import bibtexparser
import os.path

INVIS = "[](@autogenerated - invisible comment)"
with open('all.bib') as bibtex_file:
    bib_database = bibtexparser.load(bibtex_file)

#print(bib_database.entries)

print(bib_database.comments)
print(bib_database.preambles)
print(bib_database.strings)

[]
[]
OrderedDict()

AllRefs = ""
for k in bib_database.entries:
    #print k.keys()
    m = "* "
    if os.path.isfile("ArticlesPDF/"+k["ID"]+".pdf"):
        m += "[x] "
    else:
        m += "[ ] "
    m += "["+k["ID"]+"] __"+k["title"]+"__"
    if "author" in k.keys():
        m += " by "+k["author"]

    if "doi" in k.keys():
        m += ". (_DOI: ["+k["doi"]+"](https://doi.org/"+k["doi"]+")_)."
        if not os.path.isfile("ArticlesPDF/"+k["ID"]+".pdf"):
            print m.replace("{","").replace("}","")
    AllRefs += m+"\n"

* [ ] [raj_embedded_2014] __An embedded system for elasticity measurement using ultrasound waves__ by Raj, Jean and Smk, Rahman and Anand, Sneh. (_DOI: [10.13140/RG.2.1.2175.0165](https://doi.org/10.13140/RG.2.1.2175.0165)_).
* [ ] [park_implementation_2018] __Implementation of a backend system for real-time intravascular ultrasound imaging__ by Park, Jun-Won and Moon, Ju-Young and Lee, Junsu and Chang, Jin Ho. (_DOI: [10.7776/ASK2018.37.4.215](https://doi.org/10.7776/ASK2018.37.4.215)_).
* [ ] [isabel_low_2015] __A low cost pulsed wave Doppler ultrasound system on Field Programmable Gate Arrays for vascular studies.__ by Isabel, Arnaiz. (_DOI: [10.1007/978-3-319-19387-8_308](https://doi.org/10.1007/978-3-319-19387-8_308)_).
* [ ] [ramos_dependence_2000] __Dependence of pulser driving responses on electrical and motional characteristics of NDE ultrasonic probes__ by Ramos, A. and San Emeterio, J. L. and Sanz, P. T.. (_DOI: [10.1016/S0041-624X(99)00072-4](https://doi.org/10.1016/S0041-624X(99)00072-4)_).
* [ ] [nikitin_ultrasonic_2017] __Ultrasonic system and easy ILI tools for pipeline and tubular inspection__ by Nikitin, Konstantin. (_DOI: [10.13140/RG.2.2.25093.45288](https://doi.org/10.13140/RG.2.2.25093.45288)_).
* [ ] [jager_ultrasonic_2017] __Ultrasonic phased array for sound drift compensation in gas flow metering__ by Jäger, A. and Unger, A. and Wang, H. and Arnaudov, Y. and Kang, L. and Su, R. and Lines, D. and Ramadas, S. N. and Dixon, S. and Kupnik, M.. (_DOI: [10.1109/ULTSYM.2017.8092174](https://doi.org/10.1109/ULTSYM.2017.8092174)_).
* [ ] [dokmanic_acoustic_2013] __Acoustic echoes reveal room shape__ by Dokmanic, I. and Parhizkar, R. and Walther, A. and Lu, Y. M. and Vetterli, M.. (_DOI: [10.1073/pnas.1221464110](https://doi.org/10.1073/pnas.1221464110)_).

text_file = open("AllRefs.md", "w")
text_file.write(AllRefs.encode('utf8').replace("{","").replace("}","")+"\n"+INVIS)
text_file.close()

AllRefs = ""
for k in bib_database.entries:
    #print k.keys()
    m = "* "
    if os.path.isfile("ArticlesPDF/"+k["ID"]+".pdf"):
        m += "[x] "
    else:
        m += "[ ] "
    m += "["+k["ID"]+"] __"+k["title"]+"__"
    if "author" in k.keys():
        m += " by "+k["author"]

    if "doi" not in k.keys():
        if not os.path.isfile("ArticlesPDF/"+k["ID"]+".pdf"):
            print m.replace("{","").replace("}","")
    AllRefs += m+"\n"

* [ ] [thomenius_instrumentation_2018] __INSTRUMENTATION DESIGN FOR ULTRASONIC IMAGING__ by Thomenius, Kai
* [ ] [lecklider_ultrasound_2012] __Ultrasound imaging: more than skin-deep__ by Lecklider, Tom
* [ ] [wall_high-speed_2010] __A High-Speed Reconfigurable System for Ultrasound Research__ by Wall, Kieran
* [ ] [countries_future_1985] __Future use of new imaging technologies in developing countries : report of a WHO scientific group [meeting held in Geneva from 24 September to 1 October 1984]__ by Countries, WHO Scientific Group on the Future Use of New Imaging Technologies in Developing and Organization, World Health
* [ ] [lunt_handbook_1978] __Handbook of ultrasonic B-scanning in medicine__ by Lunt, R.
* [ ] [buess_system_1984] __A system for a transanal endoscopic rectum operation__ by Buess, G. and Hutterer, F. and Theiss, J. and Böbel, M. and Isselhard, W. and Pichlmaier, H.
* [ ] [kremkau_diagnostic_1989] __Diagnostic ultrasound: principles, instruments, and exercises__ by Kremkau, Frederick W.
* [ ] [holm_abdominal_1976] __Abdominal ultrasound__
* [ ] [joyner_ultrasound_1974] __Ultrasound in the diagnosis of cardiovascular-pulmonary disease__
* [ ] [carlin_ultrasonics_1960] __Ultrasonics__ by Carlin, Benson
* [ ] [ribas_logiciels_2016] __Logiciels \& objets libres: Animer une communauté autour d'un projet ouvert__ by Ribas, Stéphane and Ubeda, Stéphane and Guillaud, Patrick
* [ ] [silverman_effect_1995] __The effect of transducer bandwidth on ultrasonic image characteristics__ by Silverman, R. H. and Vinarsky, E. and Woods, S. M. and Lizzi, F. L. and Coleman, D. J.
* [ ] [lie_low_2008] __A low cost CPLD-based ultrasonic flowmeter__ by Lie, Ioan and Tiponuţ, Virgil and Bogdanov, Ivan and Ionel, Sabin
* [ ] [noauthor_sensors_nodate] __Sensors \textbar Free Full-Text \textbar Improvement of Ultrasonic Pulse Generator for Automatic Pipeline Inspection \textbar HTML__
* [ ] [karlen_mobile_2015] __Mobile point-of-care monitors and diagnostic device design__