metadata
 from .utils import get_builds, get_ggd_channels, get_species
-from .list_installed_pkgs import  get_metadata, GGD_INFO, METADATA
 
 SPECIES_LIST = sorted(get_species())
 GENOME_BUILDS = sorted(get_builds("*"))
@@ -65,7 +65,9 @@ def add_list_files(p):
 # -------------------------------------------------------------------------------------------------------------
 
 
-def in_ggd_channel(ggd_recipes, ggd_channel, C_ROOT, reporting=True, return_pkg_list = False):
+def in_ggd_channel(
+    ggd_recipes, ggd_channel, C_ROOT, reporting=True, return_pkg_list=False
+):
     """Method to check if the desired ggd recipe is in the ggd channel
 
     in_ggd_channel
@@ -111,7 +113,7 @@ def get_local_pkg_dict():
         ==================
         Load the local install ggd packages from a json file into a dict.
         """
-    
+
         ## Get local install list
         local_json_dict = get_metadata(C_ROOT, GGD_INFO, METADATA)
 
@@ -121,11 +123,10 @@ def get_local_pkg_dict():
             if value["tags"]["ggd-channel"] != ggd_channel:
                 rm_pkgs.append(pkg)
 
-        [local_json_dict["packages"].pop(key) for key in rm_pkgs] 
+        [local_json_dict["packages"].pop(key) for key in rm_pkgs]
 
         return local_json_dict
 
-
     def get_package_list(j_dict):
         """
         get_package_list
@@ -145,8 +146,7 @@ def get_package_list(j_dict):
         if len(json_dict["packages"].keys()) > 0:
             package_list = search_packages(j_dict, ggd_recipes)
 
-        return(package_list)
-
+        return package_list
 
     json_dict = {"channeldata_version": 1, "packages": {}}
     if check_for_internet_connection(3):
@@ -169,11 +169,11 @@ def get_package_list(j_dict):
     package_list = get_package_list(json_dict)
 
     ## If no pkgs, check the local installed files
-    if not all(True if recipe in package_list else False for recipe in ggd_recipes ):
+    if not all(True if recipe in package_list else False for recipe in ggd_recipes):
         json_dict["packages"].update(get_local_pkg_dict()["packages"])
         package_list = get_package_list(json_dict)
 
-    if all(True if recipe in package_list else False for recipe in ggd_recipes ):
+    if all(True if recipe in package_list else False for recipe in ggd_recipes):
         if return_pkg_list:
             return (package_list, json_dict)
         else:

ggd/install.py

@@ -201,18 +201,18 @@ def list_pkg_info(pkg_names, pkgs_dict, env_vars, conda_list, prefix, prefix_set
         print(
             (
                 "#\n# NOTE: Packages with the '{}' messages represent packages where the ggd"
-                " package(s) are installed, but the package metadata has been removed from conda storage. This" 
+                " package(s) are installed, but the package metadata has been removed from conda storage. This"
                 " happens when one of the following happen: \n 1) The package represents an ID specific meta-"
                 "recipe installed by GGD. \n 2) When the recipe is built locally using 'ggd check-recipe' and"
-                " has not been uninstalled. (Commonly for private data packages).\n  Or \n 3) The package is" 
+                " has not been uninstalled. (Commonly for private data packages).\n  Or \n 3) The package is"
                 " uninstalled using conda rather then ggd. The package is still available for use and is in"
                 " the same state as before the 'conda uninstall'. To fix the problem on conda's side, uninstall"
                 " the package with 'ggd uninstall' and re-install with 'ggd install'.\n"
             ).format(missing_message.strip())
         )
 
 
-def get_metadata(C_ROOT,GGD_INFO_DIR, METADATA_FILE):
+def get_metadata(C_ROOT, GGD_INFO_DIR, METADATA_FILE):
     """
     get_metadata
     =============
@@ -228,14 +228,14 @@ def get_metadata(C_ROOT,GGD_INFO_DIR, METADATA_FILE):
     ++++++++
     1) (dict) Metadata json file loaded as a dictionary
     """
-    
+
     try:
         metadata_dict = load_json(os.path.join(C_ROOT, GGD_INFO_DIR, METADATA_FILE))
     except IOError as e:
         print(str(e))
         sys.exit("\n:ggd:list: !!ERROR!! Unable to load the local metadata")
 
-    return(metadata_dict)
+    return metadata_dict
 
 
 def list_installed_packages(parser, args):
@@ -282,7 +282,7 @@ def list_installed_packages(parser, args):
         update_installed_pkg_metadata(prefix=CONDA_ROOT)
 
     ## Load json metadata data as dictionary
-    #metadata = load_json(os.path.join(CONDA_ROOT, GGD_INFO, METADATA))
+    # metadata = load_json(os.path.join(CONDA_ROOT, GGD_INFO, METADATA))
     metadata = get_metadata(CONDA_ROOT, GGD_INFO, METADATA)
 
     ## Get the environment variables

ggd/list_files.py

@@ -45,7 +45,7 @@ def add_pkg_info(p):
 # -------------------------------------------------------------------------------------------------------------
 
 
-def check_if_ggd_recipe(ggd_recipe, ggd_channel, prefix = conda_root()):
+def check_if_ggd_recipe(ggd_recipe, ggd_channel, prefix=conda_root()):
     """Method to check if a ggd recipe is in designated ggd channel or not 
 
     check_if_ggd_recipe
@@ -76,7 +76,9 @@ def check_if_ggd_recipe(ggd_recipe, ggd_channel, prefix = conda_root()):
         return False
 
 
-def get_meta_yaml_info(tarball_info_object, ggd_recipe, ggd_channel, prefix = conda_root()):
+def get_meta_yaml_info(
+    tarball_info_object, ggd_recipe, ggd_channel, prefix=conda_root()
+):
     """Method to get information from the meta.yaml file of an installed ggd package
 
     get_meta_yaml_info
@@ -111,11 +113,19 @@ def get_meta_yaml_info(tarball_info_object, ggd_recipe, ggd_channel, prefix = co
         )
         utils.add_yaml_literal_block(yaml)
 
-    species = yaml_dict["about"]["identifiers"]["species"] 
-    genome_build = yaml_dict["about"]["identifiers"]["genome-build"] 
+    species = yaml_dict["about"]["identifiers"]["species"]
+    genome_build = yaml_dict["about"]["identifiers"]["genome-build"]
 
-    report_species = yaml_dict["about"]["identifiers"]["species"] if "updated-species" not in yaml_dict["about"]["identifiers"] else "(Updated) " +  yaml_dict["about"]["identifiers"]["updated-species"] 
-    report_genome_build = yaml_dict["about"]["identifiers"]["genome-build"] if "updated-genome-build" not in yaml_dict["about"]["identifiers"] else "(Updated) " + yaml_dict["about"]["identifiers"]["updated-genome-build"]
+    report_species = (
+        yaml_dict["about"]["identifiers"]["species"]
+        if "updated-species" not in yaml_dict["about"]["identifiers"]
+        else "(Updated) " + yaml_dict["about"]["identifiers"]["updated-species"]
+    )
+    report_genome_build = (
+        yaml_dict["about"]["identifiers"]["genome-build"]
+        if "updated-genome-build" not in yaml_dict["about"]["identifiers"]
+        else "(Updated) " + yaml_dict["about"]["identifiers"]["updated-genome-build"]
+    )
 
     version = yaml_dict["package"]["version"]
 
@@ -125,7 +135,11 @@ def get_meta_yaml_info(tarball_info_object, ggd_recipe, ggd_channel, prefix = co
     )
     if "parent-meta-recipe" in yaml_dict["about"]["identifiers"]:
         results.append(
-            "\t" + "\033[1m" + "GGD Parent Meta-Recipe:" + "\033[0m" + " {}".format(yaml_dict["about"]["identifiers"]["parent-meta-recipe"])
+            "\t"
+            + "\033[1m"
+            + "GGD Parent Meta-Recipe:"
+            + "\033[0m"
+            + " {}".format(yaml_dict["about"]["identifiers"]["parent-meta-recipe"])
         )
     results.append(
         "\t" + "\033[1m" + "GGD-Channel:" + "\033[0m" + " ggd-{}".format(ggd_channel)
@@ -140,9 +154,15 @@ def get_meta_yaml_info(tarball_info_object, ggd_recipe, ggd_channel, prefix = co
         + "\033[0m"
         + " {}".format(yaml_dict["about"]["summary"])
     )
-    results.append("\t" + "\033[1m" + "Species:" + "\033[0m" + " {}".format(report_species))
     results.append(
-        "\t" + "\033[1m" + "Genome Build:" + "\033[0m" + " {}".format(report_genome_build)
+        "\t" + "\033[1m" + "Species:" + "\033[0m" + " {}".format(report_species)
+    )
+    results.append(
+        "\t"
+        + "\033[1m"
+        + "Genome Build:"
+        + "\033[0m"
+        + " {}".format(report_genome_build)
     )
     if "keywords" in yaml_dict["about"] and yaml_dict["about"]["keywords"]:
         results.append(
@@ -278,7 +298,7 @@ def print_recipe(tarball_info_object, ggd_recipe):
     return True
 
 
-def get_pkg_info(ggd_recipe, ggd_channel, show_recipe, prefix = conda_root()):
+def get_pkg_info(ggd_recipe, ggd_channel, show_recipe, prefix=conda_root()):
     """Method to get the package info from an installed package
 
     get_pkg_info
@@ -298,7 +318,7 @@ def get_pkg_info(ggd_recipe, ggd_channel, show_recipe, prefix = conda_root()):
     from .utils import get_conda_package_list
 
     ## Get a list of installed ggd packages using conda list
-    conda_package_list = get_conda_package_list(prefix, include_local = True)
+    conda_package_list = get_conda_package_list(prefix, include_local=True)
 
     ## Check if ggd recipe in the list
     if ggd_recipe in conda_package_list.keys():
@@ -334,10 +354,7 @@ def get_pkg_info(ggd_recipe, ggd_channel, show_recipe, prefix = conda_root()):
 def info(parser, args):
     """Main method to run list_pkg_info"""
 
-    from .utils import (
-        get_conda_prefix_path,
-        prefix_in_conda,
-    )
+    from .utils import get_conda_prefix_path, prefix_in_conda
 
     ## Check prefix
     CONDA_ROOT = (

ggd/list_installed_pkgs.py

@@ -1,10 +1,9 @@
 from __future__ import print_function
 
 import os
-
 from shutil import copyfile
 
-from .utils import get_builds, get_ggd_channels, get_species 
+from .utils import get_builds, get_ggd_channels, get_species
 
 SPECIES_LIST = sorted(get_species())
 GENOME_BUILDS = sorted(get_builds("*"))
@@ -25,7 +24,6 @@ def add_make_metarecipe(p):
         description="Make a ggd data meta-recipe",
     )
 
-
     c.add_argument(
         "-c",
         "--channel",
@@ -55,36 +53,36 @@ def add_make_metarecipe(p):
         "-s",
         "--species",
         help="The species recipe is for. Use 'meta-recipe` for a metarecipe file",
-        default = "meta-recipe"
+        default="meta-recipe",
     )
 
     c.add_argument(
         "-g",
         "--genome-build",
         help="The genome build the recipe is for. Use 'metarecipe' for a metarecipe file",
-        default = "meta-recipe"
+        default="meta-recipe",
     )
 
     c.add_argument(
         "-dv",
         "--data-version",
         help="The version of the data (itself) being downloaded and processed (EX: dbsnp-127). Use 'metarecipe' for a metarecipe",
-        default = "meta-recipe"
+        default="meta-recipe",
     )
 
     c.add_argument(
         "-cb",
         "--coordinate-base",
         choices=GENOMIC_COORDINATE_LIST,
         help="The genomic coordinate basing for the file(s) in the recipe. Use 'NA' for a metarecipe",
-        default = "NA"
+        default="NA",
     )
 
     c.add_argument(
         "--extra-scripts",
-        metavar = "Extra Scripts",
-        nargs = "*",
-        help = "Any additional scripts used for the metarecipe that are not the main bash script"
+        metavar="Extra Scripts",
+        nargs="*",
+        help="Any additional scripts used for the metarecipe that are not the main bash script",
     )
 
     c2 = c.add_argument_group("required arguments")
@@ -127,7 +125,6 @@ def add_make_metarecipe(p):
         required=True,
     )
 
-
     c2.add_argument(
         "-n",
         "--name",
@@ -137,8 +134,7 @@ def add_make_metarecipe(p):
     )
 
     c2.add_argument(
-        "script",
-        help="bash script that contains the commands for the metarecipe.",
+        "script", help="bash script that contains the commands for the metarecipe.",
     )
 
     c.set_defaults(func=make_bash)
@@ -224,8 +220,7 @@ def make_bash(parser, args):
 
     from .check_recipe import _check_build
 
-
-#    if args.genome_build != "meta-recipe":
+    #    if args.genome_build != "meta-recipe":
     print(":ggd:make-recipe: checking", args.genome_build)
     _check_build(args.species, args.genome_build)
 
@@ -300,8 +295,8 @@ def make_bash(parser, args):
         }
     yml2 = {"extra": {"authors": args.authors}}
     yml3 = {"package": {"name": name, "version": args.package_version}}
-    #yml3 = {"package": {"name": "{{ GGD_NAME_ID }}-" + args.data_provider.lower() + "-v" + args.package_version , "version": args.package_version}}
-    #yml3 = {"package": {"name": """{{ environ.get("GGD_NAME_ID") }}-""" + args.data_provider.lower() + "-v" + args.package_version , "version": args.package_version}}
+    # yml3 = {"package": {"name": "{{ GGD_NAME_ID }}-" + args.data_provider.lower() + "-v" + args.package_version , "version": args.package_version}}
+    # yml3 = {"package": {"name": """{{ environ.get("GGD_NAME_ID") }}-""" + args.data_provider.lower() + "-v" + args.package_version , "version": args.package_version}}
     yml4 = {"requirements": {"build": non_ggd_deps[:], "run": deps[:]}}
     yml5 = {"source": {"path": "."}}
     yml6 = {
@@ -429,7 +424,7 @@ def make_bash(parser, args):
         fh.write("#!/bin/sh\nset -eo pipefail -o nounset\n")
         fh.write(open(args.script).read())
 
-    ## create empty recipe.sh script 
+    ## create empty recipe.sh script
     open(os.path.join(name, "recipe.sh"), "a").close()
 
     ## Create empty checksum file
@@ -441,10 +436,8 @@ def make_bash(parser, args):
         % name
     )
 
-
     ## Copy all extra scripts to the meta recipe directory
     for f in args.extra_scripts:
         copyfile(f, os.path.join(os.getcwd(), name, os.path.basename(f)))
-        
 
     return True

ggd/list_pkg_info.py

@@ -50,13 +50,19 @@ def get_channeldata(ggd_recipes, ggd_channel):
      check_for_installation() method if it is found within the channeldata.json file
 
     """
-    
+
     from .list_files import in_ggd_channel
 
     ## Check if recipe is in the ggd channel
     package_list = []
     try:
-        package_list, jdict = in_ggd_channel(ggd_recipes, ggd_channel, conda_root(), reporting = False, return_pkg_list = True)
+        package_list, jdict = in_ggd_channel(
+            ggd_recipes,
+            ggd_channel,
+            conda_root(),
+            reporting=False,
+            return_pkg_list=True,
+        )
     except SystemExit:
         pass
 
@@ -70,7 +76,11 @@ def get_channeldata(ggd_recipes, ggd_channel):
                     % (recipe, ggd_channel)
                 )
             else:
-                print("\n:ggd:uninstall: The '{}' channel is not a ggd conda channel".format(ggd_channel))
+                print(
+                    "\n:ggd:uninstall: The '{}' channel is not a ggd conda channel".format(
+                        ggd_channel
+                    )
+                )
 
             similar_pkgs = get_similar_pkg_installed_by_conda(recipe)
             if len(similar_pkgs) > 0:
@@ -291,7 +301,7 @@ def uninstall(parser, args):
         sys.exit()
 
     ## Get the installed ggd data package names
-    installed_ggd_packages = get_conda_package_list(conda_root(), include_local = True)
+    installed_ggd_packages = get_conda_package_list(conda_root(), include_local=True)
 
     ## Check for GGD package as run deps
     ### Add them to the uninstall list