Merge branch '13645-fix-arvados-api-host-insecure'

[arvados.git] / sdk / cwl / arvados_cwl / pathmapper.py

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index bd4b5283fbe4ff3de751110e9a15fd5250697008..d083b78f5a061906164a5978530af9230e767473 100644 (file)
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -8,11 +8,13 @@ import uuid
 import os
 import urllib
 
+from arvados_cwl.util import get_current_container, get_intermediate_collection_info
 import arvados.commands.run
 import arvados.collection
 
 from schema_salad.sourceline import SourceLine
 
+from arvados.errors import ApiError
 from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
 from cwltool.workflow import WorkflowException
 
@@ -42,7 +44,7 @@ class ArvPathMapper(PathMapper):
     pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$')
 
     def __init__(self, arvrunner, referenced_files, input_basedir,
-                 collection_pattern, file_pattern, name=None, single_collection=False, **kwargs):
+                 collection_pattern, file_pattern, name=None, single_collection=False):
         self.arvrunner = arvrunner
         self.input_basedir = input_basedir
         self.collection_pattern = collection_pattern
@@ -127,19 +129,6 @@ class ArvPathMapper(PathMapper):
                                                        keep_client=self.arvrunner.keep_client,
                                                        num_retries=self.arvrunner.num_retries)
 
-        already_uploaded = self.arvrunner.get_uploaded()
-        copied_files = set()
-        for k in referenced_files:
-            loc = k["location"]
-            if loc in already_uploaded:
-                v = already_uploaded[loc]
-                self._pathmap[loc] = MapperEnt(v.resolved, self.collection_pattern % urllib.unquote(v.resolved[5:]), v.type, True)
-                if self.single_collection:
-                    basename = k["basename"]
-                    if basename not in collection:
-                        self.addentry({"location": loc, "class": v.type, "basename": basename}, collection, ".", [])
-                        copied_files.add((loc, basename, v.type))
-
         for srcobj in referenced_files:
             self.visit(srcobj, uploadfiles)
 
@@ -150,16 +139,12 @@ class ArvPathMapper(PathMapper):
                                          fnPattern="keep:%s/%s",
                                          name=self.name,
                                          project=self.arvrunner.project_uuid,
-                                         collection=collection)
+                                         collection=collection,
+                                         packed=False)
 
         for src, ab, st in uploadfiles:
             self._pathmap[src] = MapperEnt(urllib.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:],
                                            "Directory" if os.path.isdir(ab) else "File", True)
-            self.arvrunner.add_uploaded(src, self._pathmap[src])
-
-        for loc, basename, cls in copied_files:
-            fn = "keep:%s/%s" % (collection.portable_data_hash(), basename)
-            self._pathmap[loc] = MapperEnt(urllib.quote(fn, "/:+@"), self.collection_pattern % fn[5:], cls, True)
 
         for srcobj in referenced_files:
             remap = []
@@ -170,9 +155,14 @@ class ArvPathMapper(PathMapper):
                 for l in srcobj.get("listing", []):
                     self.addentry(l, c, ".", remap)
 
-                check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
-                if not check["items"]:
-                    c.save_new(owner_uuid=self.arvrunner.project_uuid)
+                container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
+                info = get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl)
+
+                c.save_new(name=info["name"],
+                           owner_uuid=self.arvrunner.project_uuid,
+                           ensure_unique_name=True,
+                           trash_at=info["trash_at"],
+                           properties=info["properties"])
 
                 ab = self.collection_pattern % c.portable_data_hash()
                 self._pathmap[srcobj["location"]] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
@@ -184,9 +174,14 @@ class ArvPathMapper(PathMapper):
                                                   num_retries=self.arvrunner.num_retries                                                  )
                 self.addentry(srcobj, c, ".", remap)
 
-                check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
-                if not check["items"]:
-                    c.save_new(owner_uuid=self.arvrunner.project_uuid)
+                container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
+                info = get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl)
+
+                c.save_new(name=info["name"],
+                           owner_uuid=self.arvrunner.project_uuid,
+                           ensure_unique_name=True,
+                           trash_at=info["trash_at"],
+                           properties=info["properties"])
 
                 ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
                 self._pathmap[srcobj["location"]] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), srcobj["basename"]),
@@ -219,6 +214,7 @@ class ArvPathMapper(PathMapper):
         else:
             return None
 
+
 class StagingPathMapper(PathMapper):
     _follow_dirs = True