diff --git a/src/caosadvancedtools/pandoc_header_tools.py b/src/caosadvancedtools/pandoc_header_tools.py
new file mode 100644
index 0000000000000000000000000000000000000000..6322da7ea71bba8e261f33f8e8a1d260e2971d6d
--- /dev/null
+++ b/src/caosadvancedtools/pandoc_header_tools.py
@@ -0,0 +1,240 @@
+#!/usr/bin/env python3
+
+# This is taken from the file manage_header.py
+# in a CaosDB management repository. The file manage_header.py
+# is not released yet, but creating a library might be useful.
+# A. Schlemmer, 04/2019
+
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+
+# Copyright (C) 2018 Research Group Biomedical Physics,
+# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+# ** end header
+# Tool to manage yaml header in markdown document
+# A. Schlemmer, 01/2019
+# D. Hornung 2019-02
+# T. Fitschen 2019-02
+
+import argparse
+import glob
+import os
+import re
+
+import yaml
+
+
+class NoValidHeader(Exception):
+ def __init__(self, filename, *args, **kwargs):
+ self.filename = filename
+ msg = ("Header missing in {}\nFix this with the modify subcommand "
+ "using -f option".format(filename))
+ super().__init__(msg, *args, **kwargs)
+
+class MetadataFileMissing(Exception):
+
+ def __init__(self, filename, *args, **kwargs):
+ self.filename = filename
+ msg = "Metadata file README.md missing in " + filename
+ super().__init__(msg, *args, **kwargs)
+
+class ParseErrorsInHeader(Exception):
+ def __init__(self, filename, reason, *args, **kwargs):
+ self.filename = filename
+ self.reason = reason
+ msg = "Invalid header in {}. Reason: {}".format(filename, reason)
+ super().__init__(msg, *args, **kwargs)
+
+TEMPLATEHEADER = """
+---
+responsible:
+description:
+...
+
+"""
+
+
+def get_header(filename, add_header=False):
+ """Open an md file identified by filename and read out the yaml
+header.
+
+filename can also be a folder. In this case folder/README.md will be used for
+getting the header.
+
+If a header is found a tuple is returned: (first yaml header line index, last+1
+yaml header line index, header)
+
+Otherwise, if `add_header` is True, a header is added and the function is called
+again.
+
+The header is normalized in the following way:
+
+- If the value to a key is a string, a list with that string as only element is
+ returned.
+
+From https://pandoc.org/MANUAL.html:
+
+A YAML metadata block is a valid YAML object, delimited by a line of three
+hyphens (---) at the top and a line of three hyphens (---) or three dots (...)
+at the bottom. A YAML metadata block may occur anywhere in the document, but if
+it is not at the beginning, it must be preceded by a blank line.
+
+ """
+
+ if os.path.isdir(filename):
+ filename = os.path.join(filename, "README.md")
+ if not os.path.exists(filename):
+ filename = filename[:-9]
+ filename = os.path.join(filename, "readme.md")
+ if not os.path.exists(filename):
+ raise MetadataFileMissing(filename)
+
+ with open(filename) as f:
+ textlines = f.readlines()
+
+ state = 0
+ found_0 = -1
+ found_1 = -1
+ found_2 = -1
+ for i, line in enumerate(textlines):
+ if len(line) == 1 and state in {-1, 0}:
+ found_0 = i
+ state = 0
+ continue
+ if line.rstrip() == "---" and state == 0:
+ found_1 = i+1
+ state = 1
+ continue
+ if (line.rstrip() == "..." or line.rstrip() == "---") and state == 1:
+ found_2 = i
+ state = 2
+ break
+ # Else: reset state to -1, unless it is 1 (in this case, leave it
+ # untouched
+ if state == 1:
+ pass
+ else:
+ state = -1
+
+ # If a header section was found:
+ if state == 2:
+ headerlines = []
+ for l in textlines[found_1:found_2]:
+ l = l.replace("\t", " ")
+ l = l.rstrip()
+ headerlines.append(l)
+ # try:
+ try:
+ yaml_part = yaml.load("\n".join(headerlines), Loader=yaml.BaseLoader)
+ except yaml.scanner.ScannerError as e:
+ raise ParseErrorsInHeader(filename, e)
+ # except yaml.error.MarkedYAMLError as e:
+ # raise NoValidHeader(filename)
+ if type(yaml_part) != dict:
+ raise NoValidHeader(filename)
+ return (found_1, found_2, clean_header(yaml_part))
+
+ if not add_header:
+ raise NoValidHeader(filename)
+ else:
+ print("Adding header in: {fn}".format(fn=filename))
+ add_header(filename)
+ return _get_header(filename)
+
+
+def save_header(filename, header_data):
+ """
+ Save a header identified by the tuple header_data to the file
+ identified by filename.
+
+ filename can also be a folder. In this case folder/README.md will
+ be used for getting the header.
+ """
+
+ if os.path.isdir(filename):
+ filename = os.path.join(filename, "README.md")
+
+ with open(filename) as f:
+ textlines = f.readlines()
+
+ while textlines[header_data[0]] != "...\n":
+ del textlines[header_data[0]]
+
+ data = header_data[2]
+ data = {key: val if len(val) > 1 else val[0] for key, val in data.items()}
+ textlines.insert(header_data[0],
+ yaml.dump(data,
+ default_flow_style=False,
+ allow_unicode=True))
+
+ with open(filename, "w") as f:
+ f.writelines(textlines)
+
+
+
+def add_header(filename, header_dict=None):
+ """
+ Add a header to an md file.
+
+ If the file does not exist it will be created.
+
+ If header_dict is a dictionary and not None the header
+ will be created based on the keys and values of that dictionary.
+ """
+
+ if os.path.isdir(filename):
+ filename = os.path.join(filename, "README.md")
+
+ if os.path.exists(filename):
+ with open(filename) as f:
+ textlines = f.readlines()
+ else:
+ textlines = ""
+
+ if header_dict is None:
+ localheader = TEMPLATEHEADER
+ else:
+ localheader = "---\n" + yaml.dump(header_dict,
+ default_flow_style=False,
+ allow_unicode=True) + "...\n"
+
+ with open(filename, "w") as f:
+ f.write(localheader)
+ f.writelines(textlines)
+
+
+def clean_header(header):
+ # Fill empty fields with empty string
+ for k, v in header.items():
+ if v == "null":
+ header[k] = ""
+ if v is None:
+ header[k] = ""
+
+ for k, v in header.items():
+ # Plain string is put into list
+ if type(v) == str:
+ header[k] = [v]
+
+ return header
+
+
+def kw_present(header, kw):
+ """
+ Check whether keywords are present in the header.
+ """
+ return kw in header and header[kw] is not None and len(header[kw]) > 0
diff --git a/src/caosadvancedtools/read_md_header.py b/src/caosadvancedtools/read_md_header.py
index c4c278cca9059a73069b306f4afd04645773768d..514117a42361cb43cf56ecceed3b708577e5e937 100644
--- a/src/caosadvancedtools/read_md_header.py
+++ b/src/caosadvancedtools/read_md_header.py
@@ -25,119 +25,125 @@
# ** end header
#
-import os
-import re
+from . import pandoc_header_tools
-import caosdb as db
-import yaml
+def get_header(fn):
+ return pandoc_header_tools.get_header(fn)[2]
-from .cfood import AbstractCFood, get_entity
-from .utils import string_to_person
+# import os
+# import re
+# import caosdb as db
+# import yaml
-def _clean_header(header):
- # Fill empty fields with empty string
+# from .cfood import AbstractCFood, get_entity
+# from .utils import string_to_person
- for k, v in header.items():
- if v == "null":
- header[k] = ""
+# TODO: I have an improved version of this tool in filesystemspecification.
- if v is None:
- header[k] = ""
+# def _clean_header(header):
+# # Fill empty fields with empty string
- for k, v in header.items():
- # Plain string is put into list
+# for k, v in header.items():
+# if v == "null":
+# header[k] = ""
- if type(v) == str:
- header[k] = [v]
+# if v is None:
+# header[k] = ""
- return header
+# for k, v in header.items():
+# # Plain string is put into list
+# if type(v) == str:
+# header[k] = [v]
-class NoValidHeader(Exception):
- pass
+# return header
-def get_header(filename):
- """Open an md file identified by filename and read out the yaml
-header.
+# class NoValidHeader(Exception):
+# pass
-filename can also be a folder. In this case folder/readme.md will be used for
-getting the header.
-If a header is found a tuple is returned: (first yaml header line index, last+1
-yaml header line index, header)
+# def get_header(filename):
+# """Open an md file identified by filename and read out the yaml
+# header.
-Otherwise, if `add_header` is True, a header is added and the function is called
-again.
+# filename can also be a folder. In this case folder/readme.md will be used for
+# getting the header.
-The header is normalized in the following way:
+# If a header is found a tuple is returned: (first yaml header line index, last+1
+# yaml header line index, header)
-- If the value to a key is a string, a list with that string as only element is
- returned.
+# Otherwise, if `add_header` is True, a header is added and the function is called
+# again.
-From https://pandoc.org/MANUAL.html:
+# The header is normalized in the following way:
-A YAML metadata block is a valid YAML object, delimited by a line of three
-hyphens (---) at the top and a line of three hyphens (---) or three dots (...)
-at the bottom. A YAML metadata block may occur anywhere in the document, but if
-it is not at the beginning, it must be preceded by a blank line.
+# - If the value to a key is a string, a list with that string as only element is
+# returned.
- """
+# From https://pandoc.org/MANUAL.html:
- if os.path.isdir(filename):
- filename = os.path.join(filename, "readme.md")
+# A YAML metadata block is a valid YAML object, delimited by a line of three
+# hyphens (---) at the top and a line of three hyphens (---) or three dots (...)
+# at the bottom. A YAML metadata block may occur anywhere in the document, but if
+# it is not at the beginning, it must be preceded by a blank line.
- with open(filename) as f:
- textlines = f.readlines()
+# """
- state = 0
- found_0 = -1
- found_1 = -1
- found_2 = -1
+# if os.path.isdir(filename):
+# filename = os.path.join(filename, "readme.md")
- for i, line in enumerate(textlines):
- if len(line) == 1 and state in {-1, 0}:
- found_0 = i
- state = 0
+# with open(filename) as f:
+# textlines = f.readlines()
- continue
+# state = 0
+# found_0 = -1
+# found_1 = -1
+# found_2 = -1
- if line.rstrip() == "---" and state == 0:
- found_1 = i+1
- state = 1
+# for i, line in enumerate(textlines):
+# if len(line) == 1 and state in {-1, 0}:
+# found_0 = i
+# state = 0
- continue
+# continue
- if line.rstrip() == "..." and state == 1:
- found_2 = i
- state = 2
+# if line.rstrip() == "---" and state == 0:
+# found_1 = i+1
+# state = 1
- break
- # Else: reset state to -1, unless it is 1 (in this case, leave it
- # untouched
+# continue
- if state == 1:
- pass
- else:
- state = -1
+# if line.rstrip() == "..." and state == 1:
+# found_2 = i
+# state = 2
- # If a header section was found:
+# break
+# # Else: reset state to -1, unless it is 1 (in this case, leave it
+# # untouched
- if state == 2:
- headerlines = []
+# if state == 1:
+# pass
+# else:
+# state = -1
- for l in textlines[found_1:found_2]:
- l = l.replace("\t", " ")
- l = l.rstrip()
- headerlines.append(l)
- try:
- yaml_part = yaml.load("\n".join(headerlines))
- except yaml.error.MarkedYAMLError as e:
- # print("Error in file {}:".format(filename))
- # print(headerlines)
- raise NoValidHeader(filename)
+# # If a header section was found:
- return _clean_header(yaml_part)
+# if state == 2:
+# headerlines = []
- raise NoValidHeader(filename)
+# for l in textlines[found_1:found_2]:
+# l = l.replace("\t", " ")
+# l = l.rstrip()
+# headerlines.append(l)
+# try:
+# yaml_part = yaml.load("\n".join(headerlines))
+# except yaml.error.MarkedYAMLError as e:
+# # print("Error in file {}:".format(filename))
+# # print(headerlines)
+# raise NoValidHeader(filename)
+
+# return _clean_header(yaml_part)
+
+# raise NoValidHeader(filename)