Added singularity def file to ease deployment

.gitignore

@@ -0,0 +1 @@
+__pycache__

README.md

@@ -15,13 +15,32 @@ The sanity checks implemented are based on experience and the bcl2fastq document
 
 # Local instance
 
-    git clone https://github.com/sequana/webapp_samplesheet check_my_sample_sheet
-    cd check_my_sample_sheet
+## Using local python
 
-    # You will need to install requirements (sequana and streamlit)
-    pip install --file requirements.txt
+If you'd like to run a local instance, you could either install streamlit and run it directly (python virtual environment is highly recommended):
 
-    # and should ne ready to test the appliction locally in your browser 
-    streamlit run app.py
+```bash
+git clone https://github.com/sequana/webapp_samplesheet check_my_sample_sheet
+cd check_my_sample_sheet/app
+pip install -r requirements.txt
+python -m streamlit run app.py
+```
 
+## Using singularity
 
+Or if you'd like to run an instance on a web server, there is a singularity definition file (requires singularity and docker to build, only singularity to run):
+
+```bash
+git clone https://github.com/sequana/webapp_samplesheet check_my_sample_sheet
+singularity build --build-arg SERVER_ADDRESS=127.0.0.1 --fakeroot sample_sheet_validator_1.0.0.sif samplesheet_validator.def
+```
+
+You can change the IP address you're listening to to suit your needs, and then run an instance of the app:
+
+```bash
+singularity instance start sample_sheet_validator_1.0.0.sif samplesheet_validatord
+```
+
+Please note: if using singularity, make sure that both `/tmp` and `$HOME` are writable. You can either set `mount tmp = yes` and `mount home = yes` in `/etc/singularity/singularity.conf`, or you can set the binds manually.
+
+By default, the app will be served on port 8501, so if you'd like to redirect http traffic through a reverse proxy, you can specify the IP address and port 8501 as the target.

app.py → app/app.py

@@ -17,14 +17,16 @@
 
 import requests
 import streamlit as st
-from sequana.iem import SampleSheet
+from samplesheet import SampleSheet
 from streamlit_option_menu import option_menu
 
 st.set_page_config(
     page_title="Illumina Sample Sheet Validator",
     page_icon="imgs/logo_256x256.png",
     layout="wide",
-    menu_items={"Report a bug": "https://github.com/sequana/webapp_samplesheet/issues/new/choose"},
+    menu_items={
+        "Report a bug": "https://github.com/sequana/webapp_samplesheet/issues/new/choose"
+    },
 )
 
 version = "1.0.0"
@@ -104,7 +106,9 @@ def add_legend(success, warning, error):
         error = counter["Error"] / S * 100
 
         completed = min(round(100 * (S / float(N))), 100)
-        bar_placeholder.markdown(colored_bar(success, warning, error, completed), unsafe_allow_html=True)
+        bar_placeholder.markdown(
+            colored_bar(success, warning, error, completed), unsafe_allow_html=True
+        )
 
     # finally add the legend
     _, col2, _ = st.columns([1, 4, 1])
@@ -126,7 +130,9 @@ def add_legend(success, warning, error):
 
 
 def main():
-    st.sidebar.write("Provided by the [Sequana teams](https://github.com/sequana/sequana)")
+    st.sidebar.write(
+        "Provided by the [Sequana teams](https://github.com/sequana/sequana)"
+    )
     st.sidebar.image("imgs/logo_256x256.png")
     st.title(f"Sample Sheet and Design Validator (v{version})")
 
@@ -135,7 +141,11 @@ def main():
     # 1. as sidebar menu
     with st.sidebar:
         choice = option_menu(
-            "Main Menu", menu, icons=["gear", "gear", "cloud-upload", ""], menu_icon="cast", default_index=0
+            "Main Menu",
+            menu,
+            icons=["gear", "gear", "cloud-upload", ""],
+            menu_icon="cast",
+            default_index=0,
         )
 
     if choice == "Sample Sheet Validation (Illumina)":
@@ -149,15 +159,21 @@ def main():
         col1, col2, col3 = st.columns([4, 1, 4])
         with col1:
             data_file = st.file_uploader(
-                "Drop a sample sheet below and press the **Process** button. ", type=["csv", "txt"]
+                "Drop a sample sheet below and press the **Process** button. ",
+                type=["csv", "txt"],
             )
         with col2:
             # Centered "OR" text
-            st.markdown("<div style='text-align: center;'><br><br>OR</div>", unsafe_allow_html=True)
+            st.markdown(
+                "<div style='text-align: center;'><br><br>OR</div>",
+                unsafe_allow_html=True,
+            )
 
         with col3:
             code = st.text_area(
-                "Paste your code here and press the **Process** button.", value=st.session_state.code, key="code_area"
+                "Paste your code here and press the **Process** button.",
+                value=st.session_state.code,
+                key="code_area",
             )
 
         if st.button(":gear: Process :gear:"):
@@ -216,9 +232,7 @@ def main():
         st.code(data, language="bash")
 
         st.subheader("3 - [Data] section with single-index and a [Settings] section")
-        url = (
-            "https://raw.githubusercontent.com/sequana/webapp_samplesheet/main/examples/sample_sheet_settings_index.csv"
-        )
+        url = "https://raw.githubusercontent.com/sequana/webapp_samplesheet/main/examples/sample_sheet_settings_index.csv"
         r = requests.get(url, allow_redirects=True)
         data = r.content.decode()
         st.code(data, language="bash")
@@ -229,7 +243,9 @@ def main():
         data = r.content.decode()
         st.code(data, language="bash")
 
-        st.subheader("5 - Example of an erroneous sample sheet (extra semicolons at the end)")
+        st.subheader(
+            "5 - Example of an erroneous sample sheet (extra semicolons at the end)"
+        )
         url = "https://raw.githubusercontent.com/sequana/webapp_samplesheet/main/examples/Bad_SampleSheet_extra_semicolons.csv"
         r = requests.get(url, allow_redirects=True)
         data = r.content.decode()
@@ -249,7 +265,9 @@ def main():
         )
     else:
         st.subheader("How to cite ? ")
-        st.info("Check My Sample Sheet application (this website):\n\nLemée L. et al [researchsquare](https://www.researchsquare.com/article/rs-5268893/v1)")
+        st.info(
+            "Check My Sample Sheet application (this website):\n\nLemée L. et al [researchsquare](https://www.researchsquare.com/article/rs-5268893/v1)"
+        )
 
         st.info(
             "The Sequana application to check the sample sheet: \n\nCokelaer T. et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI [doi:10.21105/joss.00352](https://joss.theoj.org/papers/10.21105/joss.00352)"
@@ -272,11 +290,15 @@ def process_sample_sheet(data_file, samplesheet):
     None
     """
     if data_file is not None:
-        file_details = {"Filename": data_file.name, "FileType": data_file.type, "FileSize": data_file.size}
+        file_details = {
+            "Filename": data_file.name,
+            "FileType": data_file.type,
+            "FileSize": data_file.size,
+        }
     else:
         pass
 
-    if 1 == 1:
+    if True:
 
         # read to save locally
         # samplesheet = data_file.read().decode()

app/checker.py

@@ -0,0 +1,58 @@
+#
+#  This file is part of Sequana software
+#
+#  Copyright (c) 2018-2022 - Sequana Development Team
+#
+#  Distributed under the terms of the 3-clause BSD license.
+#  The full license is in the LICENSE file, distributed with this software.
+#
+#  website: https://github.com/sequana/sequana
+#  documentation: http://sequana.readthedocs.io
+#
+##############################################################################
+
+import colorlog
+
+logger = colorlog.getLogger(__name__)
+
+
+class Checker:
+    """Utility to hold checks
+
+
+    The method :meth:`~sequana.utils.checks.Checke./tryme` calls the method or function
+    provided. This method is expected to return a dictionary
+    with 2 keys called status and msg. Status should be
+    in 'Error', 'Warning', 'Success'.
+
+    The attributes hold all calls to :meth:`tryme`
+
+    Given that func returns a dictionary as explained here above, you can run this code
+    ::
+
+        checks = Checker()
+        checks.tryme(func)
+
+    checks contains the status and mesg of each function called by checks.tryme.
+
+
+    """
+
+    def __init__(self):
+
+        self.results = []
+
+    def tryme(self, meth):
+        try:
+            status = meth()
+            if "msg" in status and "status" in status:
+                self.results.append(status)
+            else:
+                self.results.append({"status": "Success", "msg": status})
+        except Exception as err:  # pragma: no cover
+            self.results.append(
+                {"msg": err, "status": "Error", "caller": str(meth.__name__)}
+            )
+            self.results.append(
+                {"msg": err, "status": "Error", "caller": str(meth.__name__)}
+            )

requirements.txt → app/requirements.txt

@@ -1,2 +1,2 @@
-sequana==0.17.1
 streamlit_option_menu
+colorlog