File naming when exporting and always export "network" sheet

[kdahlquist]

As per #1174, following @Amelie1253 's suggestion of breaking out the file naming of files Exported to Excel as a separate issue.

[dondi]

Conditions for export file naming:

• Hardcode the network checkbox as always checked
• Append weighted when network_optimized_weights is checked, unweighted when not checked

[dondi]

Need to also revisit file naming logic when the export is a demo—the chosen expression dataset needs to be factored in and may need to replace the internal demo name

[kdahlquist]

There is another issue #1217 that is also related to this.

[kdahlquist]

I closed the previous issue (#1217) because we will use this issue to do a general audit of file-naming. I think the filenames need to be simplified. I think originally, they were modeled the names that display in the menu bar when you either load a demo or load from the database. What is displayed in the menu bar should not change because it is useful information for the user. However, we don't need that exact phrasing to be part of the exported filename.

Here is the simplified scheme that I propose:

• Begin the filename with either GRN or PPI, depending on whether it is a GRN or PPI.
• followed by an underscore
• followed by how many genes/proteins and edges as in "6-genes_8-edges" or "6-proteins_8-edges"
• follwed by an underscore
• followed by either weighted or unweighted according to the rules above
• followed by an underscore
• followed by the expression data source, only if the user is exporting expression data. For example, "Dahlquist-2018-data" or "Apweiler-2012-data". If it is user-uploaded data then it would be "user-data"

Note that we are avoiding all special characters except for underscore and hypen. No spaces, parentheses, commas, etc.

So here are some examples:

• PPI_25-proteins_30-edges_unweighted
• GRN_15-genes_32-edges_unweighted
• GRN_6-genes_8-edges_weighted
• GRN_7-genes_14-edges_unweighted_Dahlquist-2018-data
• GRN_8-genes_16-edges_weighted_Apweiler-2012-data
• GRN_9-genes_18-edges_unweighted_user-data

These rules should apply whether the file is user-uploaded, loaded from database, or a demo. So, this is going to de-couple the exported filename from what is displayed in the menu bar. We are not including the network source info in the export filename.

This also means that when a demo is exported, it's not going to say "Demo #" in the filename, it will just follow the rules above.

If the demos are exported, and the user does not change the expression data, then those files would be:

• Demo 1: "GRN_15-genes_28-edges_unweighted_Dahlquist-2018-data"
• Demo 2: "GRN_15-genes_28-edges_weighted_Dahlquist-2018-data"
• Demo 3: "GRN_21-genes_31-edges_unweighted"
• Demo 4: "GRN_21-genes_31-edges_weighted_Schade-2004-data"
• Demo5: "PPI_18-proteins_81-edges_unweighted"

If the user changes the expression data, then the last bit of the filename would reflect the new expression data source.

Note that there is a separate issue with Demo 3 in that it is not supposed to default to being colored with expression data. The nodes should be white. I'm going to start a separate issue for that.

Please let me know if you have questions.

[kdahlquist]

Also, I want to note that we should follow this naming convention when exporting to .sif or .graphml as well.