Uniform strings describing assay nodes

[Zigur]

We want to apply the following changes to the assay node names:

• The extract node will have the name: ASSAY{assay_index}-{start_node_index}-Extract{extract_index_within_subgraph} (e.g "ASSAY0-3-Extract1")
• The labeled extract node will have the name: ASSAY{assay_index}-{start_node_index}-LE{labeled_extract_index_within_subgraph} (e.g "ASSAY0-3-LE1")
• The protocol node will have the name: {technology type}_{cell name}_ASSAY{assay_index}-{start_node_index}-<data_acquisition>{protocol_index_within_subgraph} (e.g. "mass-spectrometry_A0E2_ASSAY0-3-<data_acquisition>1")
• The raw data file: {file type}_{cell name}_ASSAY{assay_index}-{start_node_index}-{file__index_within_subgraph} (e.g. "raw-spectral-data-file_A0E2_ASSAY0-3-1")

In practice, this requires to keep a counter by type (extract, labelled extract, protocol, raw data file) of the subgraph nodes as they are created.

As per discussion:
https://isateam.slack.com/archives/D0J1PUY79/p1604319144023500?thread_ts=1604316967.014800&cid=D0J1PUY79

[Zigur]

This works. The only difference with the specs is that <data_acquisition> has been changed to , as a protocol node could actually produce something else than a file as output in some configuration (at least potentially)