It seems that when using the automator installations that come with the pubmex the pubmex.py can not be found.

    for f in "$@"
    do
        pubmex.py $f
    done

The following error is displayed:

The action “Run Shell Script” encountered an error: “zsh:3: command not found: pubmex.py”

When specifying the direct location of just the pubmex.py file another error occures.

    for f in "$@"
    do
        /users/suntim/miniforge3/bin/pubmex.py $f
    done

The following error is displayed:

The action “Run Shell Script” encountered an error: “”

When specifying the direct location of python and the pubmex.py file another error occures.

    for f in "$@"
    do
        /usr/local/bin/python3 /users/suntim/miniforge3/bin/pubmex.py $f
    done

The following error is displayed:

The action “Run Shell Script” encountered an error: “Traceback (most recent call last): File "/users/suntim/miniforge3/bin/pubmex.py", line 27, in <module> from Bio import Entrez ModuleNotFoundError: No module named 'Bio'”

I have all dependencies installed pip3 install pubmex, pip3 install biopython, brew install poppler. As it says in the readme.md that biopython should be isntalled via brew I assume that was a mistake. I instead installed it via pip3.

The same error messages occure regardless of using the zsh or bash version.

[email protected]:~/Desktop/pdfs$ pubmex.py -a -r -f 1-s2.0-S1874939915001868-main.pdf ERROR: Not found in PubMed, although DOI (.ORG/10.1016/J.BBAGRM.2015.08.009) was detected in the pdf! Traceback (most recent call last): File "/home/magnus/bin/pubmex.py", line 472, in main() File "/home/magnus/bin/pubmex.py", line 451, in main title = get_title_auto_from_text(text, OPTIONS.debug, False, OPTIONS.keywords) File "/home/magnus/bin/pubmex.py", line 239, in get_title_auto_from_text return get_title_via_doi(doi, debug, reference, customed_title) File "/home/magnus/bin/pubmex.py", line 359, in get_title_via_doi pmid = get_pmid_via_doi_net(doi) File "/home/magnus/bin/pubmex.py", line 333, in get_pmid_via_doi_net return get_value('citation_pmid', content) TypeError: get_value() takes exactly 3 arguments (2 given)

The colon in 'demo/10.1261:rna.418407.pdf' causes problems in cloning from windows machines.

Cloning into 'pubmex'... remote: Enumerating objects: 426, done. remote: Counting objects: 100% (9/9), done. remote: Total 426 (delta 8), reused 8 (delta 8), pack-reused 417 eceiving obj Receiving objects: 100% (426/426), 3.79 MiB | 2.86 MiB/s, done. Resolving deltas: 100% (252/252), done. error: invalid path 'demo/10.1261:rna.418407.pdf' fatal: unable to checkout working tree warning: Clone succeeded, but checkout failed. You can inspect what was checked out with 'git status' and retry with 'git restore --source=HEAD :/'

(py37) [mx] rna$ pubmex.py ct200162x.pdf --debug
filename: .......... ct200162x.pdf
filename: .......... ct200162x.pdf
doi: ............... ct200162x
IdList.............. []
pmid: .............. False
ERROR: 		Not found in PubMed, although DOI (ct200162x) was detected in the pdf!
generate ./temp.....[OK]
out:
err:
temp is going to be opened
doi_line: .......... DX.DOI.ORG/10.1021/CT200162X | J. CHEM. THEORY COMPUT. 2011, 7, 28862902
doi is found: ...... 10.1021/CT200162X
doi: ............... 10.1021/CT200162X
IdList.............. ['21921995']
pmid: .............. 21921995
summary_dict........ {'Item': [], 'Id': '21921995', 'PubDate': '2011 Sep 13', 'EPubDate': '2011 Aug 2', 'Source': 'J Chem Theory Comput', 'AuthorList': ['Zgarbová M', 'Otyepka M', 'Sponer J', 'Mládek A', 'Banáš P', 'Cheatham TE 3rd', 'Jurečka P'], 'LastAuthor': 'Jurečka P', 'Title': 'Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.', 'Volume': '7', 'Issue': '9', 'Pages': '2886-2902', 'LangList': ['English'], 'NlmUniqueID': '101232704', 'ISSN': '1549-9618', 'ESSN': '1549-9626', 'PubTypeList': ['Journal Article'], 'RecordStatus': 'PubMed', 'PubStatus': 'ppublish+epublish', 'ArticleIds': {'pubmed': ['21921995'], 'medline': [], 'doi': '10.1021/ct200162x', 'pmc': 'PMC3171997', 'rid': '21921995', 'eid': '21921995', 'pmcid': 'pmc-id: PMC3171997;'}, 'DOI': '10.1021/ct200162x', 'History': {'pubmed': ['2011/09/17 06:00'], 'medline': ['2011/09/17 06:01'], 'received': '2011/03/08 00:00', 'entrez': '2011/09/17 06:00'}, 'References': [], 'HasAbstract': IntegerElement(1, attributes={}), 'PmcRefCount': IntegerElement(242, attributes={}), 'FullJournalName': 'Journal of chemical theory and computation', 'ELocationID': '', 'SO': '2011 Sep 13;7(9):2886-2902'}
ERROR: 		Problem! The pubmex could not find automatically a title for the pdf file! Sorry!

(py37) [mx] rna$ pubmex.py gkz1184.pdf --debug
filename: .......... gkz1184.pdf
filename: .......... gkz1184.pdf
doi: ............... gkz1184
IdList.............. []
pmid: .............. False
ERROR: 		Not found in PubMed, although DOI (gkz1184) was detected in the pdf!
generate ./temp.....[OK]
out:
err:
temp is going to be opened
doi_line: .......... 11641174 NUCLEIC ACIDS RESEARCH, 2020, VOL. 48, NO. 3 DOI: 10.1093/NAR/GKZ1184
doi is found: ...... 10.1093/NAR/GKZ1184
doi: ............... 10.1093/NAR/GKZ1184
IdList.............. ['31889193']
pmid: .............. 31889193
summary_dict........ {'Item': [], 'Id': '31889193', 'PubDate': '2020 Feb 20', 'EPubDate': '', 'Source': 'Nucleic Acids Res', 'AuthorList': ['Reißer S', 'Zucchelli S', 'Gustincich S', 'Bussi G'], 'LastAuthor': 'Bussi G', 'Title': 'Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data.', 'Volume': '48', 'Issue': '3', 'Pages': '1164-1174', 'LangList': ['English'], 'NlmUniqueID': '0411011', 'ISSN': '0305-1048', 'ESSN': '1362-4962', 'PubTypeList': ['Journal Article'], 'RecordStatus': 'PubMed - indexed for MEDLINE', 'PubStatus': 'ppublish', 'ArticleIds': {'pubmed': ['31889193'], 'medline': [], 'pii': '5691221', 'doi': '10.1093/nar/gkz1184', 'pmc': 'PMC7026608', 'rid': '31889193', 'eid': '31889193', 'pmcid': 'pmc-id: PMC7026608;'}, 'DOI': '10.1093/nar/gkz1184', 'History': {'pubmed': ['2020/01/01 06:00'], 'medline': ['2020/03/20 06:00'], 'accepted': '2019/12/09 00:00', 'revised': '2019/12/05 00:00', 'received': '2019/10/14 00:00', 'entrez': '2020/01/01 06:00'}, 'References': [], 'HasAbstract': IntegerElement(1, attributes={}), 'PmcRefCount': IntegerElement(3, attributes={}), 'FullJournalName': 'Nucleic acids research', 'ELocationID': 'doi: 10.1093/nar/gkz1184', 'SO': '2020 Feb 20;48(3):1164-1174'}
ERROR: 		Problem! The pubmex could not find automatically a title for the pdf file! Sorry!

(py37) [mx] d$ pubmex -p 10.1016/j.molcel.2020.11.004
(py37) [mx] d$ pubmex -p 10.1016/j.molcel.2020.11.004 -d
doi: ............... 10.1016/j.molcel.2020.11.004
IdList.............. ['33259809']
pmid: .............. 33259809
summary_dict........ {'Item': [], 'Id': '33259809', 'PubDate': '2020 Dec 17', 'EPubDate': '2020 Nov 5', 'Source': 'Mol Cell', 'AuthorList': ['Ziv O', 'Price J', 'Shalamova L', 'Kamenova T', 'Goodfellow I', 'Weber F', 'Miska EA'], 'LastAuthor': 'Miska EA', 'Title': 'The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2.', 'Volume': '80', 'Issue': '6', 'Pages': '1067-1077.e5', 'LangList': ['English'], 'NlmUniqueID': '9802571', 'ISSN': '1097-2765', 'ESSN': '1097-4164', 'PubTypeList': ['Journal Article'], 'RecordStatus': 'PubMed - indexed for MEDLINE', 'PubStatus': 'ppublish+epublish', 'ArticleIds': {'pubmed': ['33259809'], 'medline': [], 'pii': 'S1097-2765(20)30782-6', 'doi': '10.1016/j.molcel.2020.11.004', 'pmc': 'PMC7643667', 'rid': '33259809', 'eid': '33259809', 'pmcid': 'pmc-id: PMC7643667;'}, 'DOI': '10.1016/j.molcel.2020.11.004', 'History': {'pubmed': ['2020/12/02 06:00'], 'medline': ['2021/01/12 06:00'], 'received': '2020/07/20 00:00', 'revised': '2020/10/05 00:00', 'accepted': '2020/10/29 00:00', 'entrez': '2020/12/01 20:08'}, 'References': [], 'HasAbstract': IntegerElement(1, attributes={}), 'PmcRefCount': IntegerElement(10, attributes={}), 'FullJournalName': 'Molecular cell', 'ELocationID': 'doi: 10.1016/j.molcel.2020.11.004', 'SO': '2020 Dec 17;80(6):1067-1077.e5'}
Ziv.Miska.The.Short-Long-Range.RNA-RNA.Interactome.SARS-CoV-2.MolCell.2020.pdf