diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..94a25f7f4cb416c083d265558da75d457237d671
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="VcsDirectoryMappings">
+ <mapping directory="$PROJECT_DIR$" vcs="Git" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/geosteering-out.html b/geosteering-out.html
new file mode 100644
index 0000000000000000000000000000000000000000..c978999aafc42d68e7cd8f5b0dea9102d8663b80
--- /dev/null
+++ b/geosteering-out.html
@@ -0,0 +1,66 @@
+\ecvitem{\highlight{Publications}}{Journal Articles}
+<center> <table class="submit-table" id="deadlines">
+ <tr> <td>Authors</td><td> Wilson A. </td></tr>
+ <tr> <td>Title</td><td> New Geosteering Work Flow Integrates Real-Time Measurements With Geomodels </td></tr>
+<tr> <td>Source</td> <td> Journal of Petroleum Technology </td> </tr>
+<tr> <td>Publication Date</td> <td> 2018 </td> </tr>
+<tr> <td>URL</td> <td> <a href="https://www.spe.org/en/jpt/jpt-article-detail/?art=4530">https://www.spe.org/en/jpt/jpt-article-detail/?art=4530</a> </td> </tr>
+</table> </center>
+
+<center> <table class="submit-table" id="deadlines">
+ <tr> <td>Authors</td><td> Jakobsen M., and Tveit S. </td></tr>
+ <tr> <td>Title</td><td> Distorted Born iterative T-matrix method for inversion of CSEM data in anisotropic media </td></tr>
+<tr> <td>Source</td> <td> Geophysical Journal International </td> </tr>
+<tr> <td>Publication Date</td> <td> 2018 </td> </tr>
+<tr> <td>URL</td> <td> <a href="http://dx.doi.org/10.1093/gji/ggy197">http://dx.doi.org/10.1093/gji/ggy197</a> </td> </tr>
+</table> </center>
+
+\ecvitem{\highlight{Other publications}}{}
+<center> <table class="submit-table" id="deadlines">
+ <tr> <td>Authors</td><td> Sergey Alyaev, Erich Suter, Reidar Bratvold, Aojie Hong, and Xiaodong Luo </td></tr>
+ <tr> <td>Title</td><td> A Decision Support System for Multi-target Geosteering </td></tr>
+<tr> <td>Source</td> <td> </td> </tr>
+<tr> <td>Publication Date</td> <td> 2019 </td> </tr>
+<tr> <td>URL</td> <td> <a href="https://arxiv.org/abs/1903.03933">https://arxiv.org/abs/1903.03933</a> </td> </tr>
+</table> </center>
+
+<center> <table class="submit-table" id="deadlines">
+ <tr> <td>Authors</td><td> Suter E., KÃ¥rstad T., Escalona A., A. Friis H., Vefring E., and Alyaev S. </td></tr>
+ <tr> <td>Title</td><td> A Methodology for Effective Earth Model Management while Geosteering </td></tr>
+<tr> <td>Source</td> <td> Second EAGE/SPE Geosteering and Well Placement Workshop </td> </tr>
+<tr> <td>Publication Date</td> <td> 2018 </td> </tr>
+<tr> <td>URL</td> <td> <a href="http://dx.doi.org/10.3997/2214-4609.201803215">http://dx.doi.org/10.3997/2214-4609.201803215</a> </td> </tr>
+</table> </center>
+
+<center> <table class="submit-table" id="deadlines">
+ <tr> <td>Authors</td><td> Sommer M., and Jakobsen M. </td></tr>
+ <tr> <td>Title</td><td> Towards a Fast Integral Equation Method for Inversion of Electromagnetic Data </td></tr>
+<tr> <td>Source</td> <td> Second EAGE/SPE Geosteering and Well Placement Workshop </td> </tr>
+<tr> <td>Publication Date</td> <td> 2018 </td> </tr>
+<tr> <td>URL</td> <td> <a href="http://dx.doi.org/10.3997/2214-4609.201803216">http://dx.doi.org/10.3997/2214-4609.201803216</a> </td> </tr>
+</table> </center>
+
+<center> <table class="submit-table" id="deadlines">
+ <tr> <td>Authors</td><td> Alyaev S., Bratvold R.B., Luo X., Suter E., Vefring E.H., and others </td></tr>
+ <tr> <td>Title</td><td> An Interactive Decision Support System for Geosteering Operations </td></tr>
+<tr> <td>Source</td> <td> in SPE Norway One Day Seminar </td> </tr>
+<tr> <td>Publication Date</td> <td> 2018 </td> </tr>
+<tr> <td>URL</td> <td> <a href="http://dx.doi.org/10.2118/191337-MS">http://dx.doi.org/10.2118/191337-MS</a> </td> </tr>
+</table> </center>
+
+<center> <table class="submit-table" id="deadlines">
+ <tr> <td>Authors</td><td> Alyaev S., Suter E., Bratvold R., Vefring E., and Jahani N. </td></tr>
+ <tr> <td>Title</td><td> Ensemble-based decision-support workflow for operational geosteering </td></tr>
+<tr> <td>Source</td> <td> Second EAGE/SPE Geosteering and Well Placement Workshop </td> </tr>
+<tr> <td>Publication Date</td> <td> 2018 </td> </tr>
+<tr> <td>URL</td> <td> <a href="http://dx.doi.org/10.3997/2214-4609.201803140">http://dx.doi.org/10.3997/2214-4609.201803140</a> </td> </tr>
+</table> </center>
+
+<center> <table class="submit-table" id="deadlines">
+ <tr> <td>Authors</td><td> Alyaev S., Hong A., and B Bratvold R. </td></tr>
+ <tr> <td>Title</td><td> Are you myopic, naive or farsighted about your geosteering decisions? </td></tr>
+<tr> <td>Source</td> <td> Second EAGE/SPE Geosteering and Well Placement Workshop </td> </tr>
+<tr> <td>Publication Date</td> <td> 2018 </td> </tr>
+<tr> <td>URL</td> <td> <a href="http://dx.doi.org/10.3997/2214-4609.201803217">http://dx.doi.org/10.3997/2214-4609.201803217</a> </td> </tr>
+</table> </center>
+
diff --git a/geosteering.bib b/geosteering.bib
new file mode 100644
index 0000000000000000000000000000000000000000..aeb111fcf2a48fdaf8bfe6a2181656704abd9d3d
--- /dev/null
+++ b/geosteering.bib
@@ -0,0 +1,71 @@
+@article{jakobsen2018distorted,
+ title={Distorted Born iterative T-matrix method for inversion of CSEM data in anisotropic media},
+ author={Jakobsen, Morten and Tveit, Svenn},
+ journal={Geophysical Journal International},
+ volume={214},
+ number={3},
+ pages={1524--1537},
+ year={2018},
+ publisher={Oxford University Press},
+ doi = {10.1093/gji/ggy197}
+}
+@article{wilson2018new,
+ title={New Geosteering Work Flow Integrates Real-Time Measurements With Geomodels},
+ author={Wilson, Adam},
+ journal={Journal of Petroleum Technology},
+ volume={70},
+ number={09},
+ pages={102--105},
+ year={2018},
+ publisher={Society of Petroleum Engineers},
+ url = {https://www.spe.org/en/jpt/jpt-article-detail/?art=4530}
+}
+@inproceedings{sommer2018eage,
+ title={Towards a Fast Integral Equation Method for Inversion of Electromagnetic Data},
+ author={Sommer, M. and Jakobsen, M.},
+ journal={Second EAGE/SPE Geosteering and Well Placement Workshop },
+ year={2018},
+ publisher={SPE, EAGE},
+ doi = {10.3997/2214-4609.201803216}
+}
+@inproceedings{suter2018eage,
+ title={A Methodology for Effective Earth Model Management while Geosteering},
+ author={Suter, E. and KÃ¥rstad, T. and Escalona, A. and A. Friis, H. and Vefring, E. and Alyaev, S.},
+ journal={Second EAGE/SPE Geosteering and Well Placement Workshop },
+ year={2018},
+ publisher={SPE, EAGE},
+ doi = {10.3997/2214-4609.201803215}
+}
+@inproceedings{alyaev2018eage,
+ title={Are you myopic, naive or farsighted about your geosteering decisions?},
+ author={Alyaev, S. and Hong, A and B Bratvold, R.},
+ journal={Second EAGE/SPE Geosteering and Well Placement Workshop },
+ year={2018},
+ publisher={SPE, EAGE},
+ doi = {10.3997/2214-4609.201803217}
+}
+@inproceedings{alyaev2018eageposter,
+ title={Ensemble-based decision-support workflow for operational geosteering},
+ author={Alyaev, S. and Suter, E and Bratvold, R. and Vefring, E. and Jahani, N.},
+ journal={Second EAGE/SPE Geosteering and Well Placement Workshop },
+ year={2018},
+ publisher={SPE, EAGE},
+ doi = {10.3997/2214-4609.201803140}
+}
+@misc{alyaev2019decision,
+ title={A Decision Support System for Multi-target Geosteering},
+ author={Sergey Alyaev and Erich Suter and Reidar Bratvold and Aojie Hong and Xiaodong Luo},
+ year={2019},
+ eprint={1903.03933},
+ archivePrefix={arXiv},
+ primaryClass={cs.CE},
+ url={https://arxiv.org/abs/1903.03933}
+}
+@inproceedings{alyaev2018interactive,
+ title={An Interactive Decision Support System for Geosteering Operations},
+ author={Alyaev, Sergey and Bratvold, Reidar Brumer and Luo, Xiaodong and Suter, Erich and Vefring, Erlend H and others},
+ booktitle={SPE Norway One Day Seminar},
+ year={2018},
+ organization={Society of Petroleum Engineers},
+ doi={10.2118/191337-MS}
+}
diff --git a/parser.py b/parser.py
new file mode 100644
index 0000000000000000000000000000000000000000..e1686117d7fa152ff983d78638dcf4f79d3abb96
--- /dev/null
+++ b/parser.py
@@ -0,0 +1,497 @@
+__author__ = 'Sergey Alyaev'
+
+"""Collect command-line options in a dictionary"""
+
+
+def getopts(argv):
+ opts = {} # Empty dictionary to store key-value pairs.
+ while argv: # While there are arguments left to parse...
+ if argv[0][0] == '-': # Found a "-name value" pair.
+ opts[argv[0]] = argv[1] # Add key and value to the dictionary.
+ argv = argv[1:] # Reduce the argument list by copying it starting from index 1.
+ return opts
+
+
+
+class bibentry(object):
+
+ #staic
+ label_to_abbrev = dict()
+ abbreviations = set()
+
+ def __init__(self, entry_type, entry_label = None):
+ self.entry_type = entry_type
+ self.entry_label = entry_label
+ self.fields = dict()
+ self.abbr = None
+
+ def __str__(self):
+ return self.entry_label + ":[" + self.entry_type + "]"
+
+ def __repr__(self):
+ return self.__str__()
+
+ def strip_author_name(self, author_name, abbreviate=True, ceparator_space=' '):
+ """
+ Makes name to desired format
+ :param author_name:
+ :param abbreviate:
+ :return:
+ """
+ if abbreviate:
+ name_parts = author_name.split(',')
+ out = name_parts[0].strip()
+ if len(name_parts)>1:
+ out += ceparator_space
+ name_parts = name_parts[1].split(' ')
+ for i in range(len(name_parts)):
+ if len(name_parts[i].strip())>0:
+ out += name_parts[i].strip()[0]+'.'
+ return out
+ else:
+ return author_name.strip()
+
+
+
+
+ def get_authors(self, max_authors=3, abbreviate=True, ceparator_space=' '):
+ """
+
+ :param max_authors:
+ :return:
+ """
+ out = ""
+ if 'author' in self.fields:
+ authors = self.fields['author'].split(' and ')
+ total_len = len(authors)
+ if total_len <= 1:
+ out += self.strip_author_name(authors[0], abbreviate)
+ elif (total_len > max_authors+1):
+ for i in range(max_authors-1):
+ out += self.strip_author_name(authors[i], abbreviate)+", "
+ out += self.strip_author_name(authors[max_authors-1], abbreviate)+" et" + ceparator_space +"al."
+ else:
+ for i in range(total_len-1):
+ out += self.strip_author_name(authors[i], abbreviate)+", "
+ out += "and " + self.strip_author_name(authors[total_len-1], abbreviate)
+ else:
+ out = 'x'
+ return out
+
+
+ def get_year(self):
+ """
+
+ :return:
+ """
+ out = ''
+ if 'year' in self.fields:
+ out += (self.fields['year'].strip())
+ return out
+
+ def get_title(self):
+ """
+
+ :return:
+ """
+ out = ''
+ if 'title' in self.fields:
+ out += (self.fields['title'].strip())
+ return out
+
+ url_prefix = 'URL '
+ doi_prefix = 'http://dx.doi.org/'
+
+ def get_url_html(self, prefer_doi = True):
+ """
+
+ :return:
+ """
+ out = ''
+ added = False
+ if 'url' in self.fields:
+ out = self.fields['url']
+ added = True
+ if 'doi' in self.fields:
+ if (not added) or prefer_doi:
+ out = self.doi_prefix+self.fields['doi']
+ return out
+
+ def get_url(self, url_enviorment, prefer_doi = True):
+ """
+
+ :return:
+ """
+ out = ''
+ added = False
+ if 'url' in self.fields:
+ out = self.url_prefix + url_enviorment+'{'+ self.fields['url']+'}'
+ added = True
+ if 'doi' in self.fields:
+ if (not added) or prefer_doi:
+ out = self.url_prefix + url_enviorment+'{'+self.doi_prefix+self.fields['doi'] +'}'
+ return out
+
+
+ def get_publisher(self, always_with_publisher=False):
+ """
+ gets the publisher e.g. journal
+ :return:
+ """
+ out = ''
+ if self.entry_type.lower().find('mastersthesis')>=0:
+ out += 'Master\'s thesis. '
+ if 'school' in self.fields:
+ out += self.fields['school']
+ elif self.entry_type.lower().find('phdthesis')>=0:
+ out += 'PhD thesis. '
+ if 'school' in self.fields:
+ out += self.fields['school']
+ elif self.entry_type.lower().find('techreport')>=0:
+ out += 'Technical report. '
+ if 'institution' in self.fields:
+ out += self.fields['institution']
+ elif 'journal' in self.fields:
+ if self.entry_type.lower() == 'unpublished':
+ out += "submitted to "
+ out += self.fields['journal']
+ elif 'booktitle' in self.fields:
+ out += 'in '+ self.fields['booktitle']
+ elif 'note' in self.fields:
+ out += self.fields['note']
+
+ if always_with_publisher or len(out)==0:
+ if 'publisher' in self.fields:
+ out += ' (' + self.fields['publisher']+')'
+ elif 'organization' in self.fields:
+ out += ' (' + self.fields['organization']+')'
+ #elif 'institution' in self.fields:
+ # out += ' (' + self.fields['institution']+')'
+
+ if (len(out)>0):
+ return out
+ else:
+ return ''
+
+ def get_abbreviation(self):
+ """
+ :return abbreviation
+ """
+ #TODO test for multiple of the same to work correctly
+ if self.label_to_abbrev.has_key(self.entry_label):
+ return self.label_to_abbrev[self.entry_label]
+ abbr = ''
+ if 'author' in self.fields:
+ authors = self.fields['author'].split(' and ')
+ for a in authors:
+ abbr += a[0]
+ else:
+ abbr = 'x'
+ if 'year' in self.fields:
+ abbr += self.fields['year']
+ if abbr in self.abbreviations:
+ abbr += 'a'
+ while abbr in self.abbreviations:
+ abbr[len(abbr)] = chr(int(abbr[len(abbr)])+1)
+ self.label_to_abbrev[self.entry_label] = abbr
+ self.abbreviations.add(abbr)
+ return abbr
+
+
+
+
+
+
+def find_first_outer_brackets(st):
+ """
+ :param st:
+ :return: finds closing "{}" paranthesis non-matching
+ """
+ opened = 0
+ open_b = -1
+ index = 0
+ while index < len(st):
+ c = st[index]
+ if (c == '{'):
+ opened +=1
+ if open_b == -1:
+ open_b = index
+ if (c == '}'):
+ opened -=1
+ if opened == 0:
+ close_b = index
+ return open_b, close_b
+ if (c == '\\'):
+ index += 1
+ if opened < 0:
+ print("Incorrect parenthesis in ", st)
+ return -1, -1
+ index+=1
+ print("No bracket pairs found ", st)
+ return -1, -1
+
+def populate_entry(entry, st):
+ clean = st.strip()
+ comma_pos = clean.find(',')
+ entry.entry_label = clean[0:comma_pos]
+ while True:
+ clean = clean[comma_pos+1:].strip()
+ p_in, p_out = find_first_outer_brackets(clean)
+ if (p_in<0 or p_out<0):
+ break
+ eq_ind = clean.find('=', 0, p_in)
+ key = clean[0:eq_ind].strip()
+ value = clean[p_in+1:p_out].strip()
+ entry.fields[key] = value
+ comma_pos = clean.find(',', p_out)
+ if comma_pos < 0:
+ break
+
+
+def check_person(entry, person):
+ """
+ checks if the person is the author of the entry
+ :param entry:
+ :param person:
+ :return:
+ """
+ if person == None:
+ return True
+ if 'author' in entry.fields:
+ if entry.fields['author'].find(person) >= 0:
+ return True
+ return False
+
+
+def find_entries(st, person_name = None):
+ entries = []
+ while True:
+ index = st.find('@')
+ if index==-1:
+ break
+ st = st[index:]
+ b_in, b_out = find_first_outer_brackets(st)
+
+ #print(st[b_in+1:b_out ])
+ entry = bibentry(st[1:b_in])
+ populate_entry(entry, st[b_in+1:b_out])
+ if check_person(entry, person_name):
+ entries.append(entry)
+ st = st[b_out+1:]
+
+ return entries
+
+
+def parse_bib_file(filename, person_name):
+ file = open(filename, 'r')
+ lines = file.readlines()
+ st = ''
+ for line in lines:
+ st += line
+ file.close()
+ return find_entries(st, person_name)
+
+
+def get_sorting(entry):
+ """
+
+ :param entry: bib entry
+ :return: gets 'year'
+ """
+ if 'year' in entry.fields:
+ if 'author' in entry.fields:
+ return entry.fields['year'], entry.fields['author']
+ else:
+ return entry.fields['year'], "ZZZ"
+ else:
+ return '0000', "ZZZ"
+
+def get_year(entry):
+ """
+
+ :param entry: bib entry
+ :return: gets 'year'
+ """
+ if 'year' in entry.fields:
+ return entry.fields['year']
+ else:
+ return '0000'
+
+
+
+
+# "\\providecommand{\\url}[1]{\\texttt{#1}}\n" \
+file_prefix = "\\providecommand{\\urlprefix}{URL }\n"
+file_suffix = "\n"
+
+def entry_to_tex(entry):
+ """
+
+ :param entry:
+ :return:
+ """
+ s ="<center> <table class=\"submit-table\" id=\"deadlines\"> \n " \
+ "<tr> " \
+ " <td>Authors</td>" \
+ "<td> {0} </td>" \
+ "</tr> \n " \
+ "<tr> " \
+ " <td>Title</td>" \
+ "<td> {4} </td>" \
+ "</tr> \n" \
+ "<tr> " \
+ " <td>Source</td> " \
+ " <td> {1} </td> " \
+ "</tr> \n" \
+ "<tr> " \
+ " <td>Publication Date</td> " \
+ " <td> {2} </td> " \
+ "</tr> \n" \
+ "<tr> " \
+ " <td>URL</td> " \
+ " <td> <a href=\"{3}\">{3}</a> </td> " \
+ "</tr> \n" \
+ "</table> </center> \n \n".format(entry.get_authors(max_authors=100),
+ entry.get_publisher(False),
+ entry.get_year(),
+ entry.get_url_html(prefer_doi=True),
+ entry.get_title())
+ # s = '\\paperecvitem{'
+ # s += "\\label{" + entry.entry_label + "}"
+ # s += entry.get_authors()
+ # s += " ("+entry.get_year()+")"
+ # s += "}"
+ # s += "{"
+ # s += "\\highlight{"
+ # s += entry.get_title()
+ # s += ",} "
+ # s += entry.get_publisher(False) +' '
+ # s += entry.get_url(url_enviorment='\\url',prefer_doi=True)
+ # s += "}\n"
+ #+"}{"+"}"
+ return s
+
+
+def default_entry_filter(entry):
+ """
+ returns True
+ :param entry:
+ :return:
+ """
+ return True
+
+
+def compare_entry_filter_type(entry, type=''):
+ """
+
+ :param entry:
+ :param type:
+ :return:
+ """
+ if entry.entry_type.lower() == type.lower():
+ return True
+ return False
+
+
+def write_file_default(file, entries, entry_filter=default_entry_filter,
+ prefix='', suffix='', written=set()):
+ """
+
+ :param filename: name of a file
+ :param entries: collection of bibentries
+ :return: returns set of written items
+ """
+
+ #check if there is at lest one entry
+ count = 0
+ for entry in entries:
+ if entry_filter(entry) and (not entry in written):
+ count += 1
+ if count == 0:
+ return written
+
+ file.write(prefix)
+ #write entries
+ for entry in entries:
+ if entry_filter(entry) and (not entry in written):
+ file.write(entry_to_tex(entry))
+ written.add(entry)
+ #write suffix
+ file.write(suffix)
+
+ return written
+
+
+
+
+
+if __name__ == '__main__':
+ from sys import argv
+
+ my_args = getopts(argv)
+ if '-f' in my_args: # Example usage.
+ filename = my_args['-f']
+ print("Processing file: ", filename)
+ print(my_args)
+ else:
+ print("Usage ... -f filename -o output_file_name -p author_family_name")
+ exit()
+
+ person_name = None
+ if '-p' in my_args:
+ person_name = my_args['-p']
+ print("Filtering person: ", person_name)
+
+ entries = parse_bib_file(filename, person_name)
+ sorted_entries = sorted(entries, key=get_sorting, reverse=True)
+ #sorted_entries contain all the input
+ for entry in sorted_entries:
+ print(entry)
+
+ output_file_name = 'publications.tex'
+ if '-o' in my_args:
+ output_file_name = my_args['-o']
+ print("Outputting to: ", output_file_name)
+
+
+ file = open(output_file_name, 'w')
+ #write prefix
+
+ # file.write(file_prefix)
+ #writting out articles
+ def filter_articles(entry):
+ return compare_entry_filter_type(entry, type='article')
+
+
+ #initializing a set of written items
+ written = set()
+
+ written = write_file_default(file, sorted_entries,
+ entry_filter=filter_articles,
+ prefix='\\ecvitem{\\highlight{Publications}}{Journal Articles}\n',
+ written=written)
+
+ #writting out articles
+ def filter_exclude_reports(entry):
+ return not compare_entry_filter_type(entry, type='TechReport')
+
+ write_file_default(file, sorted_entries,
+ entry_filter=filter_exclude_reports,
+ prefix='\\ecvitem{\\highlight{Other publications}}{}\n',
+ written=written)
+
+ #writting out articles
+ def filter_reports(entry):
+ return compare_entry_filter_type(entry, type='TechReport')
+
+ write_file_default(file, sorted_entries,
+ entry_filter=filter_reports,
+ prefix='\\ecvitem{\\highlight{Technical Reports}}{}\n',
+ written=written)
+
+
+ # file.write(file_suffix)
+ file.close()
+
+
+
diff --git a/run_parser.sh b/run_parser.sh
new file mode 100644
index 0000000000000000000000000000000000000000..c0d7ed5b8424f0dad187663cd0f5ea3f7efab9b3
--- /dev/null
+++ b/run_parser.sh
@@ -0,0 +1,3 @@
+
+python parser.py -f fromScholar.bib -p Alyaev
+python parser.py -f reports.bib -p Alyaev -o reports.tex
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