Tutorial

Academic Tracker is intended to be used solely as a command line program. This tutorial describes each command and its options.

Configuration JSON File

Details about the configuration JSON file can be found in the JSON Schema section, but in general the sections of the configuration JSON file that aren’t needed for a particular command are not required. For instance, the ORCID_search section is not required for reference_search since it does not search ORCID. The same is true if the –no_ORCID option is used.

Outputs

The specific files output by Academic Tracker vary by the command used and some options, but each command always creates a new timestamped directory in the working directory. If the –test option is not used then the directory will be named tracker-YYMMDDHHMM. If the –test option is used then the directory will be named tracker-test-YYMMDDHHMM.

Search For Publications By Author

Command Line Signature

academic_tracker author_search <config_json_file> [--test --prev_pub=<file-path> --no_GoogleScholar --no_ORCID --no_Crossref --verbose --silent]

Description

For each author in the Authors section of the configuration JSON file search PubMed, ORCID, Crossref, and Google Scholar for publications they are an author on. The cutoff_year attribute for either the projects or the authors can be used to filter the publications to only those in that year or after.

Similarly, a previous publications JSON file can be used to filter out publications that are already in the file. This file can be specified manually with the –prev_pub option. If not specified manually author_search will automatically look for a publications.json file in the most recent tracker directories and if it finds one it will be used as the previous publications. To stop this automatic lookup enter “ignore” for the –prev_pub option. The output publications.json file will be a combination of the previous publications and any new publications found. To be clear the new publications.json file will be the previous publications.json file with any new entries added in.

The description of everything author_search does with the previous publications may seem arbitrary and confusing. The idea is that users will make an initial list of authors to keep track of and then run author_search every so often to look for new publications for them. To make this as easy as possible it is neceessary to both have author_search look for previous publications automatically and for the output to be cumulative so that the same publications are not reported multiple times.

Although the configuration JSON file contains projects, they are mostly there for organizational convenience and reporting. author_search queries every author in the Authors section of the configuration JSON, but the information in the projects section can affect the search. One of the first things author_search does is that it goes through each author and reconciles the information given for them with that given for any projects they are associated with. Specifically, the minimum cutoff_year is found, and affiliations and grants are concatenated. These reconciled values are then what is used when querying.

Options

–test:

The test option changes the name of the output directory from tracker-YYMMDDHHMM to tracker-test-YYMMDDHHMM and prevents any emails from being sent.

–prev_pub:

Specifies a publications.json file to use as a list of publications to ignore when searching for new publications. Set to “ignore” to prevent author_search from automatically looking for a publications.json file in tracker directories. If a publication is in prev_pub but the information has updated then it will not be ignored.

–no_GoogleScholar:

If used author_search will not search Google Scholar for publications.

–no_ORCID:

If used author_search will not search ORCID for publications. This option is assumed if the ORCID_search section of the configuration JSON file is missing.

–no_Crossref:

If used author_search will not search Crossref for publications. This option is assumed if the Crossref_search section of the configuration JSON file is missing.

–verbose:

If used HTML errors and other warnings will be printed to the screen.

–silent:

If used nothing will be printed to the screen.

Outputs

Outputs depend on the configuration JSON file and options.

A publications.json file will always be output.

An emails.json file is only created if the from_email attribute is given in either the summary_report or project_report sections of the configuration JSON file.

A summary_report.txt file is only created if the summary_report attribute is in the configuration JSON file.

Similarly, project_report.txt files are created for projects that have the project_report attribute. Project reports will either be for the whole project or individual authors and the name of the project report file will indicate this. If from_email is given in project_report then a report for the whole project is created. If the authors attribute is given in the project and from_email is not then a file for each author in the project is created. If neither authors nor from_email is given then a file is created for every author that had new publications.

Details about reports can be found in the Reporting section.

publications.json emails.json summary_report.txt projectname_project_report.txt projectname_authorname_project_report.txt

Examples

Typical run.

config_file.json:

{
  "project_descriptions": {
    "Project 1": {
      "affiliations": [
        "affiliaton1"
      ],
      "authors": [
        "Author1",
        "Author2"
      ],
      "cutoff_year": 2020,
      "grants": [
        "grant1",
        "grant2"
      ]
    }
  },
  "summary_report": {},
  "ORCID_search": {
    "ORCID_key": "orcid key",
    "ORCID_secret": "orcid secret"
  },
  "PubMed_search": {
    "PubMed_email": "email@email.com"
  },
  "Crossref_search": {
    "mailto_email": "email@email.com"
  },
  "Authors": {
    "Author1": {
      "ORCID": "Author1's ORCID ID",
      "email": "email@email.com",
      "first_name": "First",
      "last_name": "Last",
      "pubmed_name_search": "First Last"
    },
    "Author2": {
      "ORCID": "Author2's ORCID ID",
      "email": "email@email.com",
      "first_name": "Second",
      "last_name": "Last",
      "pubmed_name_search": "Second Last"
    }
  }
}

Console:

>academic_tracker author_search config_file.json
Finding author's publications. This could take a while.
Searching PubMed.
Searching ORCID.
Searching Google Scholar.
Searching Crossref.
Success. Publications and reports saved in tracker-2202020140

Create a collaborator report for an author.

config_file.json:

{
  "project_descriptions": {
    "Project 1": {
      "affiliations": [
        "affiliaton1"
      ],
      "authors": [
        "Author1",
        "Author2"
      ],
      "cutoff_year": 2020,
      "grants": [
        "grant1",
        "grant2"
      ]
    }
  },
  "ORCID_search": {
    "ORCID_key": "orcid key",
    "ORCID_secret": "orcid secret"
  },
  "PubMed_search": {
    "PubMed_email": "email@email.com"
  },
  "Crossref_search": {
    "mailto_email": "email@email.com"
  },
  "Authors": {
    "Author1": {
      "ORCID": "Author1's ORCID ID",
      "email": "email@email.com",
      "first_name": "First",
      "last_name": "Last",
      "pubmed_name_search": "First Last"
      "collaborator_report": {}
    },
    "Author2": {
      "ORCID": "Author2's ORCID ID",
      "email": "email@email.com",
      "first_name": "Second",
      "last_name": "Last",
      "pubmed_name_search": "Second Last"
    }
  }
}

Console:

>academic_tracker author_search config_file.json
Finding author's publications. This could take a while.
Searching PubMed.
Searching ORCID.
Searching Google Scholar.
Searching Crossref.
Success. Publications and reports saved in tracker-2202020140

Run in test mode so emails aren’t sent.

>academic_tracker author_search config_file.json --test
Finding author's publications. This could take a while.
Searching PubMed.
Searching ORCID.
Searching Google Scholar.
Searching Crossref.
Success. Publications and reports saved in tracker-test-2202020140

Designating a previous publications filepath instead of letting Academic Tracker find the most recent.

>academic_tracker author_search config_file.json --prev_pub prev_pub_file_path.json
Finding author's publications. This could take a while.
Searching PubMed.
Searching ORCID.
Searching Google Scholar.
Searching Crossref.
Success. Publications and reports saved in tracker-2202020140

Specifying that Academic Tracker shouldn’t use ORCID.

config_file.json:

{
  "project_descriptions": {
    "Project 1": {
      "affiliations": [
        "affiliaton1"
      ],
      "authors": [
        "Author1",
        "Author2"
      ],
      "cutoff_year": 2020,
      "grants": [
        "grant1",
        "grant2"
      ]
    }
  },
  "summary_report": {},
  "PubMed_search": {
    "PubMed_email": "email@email.com"
  },
  "Crossref_search": {
    "mailto_email": "email@email.com"
  },
  "Authors": {
    "Author1": {
      "email": "email@email.com",
      "first_name": "First",
      "last_name": "Last",
      "pubmed_name_search": "First Last"
    },
    "Author2": {
      "email": "email@email.com",
      "first_name": "Second",
      "last_name": "Last",
      "pubmed_name_search": "Second Last"
    }
  }
}

Note

A minimal example is shown, but the config can have other sections and run without error.

Console:

>academic_tracker author_search config_file.json --no_ORCID
Finding author's publications. This could take a while.
Searching PubMed.
Searching Google Scholar.
Searching Crossref.
Success. Publications and reports saved in tracker-2202020140

Search For Publications By Reference

Command Line Signature

academic_tracker reference_search <config_json_file> <references_file_or_URL> [--test --prev_pub=<file-path> --PMID_reference --MEDLINE_reference --no_Crossref --verbose --silent]

Description

Parse and tokenize the reference file or URL and then search PubMed and Crossref for the publications found. ORCID is not searched because it is a database of authors and does not support searching for publications directly. Google Scholar is not searched because it does not like bots, so cannot be easily searched without using a 3rd party paid service or proxies.

The reference_file_or_URL can be several different things. If it is a file then it can be a JSON file of already tokenized data, a docx file, or a txt file. If not a JSON file then each reference is expected to be on a single line. If it is a URL then it can be either a MyNCBI URL or not. If it is a MyNCBI URL then it is expected to be the first page of a bibliography and will be tokenized in a specific way. All other URLs are simply read as a text file and tokenized like one.

The –PMID_reference and –MEDLINE_reference options change how the reference file is interpreted. If the –PMID_reference option is used then it indicates that the given reference file is a list of PMIDs (PubMed’s unique IDs). Instead of tokenizing this file it is assumed that each line is a PMID so PubMed will be queried for each PMID and Crossref will not be queried. The idea for this option was to be able to quickly grab information from PubMed.

The –MEDLINE_reference option indicates that given reference file is a MEDLINE formatted file. This will be tokenized in a unique way since the publication information is spread out over multiple lines in this format. This format is supported because it is a dounload option on MyNCBI bibliography pages.

Details about tokenization are in the Tokenization section.

The –prev_pub option is different for reference_search than it is for author_search. First, reference_search does not automatically look for a publicaitons.json file to use since the same assumptions as described for author_search do not hold here. Second, publications in the prev_pub file are not used to ignore publications. Publications in the prev_pub file will still be in the newly created publications.json file. What this option does do is set the <is_in_comparison_file> keyword to True for matching publications in the summary report.

Options

–test:

The test option changes the name of the output directory from tracker-YYMMDDHHMM to tracker-test-YYMMDDHHMM and prevents any emails from being sent.

–prev_pub:

Specifies a publications.json file to use as a list of publications to compare with when generating the summary report.

–PMID_reference:

Specifies that the reference file is a list of PMIDs and to only return information from PubMed.

–MEDLINE_reference:

Specifies that the reference file is a MEDLINE formatted file.

–no_Crossref:

If used reference_search will not search Crossref for publications. This option is assumed if the Crossref_search section of the configuration JSON file is missing.

–verbose:

If used HTML errors and other warnings will be printed to the screen.

–silent:

If used nothing will be printed to the screen.

Outputs

Outputs depend on the configuration JSON file and options.

A publications.json file will always be output.

A tokenized_reference.json file will always be output.

An emails.json file is only created if the from_email attribute is given in the summary_report section of the configuration JSON file.

A summary_report.txt file is only created if the summary_report attribute is in the configuration JSON file.

If –PMID_reference is used no reports or emails are generated.

Details about reports can be found in the Reporting section.

publications.json tokenized_reference.json emails.json summary_report.txt

Examples

Typical run.

config_file.json:

{
  "summary_report": {},
  "PubMed_search": {
    "PubMed_email": "email@email.com"
  },
  "Crossref_search": {
    "mailto_email": "email@email.com"
  }
}

Note

A minimal example is shown, but the config can have other sections and run without error.

Console:

>academic_tracker reference_search config_file.json reference_file.txt
Finding publications. This could take a while.
Searching PubMed.
Searching Crossref.
Success. Publications and reports saved in tracker-2202020140

Run in test mode so emails aren’t sent.

>academic_tracker reference_search config_file.json reference_file.txt --test
Finding publications. This could take a while.
Searching PubMed.
Searching Crossref.
Success. Publications and reports saved in tracker-test-2202020140

Designating a previous publications filepath.

>academic_tracker reference_search config_file.json reference_file.txt --prev_pub prev_pub_file_path.json
Finding publications. This could take a while.
Searching PubMed.
Searching Crossref.
Success. Publications and reports saved in tracker-2202020140

Specifying that Academic Tracker shouldn’t use Crossref.

config_file.json:

{
  "summary_report": {},
  "PubMed_search": {
    "PubMed_email": "email@email.com"
  }
}

Note

A minimal example is shown, but the config can have other sections and run without error.

Console:

>academic_tracker reference_search config_file.json reference_file.txt --no_Crossref
Finding publications. This could take a while.
Searching PubMed.
Success. Publications and reports saved in tracker-2202020140

Find ORCID IDs for Authors

Command Line Signature

academic_tracker find_ORCID <config_json_file> [--verbose --silent]

Description

For each author in the Authors section of the configuration JSON file with a missing or blank ORCID attribute search ORCID for a match to get an ID. Matching is done using first and last names and the affiliations attribute.

Options

–verbose:

If used HTML errors and other warnings will be printed to the screen.

–silent:

If used nothing will be printed to the screen.

Outputs

If any authors are found then a new configuration.json file is created with the ORCID information updated in the Authors. If no authors are matched then there are no outputs.

configuration.json

Examples

Typical run.

config_file.json:

{
  "ORCID_search": {
    "ORCID_key": "orcid key",
    "ORCID_secret": "orcid secret"
  },
  "Authors": {
    "Author1": {
      "email": "email@email.com",
      "first_name": "First",
      "last_name": "Last",
      "pubmed_name_search": "First Last"
    },
    "Author2": {
      "email": "email@email.com",
      "first_name": "Second",
      "last_name": "Last",
      "pubmed_name_search": "Second Last"
    }
  }
}

Note

A minimal example is shown, but the config can have other sections and run without error.

Console:

>academic_tracker find_ORCID config_file.json
Searching ORCID for author's ORCID ids.
Success! configuration.json saved in tracker-2202020140

No authors found.

>academic_tracker find_ORCID config_file.json
Searching ORCID for author's ORCID ids.
No authors were matched from the ORCID results. No new file saved.

Find Scholar IDs for Authors

Command Line Signature

academic_tracker find_Google_Scholar <config_json_file> [--verbose --silent]

Description

For each author in the Authors section of the configuration JSON file with a missing or blank scholar_id attribute search Google Scholar for a match to get an ID. Matching is done using first and last names and the affiliations attribute.

Options

–verbose:

If used HTML errors and other warnings will be printed to the screen.

–silent:

If used nothing will be printed to the screen.

Outputs

If any authors are found then a new configuration.json file is created with the scholar_id information updated in the Authors. If no authors are matched then there are no outputs.

configuration.json

Examples

Typical run.

config_file.json:

{
  "Authors": {
    "Author1": {
      "ORCID": "Author1's ORCID ID",
      "email": "email@email.com",
      "first_name": "First",
      "last_name": "Last",
      "pubmed_name_search": "First Last"
    },
    "Author2": {
      "ORCID": "Author2's ORCID ID",
      "email": "email@email.com",
      "first_name": "Second",
      "last_name": "Last",
      "pubmed_name_search": "Second Last"
    }
  }
}

Note

A minimal example is shown, but the config can have other sections and run without error.

Console:

>academic_tracker find_Google_Scholar config_file.json
Searching Google Scholar for author's scholar ids.
Success! configuration.json saved in tracker-2202020140

No authors found.

>academic_tracker find_Google_Scholar config_file.json
Searching Google Scholar for author's scholar ids.
No authors were matched from the Google Scholar results. No new file saved.

Add Or Update Authors In Configuration JSON

Command Line Signature

academic_tracker add_authors <config_json_file> <authors_file> [--verbose --silent]

Description

Read in the authors_file and update the Authors section of the configuration JSON file with the information in it.

The authors_file must be a csv file. The columns are the attributes for each author and each row is one author. Including columns for each required author attribute there must also be a column named “author_id” which contains the key for the author. In all the required columns are “author_id”, “first_name”, “last_name”, “pubmed_name_search”, and “email”.

Example csv: .. code-block:: console

author_id first_name last_name pubmed_name_search email ORCID Name McName Name McName Name McName email@email.com 0000-00001-1234-1234

Options

–verbose:

If used HTML errors and other warnings will be printed to the screen.

–silent:

If used nothing will be printed to the screen.

Outputs

configuration.json

Examples

Typical run.

config_file.json:

{
  "Authors": {
    "Author1": {
      "ORCID": "Author1's ORCID ID",
      "email": "email@email.com",
      "first_name": "First",
      "last_name": "Last",
      "pubmed_name_search": "First Last"
    },
    "Author2": {
      "ORCID": "Author2's ORCID ID",
      "email": "email@email.com",
      "first_name": "Second",
      "last_name": "Last",
      "pubmed_name_search": "Second Last"
    }
  }
}

Note

A minimal example is shown, but the config can have other sections and run without error.

Console:

>academic_tracker add_authors config_file.json
Success! configuration.json saved in tracker-2202020140

Tokenize A Reference

Command Line Signature

academic_tracker tokenize_reference <references_file_or_URL> [--MEDLINE_reference --verbose --silent]

Description

Tokenize the input reference and output a tokenization report and JSON file.

Options

–MEDLINE_reference:

Specifies that the reference file is a MEDLINE formatted file.

–verbose:

If used HTML errors and other warnings will be printed to the screen.

–silent:

If used nothing will be printed to the screen.

Outputs

The information in the text report and JSON file are essentially the same, but the text report is presented in a more human readable way. They both have every publication that could be identified in the reference and tokenized, so if one does not appear that should be then there is a problem during tokenization. More detailed information about tokenization is in the Tokenization section.

tokenization_report.txt tokenized_reference.json

Examples

Typical run.

>academic_tracker tokenize_reference reference_file.txt
Searching Google Scholar for author's scholar ids.
Success! Tokenization files saved in tracker-2202020140