from .pathmapper import ArvPathMapper, trim_listing
from .arvtool import ArvadosCommandTool, set_cluster_target
from ._version import __version__
+from .util import common_prefix
from .perf import Perf
return False
-def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, set_block_style, runtimeContext, prefix, replacePrefix):
- if set_block_style and (isinstance(d, CommentedSeq) or isinstance(d, CommentedMap)):
- d.fa.set_block_style()
-
+def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix):
if isinstance(d, MutableSequence):
for i, s in enumerate(d):
if prefix and isinstance(s, str):
if s.startswith(prefix):
d[i] = replacePrefix+s[len(prefix):]
else:
- update_refs(s, baseuri, urlexpander, merged_map, jobmapper, set_block_style, runtimeContext, prefix, replacePrefix)
+ update_refs(s, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
elif isinstance(d, MutableMapping):
for field in ("id", "name"):
if isinstance(d.get(field), str) and d[field].startswith("_:"):
if isinstance(d["inputs"][inp], str) and not is_basetype(d["inputs"][inp]):
d["inputs"][inp] = rel_ref(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper)
if isinstance(d["inputs"][inp], MutableMapping):
- update_refs(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper, set_block_style, runtimeContext, prefix, replacePrefix)
+ update_refs(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
continue
if field == "$schemas":
d["$schemas"][n] = rel_ref(d["$schemas"][n], baseuri, urlexpander, merged_map, jobmapper)
continue
- update_refs(d[field], baseuri, urlexpander, merged_map, jobmapper, set_block_style, runtimeContext, prefix, replacePrefix)
+ update_refs(d[field], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
def fix_schemadef(req, baseuri, urlexpander, merged_map, jobmapper, pdh):
merged_map[mm].resolved[r] = rename
return req
+
def drop_ids(d):
if isinstance(d, MutableSequence):
for i, s in enumerate(d):
import_files = set()
include_files = set()
+ # The document loader index will have entries for all the files
+ # that were loaded in the process of parsing the entire workflow
+ # (including subworkflows, tools, imports, etc). We use this to
+ # get compose a list of the workflow file dependencies.
for w in tool.doc_loader.idx:
if w.startswith("file://"):
workflow_files.add(urllib.parse.urldefrag(w)[0])
all_files = workflow_files | import_files | include_files
- n = 7
- allmatch = True
- if firstfile:
- while allmatch:
- n += 1
- for f in all_files:
- if len(f)-1 < n:
- n -= 1
- allmatch = False
- break
- if f[n] != firstfile[n]:
- allmatch = False
- break
-
- while firstfile[n] != "/":
- n -= 1
+ # Find the longest common prefix among all the file names. We'll
+ # use this to recreate the directory structure in a keep
+ # collection with correct relative references.
+ prefix = common_prefix(firstfile, all_files)
col = arvados.collection.Collection(api_client=arvRunner.api)
+ # Now go through all the files and update references to other
+ # files. We previously scanned for file dependencies, these are
+ # are passed in as merged_map.
+ #
+ # note about merged_map: we upload dependencies of each process
+ # object (CommandLineTool/Workflow) to a separate collection.
+ # That way, when the user edits something, this limits collection
+ # PDH changes to just that tool, and minimizes situations where
+ # small changes break container reuse for the whole workflow.
+ #
for w in workflow_files | import_files:
- # 1. load YAML
+ # 1. load the YAML file
text = tool.doc_loader.fetch_text(w)
if isinstance(text, bytes):
yamlloader = schema_salad.utils.yaml_no_ts()
result = yamlloader.load(textIO)
- set_block_style = False
- if result.fa.flow_style():
- set_block_style = True
+ # If the whole document is in "flow style" it is probably JSON
+ # formatted. We'll re-export it as JSON because the
+ # ruamel.yaml round-trip mode is a lie and only preserves
+ # "block style" formatting and not "flow style" formatting.
+ export_as_json = result.fa.flow_style()
# 2. find $import, $include, $schema, run, location
# 3. update field value
- update_refs(result, w, tool.doc_loader.expand_url, merged_map, jobmapper, set_block_style, runtimeContext, "", "")
+ update_refs(result, w, tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, "", "")
- with col.open(w[n+1:], "wt") as f:
- # yamlloader.dump(result, stream=sys.stdout)
- yamlloader.dump(result, stream=f)
+ # Write the updated file to the collection.
+ with col.open(w[len(prefix):], "wt") as f:
+ if export_as_json:
+ json.dump(result, f, indent=4, separators=(',',': '))
+ else:
+ yamlloader.dump(result, stream=f)
- with col.open(os.path.join("original", w[n+1:]), "wt") as f:
+ # Also store a verbatim copy of the original files
+ with col.open(os.path.join("original", w[len(prefix):]), "wt") as f:
f.write(text)
+ # Upload files referenced by $include directives, these are used
+ # unchanged and don't need to be updated.
for w in include_files:
- with col.open(w[n+1:], "wb") as f1:
- with col.open(os.path.join("original", w[n+1:]), "wb") as f3:
+ with col.open(w[len(prefix):], "wb") as f1:
+ with col.open(os.path.join("original", w[len(prefix):]), "wb") as f3:
with open(uri_file_path(w), "rb") as f2:
dat = f2.read(65536)
while dat:
f3.write(dat)
dat = f2.read(65536)
+ # Now collect metadata: the collection name and git properties.
toolname = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
if git_info and git_info.get("http://arvados.org/cwl#gitDescribe"):
toolname = "%s (%s)" % (toolname, git_info.get("http://arvados.org/cwl#gitDescribe"))
- toolfile = tool.tool["id"][n+1:]
+ toolfile = tool.tool["id"][len(prefix):]
properties = {
"type": "workflow",
p = g.split("#", 1)[1]
properties["arv:"+p] = git_info[g]
+ # Check if a collection with the same content already exists in the target project. If so, just use that one.
existing = arvRunner.api.collections().list(filters=[["portable_data_hash", "=", col.portable_data_hash()],
["owner_uuid", "=", arvRunner.project_uuid]]).execute(num_retries=arvRunner.num_retries)
+
if len(existing["items"]) == 0:
+ toolname = toolname.replace("/", " ")
col.save_new(name=toolname, owner_uuid=arvRunner.project_uuid, ensure_unique_name=True, properties=properties)
logger.info("Workflow uploaded to %s", col.manifest_locator())
else:
logger.info("Workflow uploaded to %s", existing["items"][0]["uuid"])
- adjustDirObjs(job_order, trim_listing)
- adjustFileObjs(job_order, trim_anonymous_location)
- adjustDirObjs(job_order, trim_anonymous_location)
-
- # now construct the wrapper
+ # Now that we've updated the workflow and saved it to a
+ # collection, we're going to construct a minimal "wrapper"
+ # workflow which consists of only of input and output parameters
+ # connected to a single step that runs the real workflow.
runfile = "keep:%s/%s" % (col.portable_data_hash(), toolfile)
if submit_runner_ram:
wf_runner_resources["ramMin"] = submit_runner_ram
+ # Remove a few redundant fields from the "job order" (aka input
+ # object or input parameters). In the situation where we're
+ # creating or updating a workflow record, any values in the job
+ # order get copied over as default values for input parameters.
+ adjustDirObjs(job_order, trim_listing)
+ adjustFileObjs(job_order, trim_anonymous_location)
+ adjustDirObjs(job_order, trim_anonymous_location)
+
newinputs = []
for i in main["inputs"]:
inp = {}
if hints:
wrapper["hints"] = hints
- # 1. check for SchemaDef
- # 2. do what pack does
- # 3. fix inputs
+ # Schema definitions (this lets you define things like record
+ # types) require a special handling.
+
+ for i, r in enumerate(wrapper["requirements"]):
+ if r["class"] == "SchemaDefRequirement":
+ wrapper["requirements"][i] = fix_schemadef(r, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, col.portable_data_hash())
+
+ update_refs(wrapper, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, main["id"]+"#", "#main/")
doc = {"cwlVersion": "v1.2", "$graph": [wrapper]}
for g in git_info:
doc[g] = git_info[g]
- for i, r in enumerate(wrapper["requirements"]):
- if r["class"] == "SchemaDefRequirement":
- wrapper["requirements"][i] = fix_schemadef(r, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, col.portable_data_hash())
-
- update_refs(wrapper, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, False, runtimeContext, main["id"]+"#", "#main/")
-
# Remove any lingering file references.
drop_ids(wrapper)
projects / arvados.git / blobdiff