misc bugfixes discovered in testing

[yfan2012]

This PR fixes various bugs discovered while testing the RNA/WES/WGS that do not have any relation to the changes made to support the crispr-dav pipeline. The changes include:

SBG get_project_by_name()

• Context: This method works by calling self.api.projects.query(name=project_name), which returns a list of project objects whose names contain project_name as a substring. Then, get_project_by_name() returns the first project in that list.
• Problem: This was causing an issue in the RNA seq pipeline because the reference project name is 'RNA-Seq Reference', but there is now another project named 'RNA-Seq Reference Generate'. When trying to copy reference files from the reference project, get_project_by_name() returned the 'RNA-Seq Reference Generate' project which does not contain the needed files.
• Fix: Loop through the project list returned by self.api.projects.query(name=project_name) and check that names exactly match the query. If multiple or no names match, return None.

SBG get_file_id()

• Problem: This method derives the file_name from the file_path parameter, but then never uses file_name in the api call. This causes files in the project root to not be found when there is a leading slash in the file_path parameter.
• Fix: Actually use the file_name variable.

[golharam]

This PR has no unit test demonstrating the issue nor the fix is correct.

[yfan2012]

This PR has no unit test demonstrating the issue nor the fix is correct.

Tests are now added