Update tool GRB detection to 0.0.1+galaxy0

.github/workflows/live-preview.yaml

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+name: Preview PR on galaxy.odahub.fr
+on:
+  pull_request:
+    branches:
+      - main
+    types:
+      - opened
+      - labeled
+      - synchronize
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
+env:
+  GALAXY_FORK: galaxyproject
+  GALAXY_BRANCH: release_23.1
+
+jobs:
+  setup:
+    if: contains( github.event.pull_request.labels.*.name, 'test-live')
+    name: Determine changed repositories
+    runs-on: ubuntu-latest
+    outputs:
+      tool-list: ${{ steps.discover.outputs.tool-list }}
+    steps:
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.7"
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Fake a Planemo run to determine tool list
+      uses: galaxyproject/planemo-ci-action@v1
+      id: discover
+      with:
+        galaxy-fork: ${{ env.GALAXY_FORK }}
+        galaxy-branch: ${{ env.GALAXY_BRANCH }}
+        python-version: "3.7"
+    - name: Show tool list
+      run: echo '${{ steps.discover.outputs.tool-list }}'
+
+  # deploy the tools
+  deploy:
+    name: Deploy
+    if: contains( github.event.pull_request.labels.*.name, 'test-live') && needs.setup.outputs.tool-list
+    needs: setup
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install requirenments
+      run: sudo apt-get install -y ansible
+    - name: Install SSH key
+      uses: shimataro/ssh-key-action@v2
+      with:
+        key: ${{ secrets.SSH_PRIVATE_KEY }}
+        known_hosts: ${{ secrets.KNOWN_HOSTS }}
+    - name: Deploy tools
+      env: 
+        TOOL_LIST: ${{ needs.setup.outputs.tool-list }}
+        pr_num: ${{ github.event.pull_request.number }}
+      run: |
+        cd deploy-preview
+
+        dir_list=`for tl in $TOOL_LIST ; do echo $tl | awk -F '/' '{print $2}'; done | uniq`
+
+        for dr in $dir_list; do
+          tools_list=`for tl in $TOOL_LIST; do if [[ "$tl" == *"$dr"*  ]] ; then basename $tl ; fi ; done`
+
+          export tools_list
+          export tool_dir=$dr
+
+          ansible-playbook deploy.yml
+        done

deploy-preview/ansible.cfg

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+[defaults]
+inventory = hosts
+timeout = 60
+
+[ssh_connection]
+pipelining = true

deploy-preview/deploy.yml

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+---
+- hosts: all
+  become: true
+  become_user: root
+  vars:
+    src_tools_dir: ../tools
+    dest_tools_dir: /srv/galaxy/staging_tools
+    dest_tools_conf: /srv/galaxy/server/config/staging_tool_conf.xml
+    tools_list: "{{ lookup('env', 'tools_list').split() }}"
+    tool_dir: "{{ lookup('env', 'tool_dir') }}"
+    pr_num: "{{ lookup('env', 'pr_num') }}"
+
+
+  tasks:
+    - name: Sync tool dir
+      ansible.posix.synchronize:
+        src: "{{ src_tools_dir }}/{{ tool_dir }}/"
+        dest: "{{ dest_tools_dir }}/{{ tool_dir }}_pr{{ pr_num }}"
+        rsync_opts:
+          - "--chown=galaxy:galaxy"
+
+    - name: Make id unique
+      replace:
+        path: "{{ dest_tools_dir }}/{{ tool_dir }}_pr{{ pr_num }}/{{ item }}"
+        regexp: '<tool id="([a-z0-9_]+)"'
+        replace: '<tool id="\1_pr{{ pr_num }}"'
+      loop: "{{ tools_list }}"
+
+    - name: Make name unique
+      replace:
+        path: "{{ dest_tools_dir }}/{{ tool_dir }}_pr{{ pr_num }}/{{ item }}"
+        regexp: '<tool(.*)name="([a-z0-9_]+)"'
+        replace: '<tool\1name="\2_pr{{ pr_num }}"'
+      loop: "{{ tools_list }}"
+
+    - name: Clean previous references
+      lineinfile:
+        path: "{{ dest_tools_conf }}"
+        regexp: '^\s*<tool\s+file="{{ tool_dir }}_pr{{ pr_num }}/'
+        state: absent
+      loop: "{{ tools_list }}"
+
+    - name: Enable tools
+      lineinfile:
+        path: "{{ dest_tools_conf }}"
+        regexp: '^\s*<tool\s+file="{{ tool_dir }}_pr{{ pr_num }}/{{ item|regex_escape }}"'
+        insertafter: '<section id="astro_staging"'
+        line: '    <tool file="{{ tool_dir }}_pr{{ pr_num }}/{{ item }}" />'
+      loop: "{{ tools_list }}"

deploy-preview/hosts

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+[all]
+galaxy.odahub.fr ansible_ssh_user=ubuntu

tools/grb-detection/detectgrb.py

@@ -0,0 +1,252 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# In[ ]:
+
+
+import json
+import os
+import shutil
+import sys
+
+try:
+    import numpy as np
+    _numpy_available = True
+except ImportError:
+    _numpy_available = False
+
+try:
+    from oda_api.json import CustomJSONEncoder
+except ImportError:
+    from json import JSONEncoder as CustomJSONEncoder
+
+_galaxy_wd = os.getcwd()
+
+
+# In[1]:
+
+
+T1 = "2023-01-16T04:53:33.9" # http://odahub.io/ontology#StartTime
+T2 = "2023-01-16T04:55:33.9" # http://odahub.io/ontology#EndTime
+detection_time_scales = "1,10"
+lc_time_scale = 0.1 # https://odahub.io/ontology#TimeIntervalSeconds
+background_age = 10 # oda:TimeIntervalSeconds
+min_sn = 5 # https://odahub.io/ontology#SignalToNoiseRatio
+
+
+# In[ ]:
+
+
+with open('inputs.json', 'r') as fd:
+    inp_dic = json.load(fd)
+if '_data_product' in inp_dic.keys():
+    inp_pdic = inp_dic['_data_product']
+else:
+    inp_pdic = inp_dic
+
+for vn, vv in inp_pdic.items():
+    if vn != '_selector':
+        globals()[vn] = type(globals()[vn])(vv)
+
+
+# In[2]:
+
+
+import numpy as np
+from astropy.time import Time
+from oda_api.data_products import LightCurveDataProduct, BinaryData, PictureProduct
+from matplotlib import pylab as plt
+
+
+# In[3]:
+
+
+from oda_api.api import DispatcherAPI
+disp=DispatcherAPI(url='https://www.astro.unige.ch/mmoda//dispatch-data', instrument='mock')
+
+par_dict={
+    "T1": T1,
+    "T2": T2,
+    "T_format": "isot",
+    "instrument": "spi_acs",
+    "product": "spi_acs_lc",
+    "product_type": "Real",
+    "time_bin": lc_time_scale,
+    "time_bin_format": "sec",
+}
+
+data_collection = disp.get_product(**par_dict)
+
+lc = data_collection.spi_acs_lc_0_query.data_unit[1].data
+
+
+# In[4]:
+
+
+lc['TIME'] =  lc['TIME']/24/3600 + (Time(T1).mjd  + Time(T2).mjd)/2. # TODO: more accurately
+
+
+# In[5]:
+
+
+def rebin(x, n):
+    N = int(len(x)/n)
+    return np.array(x[:N*n]).reshape((N, n)).sum(1)
+
+
+
+# In[6]:
+
+
+lc = LightCurveDataProduct.from_arrays(
+        times=Time(
+            lc['TIME'], 
+            format="mjd"),
+        fluxes=lc['RATE'],
+        errors=lc['ERROR']
+    )
+
+obj_results = [lc.encode()]
+
+
+# In[7]:
+
+
+T0_ijd = lc.data_unit[1].data['TIME'][np.argmax(lc.data_unit[1].data['FLUX'])]
+
+
+# In[8]:
+
+
+ijd2plot = lambda x:(x - T0_ijd)*24*3600
+
+
+m_bkg = ijd2plot(lc.data_unit[1].data['TIME']) < background_age
+np.sum(m_bkg)
+bkg = np.mean(lc.data_unit[1].data['FLUX'][m_bkg])
+bkg
+
+
+# In[9]:
+
+
+from matplotlib import pylab as plt
+
+plt.figure(figsize=(10, 6))
+
+plt.errorbar(
+    ijd2plot(lc.data_unit[1].data['TIME']),
+    lc.data_unit[1].data['FLUX'],
+    lc.data_unit[1].data['ERROR'],
+    label=f"{lc_time_scale} s",
+    alpha=0.5,
+)
+
+best_detection = {
+    'sn': None,
+    'timescale': None,
+    't_max_sn': None
+}
+
+for detection_time_scale in detection_time_scales.split(","):
+    n = int(float(detection_time_scale.strip()) / lc_time_scale)
+
+    r_t = rebin(lc.data_unit[1].data['TIME'], n) / n
+    r_c = rebin(lc.data_unit[1].data['FLUX'], n) / n 
+    r_ce = rebin(lc.data_unit[1].data['ERROR']**2, n)**0.5/n
+
+    sn = (r_c - bkg) / r_ce
+    imax = sn.argmax()
+
+    if best_detection['sn'] is None or best_detection['sn'] < sn[imax]:
+        best_detection['sn'] = sn[imax]
+        best_detection['timescale'] = detection_time_scale
+        best_detection['t_max_sn'] = Time(r_t[imax], format='mjd').isot
+
+    plt.errorbar(
+        ijd2plot(r_t),
+        r_c,
+        r_ce,
+        label=f"{detection_time_scale} s, S/N = {sn[imax]:.1f}"
+    )
+
+
+plt.axhline(bkg, lw=3, ls=":", c="k")
+
+plt.grid()
+plt.legend()
+
+plt.ylabel('Flux')
+plt.xlabel('Time, MJD')
+
+plt.title(best_detection)
+
+plt.savefig("annotated-lc.png")
+
+
+# In[10]:
+
+
+Time(r_t, format='mjd').isot
+
+
+# In[11]:
+
+
+bin_image = PictureProduct.from_file('annotated-lc.png')
+
+detection_note = str(dict(best_detection=best_detection))
+
+
+# In[12]:
+
+
+lc=lc # http://odahub.io/ontology#LightCurve
+
+detection_comment = detection_note # http://odahub.io/ontology#ODATextProduct
+image_output = bin_image # http://odahub.io/ontology#ODAPictureProduct
+
+
+# In[ ]:
+
+
+_simple_outs, _oda_outs = [], []
+_galaxy_meta_data = {}
+_oda_outs.append(('out_detectgrb_lc', 'lc_galaxy.output', lc))
+_oda_outs.append(('out_detectgrb_detection_comment', 'detection_comment_galaxy.output', detection_comment))
+_oda_outs.append(('out_detectgrb_image_output', 'image_output_galaxy.output', image_output))
+
+for _outn, _outfn, _outv in _oda_outs:
+    _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
+    if isinstance(_outv, str) and os.path.isfile(_outv):
+        shutil.move(_outv, _galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {'ext': '_sniff_'}
+    elif getattr(_outv, "write_fits_file", None):
+        _outv.write_fits_file(_galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {'ext': 'fits'}
+    elif getattr(_outv, "write_file", None):
+        _outv.write_file(_galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {'ext': '_sniff_'}
+    else:
+        with open(_galaxy_outfile_name, 'w') as fd:
+            json.dump(_outv, fd, cls=CustomJSONEncoder)
+        _galaxy_meta_data[_outn] = {'ext': 'json'}
+
+for _outn, _outfn, _outv in _simple_outs:
+    _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
+    if isinstance(_outv, str) and os.path.isfile(_outv):
+        shutil.move(_outv, _galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {'ext': '_sniff_'}
+    elif _numpy_available and isinstance(_outv, np.ndarray):
+        with open(_galaxy_outfile_name, 'wb') as fd:
+            np.savez(fd, _outv)
+        _galaxy_meta_data[_outn] = {'ext': 'npz'}
+    else:
+        with open(_galaxy_outfile_name, 'w') as fd:
+            json.dump(_outv, fd)
+        _galaxy_meta_data[_outn] = {'ext': 'expression.json'}
+
+with open(os.path.join(_galaxy_wd, 'galaxy.json'), 'w') as fd:
+    json.dump(_galaxy_meta_data, fd)
+print("*** Job finished successfully ***")
+