Merge branch 'master' into cwlprov-log-filename

Author: mr-c

README.rst

@@ -180,13 +180,17 @@ By default, cwltool searches https://dockstore.org/ .  Use ``--add-tool-registry
 
 For example ::
 
-  cwltool --non-strict quay.io/collaboratory/dockstore-tool-bamstats:master test.json
+  cwltool quay.io/collaboratory/dockstore-tool-bamstats:develop test.json
 
 and (defaults to latest when a version is not specified) ::
 
-  cwltool --non-strict quay.io/collaboratory/dockstore-tool-bamstats test.json
+  cwltool quay.io/collaboratory/dockstore-tool-bamstats test.json
 
-For this example, grab the test.json (and input file) from https://github.com/CancerCollaboratory/dockstore-tool-bamstats
+For this example, grab the test.json (and input file) from https://github.com/CancerCollaboratory/dockstore-tool-bamstats ::
+
+  wget https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-bamstats/versions/develop/PLAIN-CWL/descriptor/test.json
+  wget https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/rna.SRR948778.bam
+  
 
 .. _`GA4GH Tool Registry API`: https://github.com/ga4gh/tool-registry-schemas
 

cwltool/resolver.py

@@ -47,14 +47,16 @@ def tool_resolver(document_loader, uri):
     return None
 
 
-ga4gh_tool_registries = ["https://dockstore.org:8443"]
+ga4gh_tool_registries = ["https://dockstore.org/api"]
+GA4GH_TRS = "{0}/api/ga4gh/v2/tools/{1}/versions/{2}/plain-CWL/descriptor"
 
 def resolve_ga4gh_tool(document_loader, uri):
     path, version = uri.partition(":")[::2]
     if not version:
         version = "latest"
     for reg in ga4gh_tool_registries:
-        ds = "{0}/api/ga4gh/v1/tools/{1}/versions/{2}/plain-CWL/descriptor".format(reg, urllib.parse.quote(path, ""), urllib.parse.quote(version, ""))
+        ds = GA4GH_TRS.format(reg, urllib.parse.quote(path, ""),
+                              urllib.parse.quote(version, ""))
         try:
             resp = document_loader.session.head(ds)
             resp.raise_for_status()