pivot back to microSALT

Author: karlnyr

.github/pull_request_template.md

@@ -1,4 +1,5 @@
 # Description
+
 _##Remove elements in cursive as needed.##_
 
 _The features of this PR primarily concerns end-users/bioinformaticians/internals_
@@ -8,33 +9,38 @@ _Summary of the changes made:_
 _If not self-evident, mention what prompted the change._
 
 ## Primary function of PR
-- [ ] Hotfix
-- [ ] Patch
-- [ ] Minor functionality improvement
-- [ ] New type of analysis
-- [ ] Backward-breaking functionality improvement
-- [ ] This change requires internal documents to be updated
-- [ ] This change requires another repository to be updated
+
+-   [ ] Hotfix
+-   [ ] Patch
+-   [ ] Minor functionality improvement
+-   [ ] New type of analysis
+-   [ ] Backward-breaking functionality improvement
+-   [ ] This change requires internal documents to be updated
+-   [ ] This change requires another repository to be updated
 
 # Testing
+
 _If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR._
 
 _Test routine to verify the stability of the PR:_
-- _`bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAME`_
-- _`us`_
-- _`conda activate S_microSALT`_
-- _(SITUATIONAL) `export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json`_
-- _Select a relevant subset of the following:_
-- _`microsalt analyse project MIC3109`_
-- _`microsalt analyse project MIC4107`_
-- _`microsalt analyse project MIC4109`_
-- _`microsalt analyse project ACC5551`_
+
+-   _`bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microSALT-stage.sh BRANCHNAME`_
+-   _`us`_
+-   _`conda activate S_microSALT`_
+-   _(SITUATIONAL) `export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json`_
+-   _Select a relevant subset of the following:_
+-   _`microSALT analyse project MIC3109`_
+-   _`microSALT analyse project MIC4107`_
+-   _`microSALT analyse project MIC4109`_
+-   _`microSALT analyse project ACC5551`_
 
 _Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, Microbial_WGS.xlsx_
 
 ## Test results
+
 _These are the results of the tests, and necessary conclusions, that prove the stability of the PR._
 
 # Sign-offs
-- [ ] Code tested by @octocat
-- [ ] Approved to run at Clinical-Genomics by @karlnyr 
+
+-   [ ] Code tested by @octocat
+-   [ ] Approved to run at Clinical-Genomics by @karlnyr

.github/workflows/run_tests.yml

@@ -38,7 +38,7 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest --cov=microsalt tests
+        pytest --cov=microSALT tests
     - name: Run Coveralls
       run: |
         coveralls

.gitignore

@@ -1,7 +1,7 @@
 .DS_Store
 
-microsalt/__pycache__
-microsalt.log
+microSALT/__pycache__
+microSALT.log
 instance/sqlalchemy_config.py
 instance/paths.yml
 unique_references/*.n*

DEPLOYMENT.md

@@ -5,33 +5,32 @@ When all tests done and successful and PR is approved by codeowners, follow thes
 1. Ensure that you update the version in `microSALT/__init__.py`
 2. Select "Squash and merge" to merge branch into default branch (master).
 3. Deploy master to stage:
-   1. Log in to appropriate server `ssh <server.scilifelab.se>`
-   2. `us`
-   3. Install microSALT using **one** of the following commands
-      1. If you have updated the `environment.yml`:
-         ```shell
-         sudo -iu hiseq.clinical
-         us
-         bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh master
-         ```
-      2. Otherwise run:
-         ```shell
-         bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_microSALT -t microSALT -b master
-         ```
-   4. Make sure that the installation was successful
+    1. Log in to appropriate server `ssh <server.scilifelab.se>`
+    2. `us`
+    3. Install microSALT using **one** of the following commands
+        1. If you have updated the `environment.yml`:
+            ```shell
+            sudo -iu hiseq.clinical
+            us
+            bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microSALT-stage.sh master
+            ```
+        2. Otherwise run:
+            ```shell
+            bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_microSALT -t microSALT -b master
+            ```
+    4. Make sure that the installation was successful
 4. Deploy master to production:
-   1. Log in to appropriate server `ssh <server.scilifelab.se>`
-   2. `up`
-   3. Install microSALT using **one** of the following commands
-      1. If you have updated the `environment.yml`:
-         ```shell
-         sudo -iu hiseq.clinical
-         up
-         bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-prod.sh
-         ```
-      2. Otherwise run:
-         ```shell
-         bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-prod.sh -e P_microSALT -t microSALT -b master
-         ```
-   4. Make sure that the installation was successful
-
+    1. Log in to appropriate server `ssh <server.scilifelab.se>`
+    2. `up`
+    3. Install microSALT using **one** of the following commands
+        1. If you have updated the `environment.yml`:
+            ```shell
+            sudo -iu hiseq.clinical
+            up
+            bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microSALT-prod.sh
+            ```
+        2. Otherwise run:
+            ```shell
+            bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-prod.sh -e P_microSALT -t microSALT -b master
+            ```
+    4. Make sure that the installation was successful

README.md

@@ -1,17 +1,17 @@
-[![Build status](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml/badge.svg)](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml)
+[![Build status](https://github.com/clinical-genomics/microSALT/actions/workflows/run_tests.yml/badge.svg)](https://github.com/clinical-genomics/microSALT/actions/workflows/run_tests.yml)
 [![Coverage Status](https://coveralls.io/repos/github/Clinical-Genomics/microSALT/badge.svg?branch=master)](https://coveralls.io/github/Clinical-Genomics/microSALT?branch=master)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4026043.svg)](https://doi.org/10.5281/zenodo.4026043)
 
 <p align="center">
   <a href="https://github.com/sylvinite/microSALT">
-    <img width="1000" height="250" src="artwork/microsalt.jpg"/>
+    <img width="1000" height="250" src="artwork/microSALT.jpg"/>
   </a>
 </p>
 
-__Microbial Sequence Analysis and Loci-based Typing pipeline__
+**Microbial Sequence Analysis and Loci-based Typing pipeline**
 
 _The microbial sequence analysis and loci-based typing pipeline (microSALT) is
-used to analyse microbial samples.  It produces a quality control of the
+used to analyse microbial samples. It produces a quality control of the
 sample, determines a sample's organism specific sequence type, and its
 resistance pattern. microSALT also provides a database storage solution and
 report generation of these results._
@@ -42,17 +42,17 @@ cp configExample.json /MY/FAV/FOLDER/config.json
 export MICROSALT_CONFIG=/MY/FAV/FOLDER/config.json
 ```
 
-__Then edit the fields to match your environment__.
+**Then edit the fields to match your environment**.
 
 ## Usage
 
-- `microsalt analyse` contains functions to start sbatch job(s) & produce
-  output to `folders['results']`. Afterwards the parsed results  are uploaded
-  to the SQL back-end and produce reports (HTML), which are then automatically
-  e-mailed to the user.
-- `microsalt utils` contains various functionality, including generating the
-  sample description json, manually adding new reference organisms and
-  re-generating reports.
+-   `microSALT analyse` contains functions to start sbatch job(s) & produce
+    output to `folders['results']`. Afterwards the parsed results are uploaded
+    to the SQL back-end and produce reports (HTML), which are then automatically
+    e-mailed to the user.
+-   `microSALT utils` contains various functionality, including generating the
+    sample description json, manually adding new reference organisms and
+    re-generating reports.
 
 ## Databases
 
@@ -71,14 +71,14 @@ Any definitions will work, as long as they retain the same formatting.
 
 ### Hardware
 
-- A [SLURM](https://slurm.schedmd.com) enabled HPC system
-- A (clarity) LIMS server
+-   A [SLURM](https://slurm.schedmd.com) enabled HPC system
+-   A (clarity) LIMS server
 
 ### Software
 
-- [Conda](https://conda.io)
-- Python 3.6
-- [SQLite](https://www.sqlite.org)
+-   [Conda](https://conda.io)
+-   Python 3.6
+-   [SQLite](https://www.sqlite.org)
 
 ## Contributing to this repo
 
@@ -87,7 +87,7 @@ For more information, see https://guides.github.com/introduction/flow/
 
 ## Credits
 
-- Isak Sylvin - Lead developer
-- Emma Sernstad - Accreditation ready reports
-- Tanja Normark - Various issues
-- Maya Brandi - Various issues
+-   Isak Sylvin - Lead developer
+-   Emma Sernstad - Accreditation ready reports
+-   Tanja Normark - Various issues
+-   Maya Brandi - Various issues

configExample.json

@@ -22,7 +22,7 @@
     "_comment": "Report collection folder",
     "reports": "/tmp/MLST/reports/",
     "_comment": "Log file position and name",
-    "log_file": "/tmp/microsalt.log",
+    "log_file": "/tmp/microSALT.log",
     "_comment": "Root folder for input fasta sequencing data",
     "seqdata": "/tmp/projects/",
     "_comment": "ST profiles. Each ST profile file under 'profiles' have an identicial folder under references",
@@ -38,7 +38,7 @@
   },
   "_comment": "Database/Flask configuration",
   "database": {
-    "SQLALCHEMY_DATABASE_URI": "sqlite:////tmp/microsalt.db",
+    "SQLALCHEMY_DATABASE_URI": "sqlite:////tmp/microSALT.db",
     "SQLALCHEMY_TRACK_MODIFICATIONS": "False",
     "DEBUG": "True"
   },

microSALT/cli.py

@@ -9,15 +9,15 @@
 import sys
 import logging
 
-from microsalt import __version__
-from microsalt.store.database import initialize_database
-from microsalt.store.db_manipulator import DB_Manipulator
-from microsalt.server.app import initialize_app, get_app
-from microsalt.utils.config_loader import load_config
-from microsalt.utils.scraper import Scraper
-from microsalt.utils.job_creator import Job_Creator
-from microsalt.utils.reporter import Reporter
-from microsalt.utils.referencer import Referencer
+from microSALT import __version__
+from microSALT.store.database import initialize_database
+from microSALT.store.db_manipulator import DB_Manipulator
+from microSALT.server.app import initialize_app, get_app
+from microSALT.utils.config_loader import load_config
+from microSALT.utils.scraper import Scraper
+from microSALT.utils.job_creator import Job_Creator
+from microSALT.utils.reporter import Reporter
+from microSALT.utils.referencer import Referencer
 
 default_sampleinfo = {
     "CG_ID_project": "XXX0000",
@@ -461,7 +461,7 @@ def overwrite(ctx, sample_name, force):
 
 @root.command()
 def init_db():
-    from microsalt.store.orm_models import db
+    from microSALT.store.orm_models import db
 
     app = get_app()
     db.init_app(app)

microSALT/server/app.py

@@ -1,4 +1,3 @@
-
 import logging
 import os
 from pathlib import Path
@@ -7,12 +6,14 @@
 import sys
 
 from flask import Flask
-from microsalt.server.views import bp
-from microsalt.store.orm_models import db
+from microSALT.server.views import bp
+from microSALT.store.orm_models import db
+
 logger = logging.getLogger("main_logger")
 
 APP: Flask = None
 
+
 def initialize_app(config: dict) -> None:
     global APP
     APP = Flask(__name__, template_folder="templates")
@@ -23,11 +24,13 @@ def initialize_app(config: dict) -> None:
     db.init_app(APP)
     APP.register_blueprint(bp)
 
+
 def get_app() -> Flask:
     if not APP:
         raise ValueError("App not initialized")
     return APP
 
+
 def create_path(path: str, logger: logging.Logger):
     if not Path(path).exists():
         os.makedirs(path)
@@ -37,7 +40,7 @@ def create_path(path: str, logger: logging.Logger):
 
 
 def handle_config_entry(entry, value, logger):
-    
+
     if isinstance(value, str) and "/" in value and entry not in ["genologics"]:
         if os.path.abspath(value) == "/path":
             logger.error(f"Path for {entry} is not set.")
@@ -76,6 +79,7 @@ def check_database_integrity(db_file, logger):
 
     logger.info("Database integrity check passed.")
 
+
 def _setup_app_from_config(app: Flask, config: dict):
     app.config.update(config["database"])
     app.config["folders"] = config.get("folders", {})
@@ -87,23 +91,23 @@ def _setup_app_from_config(app: Flask, config: dict):
     app.config["mlst_span_threshold"] = config["threshold"]["mlst_span"]
     app.config["motif_id_threshold"] = config["threshold"]["motif_id"]
     app.config["motif_span_threshold"] = config["threshold"]["motif_span"]
-    
-    
-    
+
     # Create paths mentioned in config
     create_paths(app.config["folders"], logger)
-    
+
     # Integrity check database
     db_file = re.search(
         "sqlite:///(.+)",
         config["database"]["SQLALCHEMY_DATABASE_URI"],
     )[1]
     check_database_integrity(db_file, logger)
 
+
 if __name__ == "__main__":
-    
+
     from microSALT.utils.config_loader import load_config
-    config = load_config('/Users/karlnyren/github/microSALT/tests/testdata/config.json')
+
+    config = load_config("/Users/karlnyren/github/microSALT/tests/testdata/config.json")
     initialize_app(config)
     app = get_app()
     app.run(host="127.0.0.1", port=5001, debug=True, use_reloader=False)

microSALT/server/templates/STtracker_page.html

@@ -6,7 +6,7 @@
           <!-- Summary pages  -->
           <footer>
             <div class="panel"><div class="panel-body">
-              <a href="https://github.com/Clinical-Genomics/microSALT"><img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/microsalt.jpg?raw=true" alt="MicroSALT Logo" align="left" style="position:absolute;left:15px;width:400px;height:100px;display:flex;"></a>
+              <a href="https://github.com/Clinical-Genomics/microSALT"><img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/microSALT.jpg?raw=true" alt="MicroSALT Logo" align="left" style="position:absolute;left:15px;width:400px;height:100px;display:flex;"></a>
               <!--<img src="swedac.jpg" alt="Swedac Logo" align="right" style="display:flex;">-->
               <h2 class="page-header">
                 <small><br><br><br>Sekvenstypsuppdateringar</small>

microSALT/server/templates/alignment_page.html

@@ -7,7 +7,7 @@
           <footer>
             <div class="panel"><div class="panel-body">
               <a href="https://github.com/Clinical-Genomics/microSALT">
-              <img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/microsalt.jpg?raw=true" \
+              <img src="https://github.com/Clinical-Genomics/microSALT/blob/master/artwork/microSALT.jpg?raw=true" \
               alt="MicroSALT Logo" align="left" \
               style="position:absolute;left:15px;width:400px;height:100px;display:flex;"></a>
               {% if 'MW' in topsample.application_tag %}
@@ -35,8 +35,8 @@ <h4>{{topsample.projects.Customer_ID}}</h4><br>
                 </address>
                 <address>
                   <strong>microSALT-teamet</strong><br>
-                  <abbr title="F&ouml;rslagsl&aring;da">E:</abbr><a href="mailto:microsalt-suggestions@scilifelab.se?subject=F&ouml;rb&auml;ttringsf&ouml;rslag">
-                  microsalt-suggestions@scilifelab.se
+                  <abbr title="F&ouml;rslagsl&aring;da">E:</abbr><a href="mailto:microSALT-suggestions@scilifelab.se?subject=F&ouml;rb&auml;ttringsf&ouml;rslag">
+                  microSALT-suggestions@scilifelab.se
                   </a>
                 </address>
               </div>
@@ -237,7 +237,7 @@ <h3>Analysbegr&auml;nsningar f&ouml;r: {{topsample.application_tag}}<br></h3>
 
               <h3>F&ouml;rb&auml;ttringsf&ouml;rslag<br></h3>
               <p>
-              Alla typer av f&ouml;rb&auml;ttringsf&ouml;rslag mailas med f&ouml;rdel till microsalt-suggestions@scilifelab.se<br>
+              Alla typer av f&ouml;rb&auml;ttringsf&ouml;rslag mailas med f&ouml;rdel till microSALT-suggestions@scilifelab.se<br>
               Din &aring;terkopplling uppskattas!
               </p>