automatically set calculation_file_uri

common/python/nomadcore/simple_parser.py

@@ -20,6 +20,9 @@ from nomadcore.unit_conversion import unit_conversion
 from nomadcore.caching_backend import CachingLevel, ActiveBackend
 from nomadcore.annotator import Annotator
 import io
+from future.standard_library import install_aliases
+install_aliases()
+from urllib.parse import urlparse, urlunparse
 
 logger = logging.getLogger("nomadcore.simple_parser")
 annotate = False
@@ -59,6 +62,16 @@ class PushbackLineFile(object):
         self.lines.append(line)
         self.lineNr -= 1
 
+def uriFromRelPath(baseUri, basePath, newPath):
+    """returns an uri corresponding to newPath assuming that base path has uri baseUri.
+This will never change the net location (archive)."""
+    p1 = os.path.normpath(os.path.abspath(basePath))
+    p2 = os.path.normpath(os.path.abspath(newPath))
+    rPath = os.path.relpath(p2,p1)
+    bUri = urlparse(baseUri)
+    nUri = bUri._replace(path = os.path.normpath(os.path.join(bUri.path, rPath)))
+    return urlunparse(nUri)
+
 class SimpleMatcher(object):
     """A Something that matches either a single line, or multiple lines grouped together.
     This is the base of a declarative parser."""
@@ -1071,8 +1084,8 @@ class SimpleParserBuilder(object):
             logger.info("Parsing tree after optimization:")
             self.rootMatcher.printParsingTree()
 
-    def buildParser(self, fIn, backend, superContext):
-        return SimpleParser(self, fIn, backend, superContext)
+    def buildParser(self, fIn, backend, superContext, baseUri, basePath):
+        return SimpleParser(self, fIn, backend, superContext, baseUri, basePath)
 
     def writeMatchers(self, outF, extraIndent = 0):
         outF.write("[")
@@ -1102,7 +1115,7 @@ class SimpleParserBuilder(object):
         outF.write("}")
 
 class SimpleParser(object):
-    def __init__(self, parserBuilder, fIn, backend, superContext = None):
+    def __init__(self, parserBuilder, fIn, backend, superContext = None, baseUri = None, basePath = None):
         self.parserBuilder = parserBuilder
         self.fIn = fIn
         self.backend = backend
@@ -1110,6 +1123,13 @@ class SimpleParser(object):
         self.skipped = 0
         self.superContext = superContext
         self.lastMatch = {}
+        self.baseUri = baseUri
+        self.basePath = basePath
+        if backend.sectionManagers is not None:
+            r=backend.sectionManagers.get("section_run")
+            if r:
+                r.onOpen.append(self.emitBaseUri)
+
         annofilename = None
         # by default, ignore empty lines in coverage analysis
         self.coverageIgnore = getattr(superContext, 'coverageIgnore',
@@ -1128,6 +1148,17 @@ class SimpleParser(object):
             for k,v in sorted(compiledRootMatcher.matcher.fixedStartValues.items()):
                 compiledRootMatcher.addValue(backend, k, v)
 
+    def uriForPath(self, path):
+        """return the uri corresponding to the given path"""
+        if self.baseUri and self.basePath and path:
+            return uriFromRelPath(self.baseUri, self.basePath, path)
+        return path
+
+    def emitBaseUri(self, backend, gIndex, section):
+        """writes out the uri to the sources"""
+        if self.baseUri:
+            backend.addValue("calculation_file_uri", self.baseUri)
+
     def enterInState(self, stateIndex):
         compiledMatcher = self.parserBuilder.compiledMatchers[stateIndex]
         sects = OrderedDict()
@@ -1285,9 +1316,9 @@ def compileParser(simpleParser, metaInfo, metaInfoToKeep, default_units=None, me
         logger.debug(s.getvalue())
     return parserBuilder
 
-def runParser(compiledParser, backend, superContext, fIn):
+def runParser(compiledParser, backend, superContext, fIn, uri, path):
     """parses the open file fIn with the given compiledParser into the backend using superContext as parser SuperContext"""
-    parser = compiledParser.buildParser(PushbackLineFile(fIn), backend, superContext = superContext)
+    parser = compiledParser.buildParser(PushbackLineFile(fIn), backend, superContext = superContext, baseUri = uri, basePath = path)
     try:
         superContext.startedParsing(fIn.name, parser)
     except AttributeError:
@@ -1301,7 +1332,7 @@ def defaultParseFile(parserInfo):
         with open(path, "r") as fIn:
             backend.startedParsingSession(uri, parserInfo)
             try:
-                parsingStats = runParser(parserBuilder, backend, superContext, fIn)
+                parsingStats = runParser(parserBuilder, backend, superContext, fIn, uri, path)
                 backend.finishedParsingSession(
                     "ParseSuccess", None,
                     parsingStats=parsingStats)
@@ -1538,6 +1569,7 @@ class AncillaryParser(object):
             parser: The mains parser that is already running. It is used to get the current metadata and backend.
             superContext: Context for the ancillary parser.
         """
+        self.mainParser = parser
         default_units = parser.parserBuilder.default_units
         metainfo_units = parser.parserBuilder.metainfo_units
         # compile parser
@@ -1568,7 +1600,10 @@ class AncillaryParser(object):
         Args:
             fIn: File that is parsed.
         """
-        runParser(self.compiledParser, self.backend, self.superContext, PushbackLineFile(fIn))
+        currentUri = self.mainParser.uriForPath(fIn.name)
+        if currentUri:
+            self.backend.superBackend.addValue("calculation_file_uri", currentUri)
+        runParser(self.compiledParser, self.backend, self.superContext, PushbackLineFile(fIn), self.mainParser.baseUri, self.mainParser.basePath)
 
 
 class ParserOptimizer(object):