From d422d711a6cf9d58fc339ca49c250fd8282f8e49 Mon Sep 17 00:00:00 2001 From: Fawzi Mohamed Date: Tue, 2 Aug 2016 15:08:20 +0200 Subject: [PATCH] first skeleton for the elk parser --- .gitignore | 54 +++++++++++++++ parser/parser-elk/parser_elk.py | 69 +++++++++++++++++++ parser/parser-elk/setup_paths.py | 6 ++ .../eu/nomad_lab/parsers/ElkParser.scala | 42 +++++++++++ .../eu/nomad_lab/parsers/ElkParserSpec.scala | 14 ++++ test/examples/README.md | 1 + 6 files changed, 186 insertions(+) create mode 100644 .gitignore create mode 100644 parser/parser-elk/parser_elk.py create mode 100644 parser/parser-elk/setup_paths.py create mode 100644 src/main/scala/eu/nomad_lab/parsers/ElkParser.scala create mode 100644 src/test/scala/eu/nomad_lab/parsers/ElkParserSpec.scala create mode 100644 test/examples/README.md diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a6cb8b6 --- /dev/null +++ b/.gitignore @@ -0,0 +1,54 @@ +# use glob syntax. +syntax: glob +*.ser +*.class +*~ +*.bak +#*.off +*.old +*.pyc +*.bk +*.swp +.DS_Store + +# logging files +detailed.log + +# eclipse conf file +.settings +.classpath +.project +.manager +.scala_dependencies + +# idea +.idea +*.iml + +# building +target +build +null +tmp* +temp* +dist +test-output +build.log + +# other scm +.svn +.CVS +.hg* + +# switch to regexp syntax. +# syntax: regexp +# ^\.pc/ + +#SHITTY output not in target directory +build.log + +#emacs TAGS +TAGS + +lib/ +env/ diff --git a/parser/parser-elk/parser_elk.py b/parser/parser-elk/parser_elk.py new file mode 100644 index 0000000..845d11f --- /dev/null +++ b/parser/parser-elk/parser_elk.py @@ -0,0 +1,69 @@ +from builtins import object +import setup_paths +from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel +from nomadcore.simple_parser import SimpleMatcher as SM +from nomadcore.local_meta_info import loadJsonFile, InfoKindEl +import os, sys, json + +class ElkContext(object): + """context for elk parser""" + + def __init__(self): + self.parser = None + + def initialize_values(self): + """allows to reset values if the same superContext is used to parse different files""" + self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv + + def startedParsing(self, path, parser): + """called when parsing starts""" + self.parser = parser + # allows to reset values if the same superContext is used to parse different files + self.initialize_values() + +# description of the input +mainFileDescription = SM( + name = 'root', + weak = True, + startReStr = "", + subMatchers = [ + SM(name = 'newRun', + startReStr = r"\s*:LABEL[0-9]+: using WIEN2k_(?:[0-9.]+) \(Release (?:[0-9/.]+)\) in ", + repeats = True, + required = True, + forwardMatch = True, + sections = ['section_run', 'section_method', 'section_system', 'section_single_configuration_calculation'], + subMatchers = [ + SM( + name = 'header', + startReStr = r"\s*:LABEL[0-9]+: using WIEN2k_(?P[0-9.]+) \(Release (?P[0-9/.]+)\) in ", + sections=["x_wien2k_header"], + fixedStartValues={'program_name': 'WIEN2k', 'program_basis_set_type': '(L)APW+lo' } + ), SM( + name = "scf iteration", + startReStr = r"\s*:ITE(?P[0-9]+):\s*[0-9]*. ITERATION", + sections=["section_scf_iteration"], + repeats = True, + subMatchers=[ + SM(r":NATO :\s*(?P[0-9]+)INDEPENDENT AND\s*(?P[0-9]+)\s*TOTAL ATOMS IN UNITCELL"), + SM(r"\s*SUBSTANCE: (?P.*)"), + SM(r":POT\s*:\s*POTENTIAL OPTION\s*(?P[0-9]+)"), + SM(r":VOL\s*:\s*UNIT CELL VOLUME\s*=\s*(?P[0-9.]+)") + ] + ) + ] + ) + ]) + +# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json + +parserInfo = { + "name": "Elk" +} + +metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/elk.nomadmetainfo.json")) +metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None) + +if __name__ == "__main__": + superContext = ElkContext() + mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext) diff --git a/parser/parser-elk/setup_paths.py b/parser/parser-elk/setup_paths.py new file mode 100644 index 0000000..e0a0fb0 --- /dev/null +++ b/parser/parser-elk/setup_paths.py @@ -0,0 +1,6 @@ +import sys, os, os.path +baseDir = os.path.dirname(os.path.abspath(__file__)) +commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python")) + +if not commonDir in sys.path: + sys.path.insert(0, commonDir) diff --git a/src/main/scala/eu/nomad_lab/parsers/ElkParser.scala b/src/main/scala/eu/nomad_lab/parsers/ElkParser.scala new file mode 100644 index 0000000..be23be3 --- /dev/null +++ b/src/main/scala/eu/nomad_lab/parsers/ElkParser.scala @@ -0,0 +1,42 @@ +package eu.nomad_lab.parsers + +import eu.nomad_lab +import eu.nomad_lab.DefaultPythonInterpreter +import org.{ json4s => jn } +import eu.{ nomad_lab => lab } +import scala.collection.breakOut + +object ElkParser extends SimpleExternalParserGenerator( + name = "ElkParser", + parserInfo = jn.JObject( + ("name" -> jn.JString("Elk")) :: + ("parserId" -> jn.JString("Elk" + lab.ElkVersionInfo.version)) :: + ("versionInfo" -> jn.JObject( + ("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map { + case (k, v) => k -> jn.JString(v.toString) + }(breakOut): List[(String, jn.JString)])) :: + (lab.ElkVersionInfo.toMap.map { + case (key, value) => + (key -> jn.JString(value.toString)) + }(breakOut): List[(String, jn.JString)]) + )) :: Nil + ), + mainFileTypes = Seq("text/.*"), + mainFileRe = """:LABEL[0-9]+: using WIEN2k_(?[0-9.]+) \(Release (?[0-9/.]+)\) in """.r, + cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/elk/parser/parser-elk/parser_elk.py", + "--uri", "${mainFileUri}", "${mainFilePath}"), + resList = Seq( + "parser-elk/parser_elk.py", + "parser-elk/setup_paths.py", + "nomad_meta_info/public.nomadmetainfo.json", + "nomad_meta_info/common.nomadmetainfo.json", + "nomad_meta_info/meta_types.nomadmetainfo.json", + "nomad_meta_info/elk.nomadmetainfo.json" + ) ++ DefaultPythonInterpreter.commonFiles(), + dirMap = Map( + "parser-elk" -> "parsers/elk/parser/parser-elk", + "nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info", + "python" -> "python-common/common/python/nomadcore" + ) ++ DefaultPythonInterpreter.commonDirMapping(), + metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.elk) +) diff --git a/src/test/scala/eu/nomad_lab/parsers/ElkParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/ElkParserSpec.scala new file mode 100644 index 0000000..eccb411 --- /dev/null +++ b/src/test/scala/eu/nomad_lab/parsers/ElkParserSpec.scala @@ -0,0 +1,14 @@ +package eu.nomad_lab.parsers + +import org.specs2.mutable.Specification + +object ElkTests extends Specification { + "ElkParserTest" >> { + "test with json-events" >> { + ParserRun.parse(Wien2kParser, "parsers/elk/test/examples/ok/ok.scf", "json-events") must_== ParseResult.ParseSuccess + } + "test with json" >> { + ParserRun.parse(Wien2kParser, "parsers/elk/test/examples/ok/ok.scf", "json") must_== ParseResult.ParseSuccess + } + } +} diff --git a/test/examples/README.md b/test/examples/README.md new file mode 100644 index 0000000..aee68a4 --- /dev/null +++ b/test/examples/README.md @@ -0,0 +1 @@ +sample files to test the parser -- GitLab