8460: Merge branch 'master' into 8460-websocket-go

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

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 9d3fe1c1ba7b699f3491a3b69b30750051aadd33..500ea0f4203793fac7fdf418f79b0ae562f64334 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -2,9 +2,13 @@ import fnmatch
 import os
 import errno
 import urlparse
+import re
+
+import ruamel.yaml as yaml
 
 import cwltool.stdfsaccess
 from cwltool.pathmapper import abspath
+import cwltool.resolver
 
 import arvados.util
 import arvados.collection
@@ -127,17 +131,23 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 class CollectionFetcher(DefaultFetcher):
     def __init__(self, cache, session, api_client=None, keep_client=None):
         super(CollectionFetcher, self).__init__(cache, session)
+        self.api_client = api_client
         self.fsaccess = CollectionFsAccess("", api_client=api_client, keep_client=keep_client)
 
     def fetch_text(self, url):
         if url.startswith("keep:"):
-            with self.fsaccess.open(url) as f:
+            with self.fsaccess.open(url, "r") as f:
                 return f.read()
+        if url.startswith("arvwf:"):
+            return self.api_client.workflows().get(uuid=url[6:]).execute()["definition"]
         return super(CollectionFetcher, self).fetch_text(url)
 
     def check_exists(self, url):
         if url.startswith("keep:"):
             return self.fsaccess.exists(url)
+        if url.startswith("arvwf:"):
+            if self.fetch_text(url):
+                return True
         return super(CollectionFetcher, self).check_exists(url)
 
     def urljoin(self, base_url, url):
@@ -145,29 +155,52 @@ class CollectionFetcher(DefaultFetcher):
             return base_url
 
         urlsp = urlparse.urlsplit(url)
-        if urlsp.scheme:
+        if urlsp.scheme or not base_url:
             return url
 
         basesp = urlparse.urlsplit(base_url)
-        if basesp.scheme == "keep":
+        if basesp.scheme in ("keep", "arvwf"):
             if not basesp.path:
                 raise IOError(errno.EINVAL, "Invalid Keep locator", base_url)
 
             baseparts = basesp.path.split("/")
-            urlparts = urlsp.path.split("/")
+            urlparts = urlsp.path.split("/") if urlsp.path else []
 
             pdh = baseparts.pop(0)
 
-            if not arvados.util.keep_locator_pattern.match(pdh):
+            if basesp.scheme == "keep" and not arvados.util.keep_locator_pattern.match(pdh):
                 raise IOError(errno.EINVAL, "Invalid Keep locator", base_url)
 
             if urlsp.path.startswith("/"):
                 baseparts = []
+                urlparts.pop(0)
 
-            if baseparts and urlparts:
+            if baseparts and urlsp.path:
                 baseparts.pop()
 
             path = "/".join([pdh] + baseparts + urlparts)
-            return urlparse.urlunsplit(("keep", "", path, "", urlsp.fragment))
+            return urlparse.urlunsplit((basesp.scheme, "", path, "", urlsp.fragment))
 
         return super(CollectionFetcher, self).urljoin(base_url, url)
+
+workflow_uuid_pattern = re.compile(r'[a-z0-9]{5}-7fd4e-[a-z0-9]{15}')
+pipeline_template_uuid_pattern = re.compile(r'[a-z0-9]{5}-p5p6p-[a-z0-9]{15}')
+
+def collectionResolver(api_client, document_loader, uri):
+    if workflow_uuid_pattern.match(uri):
+        return "arvwf:%s#main" % (uri)
+
+    if pipeline_template_uuid_pattern.match(uri):
+        pt = api_client.pipeline_templates().get(uuid=uri).execute()
+        return "keep:" + pt["components"].values()[0]["script_parameters"]["cwl:tool"]
+
+    p = uri.split("/")
+    if arvados.util.keep_locator_pattern.match(p[0]):
+        return "keep:%s" % (uri)
+
+    if arvados.util.collection_uuid_pattern.match(p[0]):
+        return "keep:%s%s" % (api_client.collections().
+                              get(uuid=p[0]).execute()["portable_data_hash"],
+                              uri[len(p[0]):])
+
+    return cwltool.resolver.tool_resolver(document_loader, uri)