A simple tool to retrieve DOIs and abstracts of research articles inserted as spreadsheet.
First, we need some set-up:
We will now create a copy of the program:
https://github.com/<your-username>/abstract_doi_finder
, where <your-username>
is your username (aubertc
in the example below). We will now upload our own spreadsheet. Click on the "abstract_doi_finder" folder:
then click on the "input" folder, and click on the "Upload files" button hidden under the "Add file" button:
Upload your spreadsheet, and click on "Commit changes":
Now we will delete the spreadsheet loaded by default.
Go back in the "input" folder, and click on the "test_input.xlsx" file. On the right of the screen, click on the three dots, then on "Delete file":
Finally, click on "Commit changes…" twice:
Now, we will execute the program on our spreadsheet and download the resulting spreadsheet.
Click on "action", and then on "I understand my workflows, go ahead and enable them":
Then, click on "Remote Execution", then on "Run workflow" (twice):
Be patient, your workflow will be executed:
Once it is over, a green check will replace the orange wheel. Click on it:
Then, scroll down and click on "Remote_execution" under "Artifacts":
That's it, your download of the resulting spreadsheet should begin!
[!NOTE] If you want to run execute the program on a different sheet, simply upload your updated spreadsheet and head over to the "Actions" tab: if you there is only one sheet in the
input/
folder and the workflows have already been enabled, then they will execute automatically when the file ininput/
is edited.
[!CAUTION] Be aware that
- executing our program as indicated above (that is, on github servers) will make your spreadsheet publicly accessible while the program is being executed, and after if you don't delete your fork.
- even if our program is not supposed to edit your spreadsheet, always backing up your data before running this program is a good practise.
Your speardsheet must
xlsx
format and extension,Your spreadsheet can
Your spreadsheet must not
[!WARNING]
The program will not override your data, but create a copy of the original sheet. Furthermore, if you have data in existing cells for both the abstract and DOI, the program will not overwrite your data. However, if even one of them is missing, the program will search PubMed for the abstract and DOI, then overwrite the data in its output spreadsheet.
An example sheet that can be used as a template is provided.
cd abstract_doi_finder/
mvn compile
mvn exec:java -Dexec.mainClass="popbr.AbstractDoiFinder" -Dexec.args="input_file.xlsx 1,3"
In the command line above,
input_file.xlsx
is the name of the spreadsheet placed in the abstract_doi_finder/input/
folder (this argument is optional if only one sheet is in the input/
folder, mandatory otherwise), and1,3
are the sheets you want to run the program on. Please separate the values with commas, exclude spaces, or follow the examples below.The range can be provided (or omitted) in a multitude of ways including:
[!NOTE]
When entering your sheet range, it is important to take note that each number is subtracted by 1, so it runs on your intended files. For example: The user inputs '1,2,3' which would run on the first sheet, the second sheet, and the third. But the program will use the indices 0, 1, and 2 to run on the specified sheets. Therefore, it is important to not use 0, as this was done for user convenience.